Author: "Sherman, Mark E" / Database: OAIster - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Sherman, Mark E"' showing total 84 results

Start Over Author "Sherman, Mark E" Database OAIster

84 results on '"Sherman, Mark E"'

1. p53 and ovarian carcinoma survival: an Ovarian Tumor Tissue Analysis consortium study

Author: Köbel, Martin, Köbel, Martin, Kang, Eun‐Young, Weir, Ashley, Rambau, Peter F, Lee, Cheng‐Han, Nelson, Gregg S, Ghatage, Prafull, Meagher, Nicola S, Riggan, Marjorie J, Alsop, Jennifer, Anglesio, Michael S, Beckmann, Matthias W, Bisinotto, Christiani, Boisen, Michelle, Boros, Jessica, Brand, Alison H, Brooks‐Wilson, Angela, Carney, Michael E, Coulson, Penny, Courtney‐Brooks, Madeleine, Cushing‐Haugen, Kara L, Cybulski, Cezary, Deen, Suha, El‐Bahrawy, Mona A, Elishaev, Esther, Erber, Ramona, Fereday, Sian, Group, AOCS, Fischer, Anna, Gayther, Simon A, Barquin‐Garcia, Arantzazu, Gentry‐Maharaj, Aleksandra, Gilks, C Blake, Gronwald, Helena, Grube, Marcel, Harnett, Paul R, Harris, Holly R, Hartkopf, Andreas D, Hartmann, Arndt, Hein, Alexander, Hendley, Joy, Hernandez, Brenda Y, Huang, Yajue, Jakubowska, Anna, Jimenez‐Linan, Mercedes, Jones, Michael E, Kennedy, Catherine J, Kluz, Tomasz, Koziak, Jennifer M, Lesnock, Jaime, Lester, Jenny, Lubiński, Jan, Longacre, Teri A, Lycke, Maria, Mateoiu, Constantina, McCauley, Bryan M, McGuire, Valerie, Ney, Britta, Olawaiye, Alexander, Orsulic, Sandra, Osorio, Ana, Paz‐Ares, Luis, Ramón y Cajal, Teresa, Rothstein, Joseph H, Ruebner, Matthias, Schoemaker, Minouk J, Shah, Mitul, Sharma, Raghwa, Sherman, Mark E, Shvetsov, Yurii B, Singh, Naveena, Steed, Helen, Storr, Sarah J, Talhouk, Aline, Traficante, Nadia, Wang, Chen, Whittemore, Alice S, Widschwendter, Martin, Wilkens, Lynne R, Winham, Stacey J, Benitez, Javier, Berchuck, Andrew, Bowtell, David D, dos Reis, Francisco J Candido, Campbell, Ian, Cook, Linda S, DeFazio, Anna, Doherty, Jennifer A, Fasching, Peter A, Fortner, Renée T, García, María J, Goodman, Marc T, Goode, Ellen L, Gronwald, Jacek, Huntsman, David G, Karlan, Beth Y, Kelemen, Linda E, Kommoss, Stefan, Le, Nhu D, Martin, Stewart G, Köbel, Martin, Köbel, Martin, Kang, Eun‐Young, Weir, Ashley, Rambau, Peter F, Lee, Cheng‐Han, Nelson, Gregg S, Ghatage, Prafull, Meagher, Nicola S, Riggan, Marjorie J, Alsop, Jennifer, Anglesio, Michael S, Beckmann, Matthias W, Bisinotto, Christiani, Boisen, Michelle, Boros, Jessica, Brand, Alison H, Brooks‐Wilson, Angela, Carney, Michael E, Coulson, Penny, Courtney‐Brooks, Madeleine, Cushing‐Haugen, Kara L, Cybulski, Cezary, Deen, Suha, El‐Bahrawy, Mona A, Elishaev, Esther, Erber, Ramona, Fereday, Sian, Group, AOCS, Fischer, Anna, Gayther, Simon A, Barquin‐Garcia, Arantzazu, Gentry‐Maharaj, Aleksandra, Gilks, C Blake, Gronwald, Helena, Grube, Marcel, Harnett, Paul R, Harris, Holly R, Hartkopf, Andreas D, Hartmann, Arndt, Hein, Alexander, Hendley, Joy, Hernandez, Brenda Y, Huang, Yajue, Jakubowska, Anna, Jimenez‐Linan, Mercedes, Jones, Michael E, Kennedy, Catherine J, Kluz, Tomasz, Koziak, Jennifer M, Lesnock, Jaime, Lester, Jenny, Lubiński, Jan, Longacre, Teri A, Lycke, Maria, Mateoiu, Constantina, McCauley, Bryan M, McGuire, Valerie, Ney, Britta, Olawaiye, Alexander, Orsulic, Sandra, Osorio, Ana, Paz‐Ares, Luis, Ramón y Cajal, Teresa, Rothstein, Joseph H, Ruebner, Matthias, Schoemaker, Minouk J, Shah, Mitul, Sharma, Raghwa, Sherman, Mark E, Shvetsov, Yurii B, Singh, Naveena, Steed, Helen, Storr, Sarah J, Talhouk, Aline, Traficante, Nadia, Wang, Chen, Whittemore, Alice S, Widschwendter, Martin, Wilkens, Lynne R, Winham, Stacey J, Benitez, Javier, Berchuck, Andrew, Bowtell, David D, dos Reis, Francisco J Candido, Campbell, Ian, Cook, Linda S, DeFazio, Anna, Doherty, Jennifer A, Fasching, Peter A, Fortner, Renée T, García, María J, Goodman, Marc T, Goode, Ellen L, Gronwald, Jacek, Huntsman, David G, Karlan, Beth Y, Kelemen, Linda E, Kommoss, Stefan, Le, Nhu D, and Martin, Stewart G
Abstract: Our objective was to test whether p53 expression status is associated with survival for women diagnosed with the most common ovarian carcinoma histotypes (high-grade serous carcinoma [HGSC], endometrioid carcinoma [EC], and clear cell carcinoma [CCC]) using a large multi-institutional cohort from the Ovarian Tumor Tissue Analysis (OTTA) consortium. p53 expression was assessed on 6,678 cases represented on tissue microarrays from 25 participating OTTA study sites using a previously validated immunohistochemical (IHC) assay as a surrogate for the presence and functional effect of TP53 mutations. Three abnormal expression patterns (overexpression, complete absence, and cytoplasmic) and the normal (wild type) pattern were recorded. Survival analyses were performed by histotype. The frequency of abnormal p53 expression was 93.4% (4,630/4,957) in HGSC compared to 11.9% (116/973) in EC and 11.5% (86/748) in CCC. In HGSC, there were no differences in overall survival across the abnormal p53 expression patterns. However, in EC and CCC, abnormal p53 expression was associated with an increased risk of death for women diagnosed with EC in multivariate analysis compared to normal p53 as the reference (hazard ratio [HR] = 2.18, 95% confidence interval [CI] 1.36-3.47, p = 0.0011) and with CCC (HR = 1.57, 95% CI 1.11-2.22, p = 0.012). Abnormal p53 was also associated with shorter overall survival in The International Federation of Gynecology and Obstetrics stage I/II EC and CCC. Our study provides further evidence that functional groups of TP53 mutations assessed by abnormal surrogate p53 IHC patterns are not associated with survival in HGSC. In contrast, we validate that abnormal p53 IHC is a strong independent prognostic marker for EC and demonstrate for the first time an independent prognostic association of abnormal p53 IHC with overall survival in patients with CCC.
Published: 2023

2. Automated quantification of levels of breast terminal duct lobular (TDLU) involution using deep learning

Author: Bel, T. de, Litjens, G.J., Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Sherman, Mark E., Laak, J.A.W.M. van der, Bel, T. de, Litjens, G.J., Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Sherman, Mark E., and Laak, J.A.W.M. van der
Abstract: Contains fulltext : 245928.pdf (Publisher’s version ) (Open Access)
Published: 2022

3. Towards defining morphologic parameters of normal parous and nulliparous breast tissues by artificial intelligence

Author: Ogony, Joshua, de Bel, Thomas, Radisky, Derek C., Kachergus, Jennifer, Thompson, E. Aubrey, Degnim, Amy C., Ruddy, Kathryn J., Hilton, Tracy, Stallings-Mann, Melody, Vachon, Celine, Hoskin, Tanya L., Heckman, Michael G., Vierkant, Robert A., White, Launia J., Moore, Raymond M., Carter, Jodi, Jensen, Matthew, Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Winham, Stacey J., van der Laak, Jeroen, Sherman, Mark E., Ogony, Joshua, de Bel, Thomas, Radisky, Derek C., Kachergus, Jennifer, Thompson, E. Aubrey, Degnim, Amy C., Ruddy, Kathryn J., Hilton, Tracy, Stallings-Mann, Melody, Vachon, Celine, Hoskin, Tanya L., Heckman, Michael G., Vierkant, Robert A., White, Launia J., Moore, Raymond M., Carter, Jodi, Jensen, Matthew, Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Winham, Stacey J., van der Laak, Jeroen, and Sherman, Mark E.
Abstract: Background Breast terminal duct lobular units (TDLUs), the source of most breast cancer (BC) precursors, are shaped by age-related involution, a gradual process, and postpartum involution (PPI), a dramatic inflammatory process that restores baseline microanatomy after weaning. Dysregulated PPI is implicated in the pathogenesis of postpartum BCs. We propose that assessment of TDLUs in the postpartum period may have value in risk estimation, but characteristics of these tissues in relation to epidemiological factors are incompletely described. Methods Using validated Artificial Intelligence and morphometric methods, we analyzed digitized images of tissue sections of normal breast tissues stained with hematoxylin and eosin from donors <= 45 years from the Komen Tissue Bank (180 parous and 545 nulliparous). Metrics assessed by AI, included: TDLU count; adipose tissue fraction; mean acini count/TDLU; mean dilated acini; mean average acini area; mean "capillary" area; mean epithelial area; mean ratio of epithelial area versus intralobular stroma; mean mononuclear cell count (surrogate of immune cells); mean fat area proximate to TDLUs and TDLU area. We compared epidemiologic characteristics collected via questionnaire by parity status and race, using a Wilcoxon rank sum test or Fishers exact test. Histologic features were compared between nulliparous and parous women (overall and by time between last birth and donation [recent birth: <= 5 years versus remote birth: > 5 years]) using multivariable regression models. Results Normal breast tissues of parous women contained significantly higher TDLU counts and acini counts, more frequent dilated acini, higher mononuclear cell counts in TDLUs and smaller acini area per TDLU than nulliparas (all multivariable analyses p < 0.001). Differences in TDLU counts and average acini size persisted for > 5 years postpartum, whereas increases in immune cells were most marked <= 5 years of a birth., Funding Agencies|National Institutes of Health [CA RO1 CA229811, R01 CA262393]; Mayo Clinic Comprehensive Cancer Center [P30CA15083-45]
Published: 2022
Full Text: View/download PDF

4. Towards defining morphologic parameters of normal parous and nulliparous breast tissues by artificial intelligence

Author: Ogony, Joshua, de Bel, Thomas, Radisky, Derek C., Kachergus, Jennifer, Thompson, E. Aubrey, Degnim, Amy C., Ruddy, Kathryn J., Hilton, Tracy, Stallings-Mann, Melody, Vachon, Celine, Hoskin, Tanya L., Heckman, Michael G., Vierkant, Robert A., White, Launia J., Moore, Raymond M., Carter, Jodi, Jensen, Matthew, Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Winham, Stacey J., van der Laak, Jeroen, Sherman, Mark E., Ogony, Joshua, de Bel, Thomas, Radisky, Derek C., Kachergus, Jennifer, Thompson, E. Aubrey, Degnim, Amy C., Ruddy, Kathryn J., Hilton, Tracy, Stallings-Mann, Melody, Vachon, Celine, Hoskin, Tanya L., Heckman, Michael G., Vierkant, Robert A., White, Launia J., Moore, Raymond M., Carter, Jodi, Jensen, Matthew, Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Winham, Stacey J., van der Laak, Jeroen, and Sherman, Mark E.
Abstract: Background Breast terminal duct lobular units (TDLUs), the source of most breast cancer (BC) precursors, are shaped by age-related involution, a gradual process, and postpartum involution (PPI), a dramatic inflammatory process that restores baseline microanatomy after weaning. Dysregulated PPI is implicated in the pathogenesis of postpartum BCs. We propose that assessment of TDLUs in the postpartum period may have value in risk estimation, but characteristics of these tissues in relation to epidemiological factors are incompletely described. Methods Using validated Artificial Intelligence and morphometric methods, we analyzed digitized images of tissue sections of normal breast tissues stained with hematoxylin and eosin from donors <= 45 years from the Komen Tissue Bank (180 parous and 545 nulliparous). Metrics assessed by AI, included: TDLU count; adipose tissue fraction; mean acini count/TDLU; mean dilated acini; mean average acini area; mean "capillary" area; mean epithelial area; mean ratio of epithelial area versus intralobular stroma; mean mononuclear cell count (surrogate of immune cells); mean fat area proximate to TDLUs and TDLU area. We compared epidemiologic characteristics collected via questionnaire by parity status and race, using a Wilcoxon rank sum test or Fishers exact test. Histologic features were compared between nulliparous and parous women (overall and by time between last birth and donation [recent birth: <= 5 years versus remote birth: > 5 years]) using multivariable regression models. Results Normal breast tissues of parous women contained significantly higher TDLU counts and acini counts, more frequent dilated acini, higher mononuclear cell counts in TDLUs and smaller acini area per TDLU than nulliparas (all multivariable analyses p < 0.001). Differences in TDLU counts and average acini size persisted for > 5 years postpartum, whereas increases in immune cells were most marked <= 5 years of a birth., Funding Agencies|National Institutes of Health [CA RO1 CA229811, R01 CA262393]; Mayo Clinic Comprehensive Cancer Center [P30CA15083-45]
Published: 2022
Full Text: View/download PDF

5. Common variants in breast cancer risk loci predispose to distinct tumor subtypes

Author: Ahearn, Thomas U., Zhang, Haoyu, Michailidou, Kyriaki, Milne, Roger L., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Lush, Michael, Wang, Qin, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Augustinsson, Annelie, Baten, Adinda, Becher, Heiko, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brooks-Wilson, Angela, Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Collee, J. Margriet, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Dork, Thilo, Dwek, Miriam, Eccles, Diana M., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kauppila, Saila, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kubelka-Sabit, Katerina, Kurian, Allison W., Kyriacou, Kyriacos, Lambrechts, Diether, Lee, Derrick G., Lindblom, Annika, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, Lo, Wing-Yee, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, McLean, Catriona, Meindl, Alfons, Menon, Usha, Nevanlinna, Heli, Newman, William G., Nodora, Jesse, Offit, Kenneth, Olsson, Hakan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa, V, Peto, Julian, Pita, Guillermo, Plaseska-Karanfilska, Dijana, Prentice, Ross, Punie, Kevin, Pylkas, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Schottker, Ben, Sherman, Mark E., Shu, Xiao-Ou, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teras, Lauren R., Terry, Mary Beth, Torres, Diana, Troester, Melissa A., Vachon, Celine M., van Deurzen, Carolien H. M., van Veen, Elke M., Wagner, Philippe, Weinberg, Clarice R., Wendt, Camilla, Wesseling, Jelle, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Couch, Fergus J., Simard, Jacques, Kraft, Peter, Easton, Douglas F., Pharoah, Paul D. P., Schmidt, Marjanka K., Garcia-Closas, Montserrat, Chatterjee, Nilanjan, Ahearn, Thomas U., Zhang, Haoyu, Michailidou, Kyriaki, Milne, Roger L., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Lush, Michael, Wang, Qin, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Augustinsson, Annelie, Baten, Adinda, Becher, Heiko, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brooks-Wilson, Angela, Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Collee, J. Margriet, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Dork, Thilo, Dwek, Miriam, Eccles, Diana M., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kauppila, Saila, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kubelka-Sabit, Katerina, Kurian, Allison W., Kyriacou, Kyriacos, Lambrechts, Diether, Lee, Derrick G., Lindblom, Annika, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, Lo, Wing-Yee, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, McLean, Catriona, Meindl, Alfons, Menon, Usha, Nevanlinna, Heli, Newman, William G., Nodora, Jesse, Offit, Kenneth, Olsson, Hakan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa, V, Peto, Julian, Pita, Guillermo, Plaseska-Karanfilska, Dijana, Prentice, Ross, Punie, Kevin, Pylkas, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Schottker, Ben, Sherman, Mark E., Shu, Xiao-Ou, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teras, Lauren R., Terry, Mary Beth, Torres, Diana, Troester, Melissa A., Vachon, Celine M., van Deurzen, Carolien H. M., van Veen, Elke M., Wagner, Philippe, Weinberg, Clarice R., Wendt, Camilla, Wesseling, Jelle, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Couch, Fergus J., Simard, Jacques, Kraft, Peter, Easton, Douglas F., Pharoah, Paul D. P., Schmidt, Marjanka K., Garcia-Closas, Montserrat, and Chatterjee, Nilanjan
Abstract: Background Genome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear. Methods Among 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes. Results Eighty-five of 173 variants were associated with at least one tumor feature (false discovery rate < 5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at p < 0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions. Conclusion This report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.
Published: 2022
Full Text: View/download PDF

6. Automated quantification of levels of breast terminal duct lobular (TDLU) involution using deep learning

Author: de Bel, Thomas, Litjens, Geert, Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Radisky, Derek C., Vierkant, Robert A., Broderick, Brendan, Hoskin, Tanya L., Winham, Stacey J., Frost, Marlene H., Visscher, Daniel W., Allers, Teresa, Degnim, Amy C., Sherman, Mark E., van der Laak, Jeroen, de Bel, Thomas, Litjens, Geert, Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Radisky, Derek C., Vierkant, Robert A., Broderick, Brendan, Hoskin, Tanya L., Winham, Stacey J., Frost, Marlene H., Visscher, Daniel W., Allers, Teresa, Degnim, Amy C., Sherman, Mark E., and van der Laak, Jeroen
Abstract: Convolutional neural networks (CNNs) offer the potential to generate comprehensive quantitative analysis of histologic features. Diagnostic reporting of benign breast disease (BBD) biopsies is usually limited to subjective assessment of the most severe lesion in a sample, while ignoring the vast majority of tissue features, including involution of background terminal duct lobular units (TDLUs), the structures from which breast cancers arise. Studies indicate that increased levels of age-related TDLU involution in BBD biopsies predict lower breast cancer risk, and therefore its assessment may have potential value in risk assessment and management. However, assessment of TDLU involution is time-consuming and difficult to standardize and quantitate. Accordingly, we developed a CNN to enable automated quantitative measurement of TDLU involution and tested its performance in 174 specimens selected from the pathology archives at Mayo Clinic, Rochester, MN. The CNN was trained and tested on a subset of 33 biopsies, delineating important tissue types. Nine quantitative features were extracted from delineated TDLU regions. Our CNN reached an overall dice-score of 0.871 (+/- 0.049) for tissue classes versus reference standard annotation. Consensus of four reviewers scoring 705 images for TDLU involution demonstrated substantial agreement with the CNN method (unweighted kappa = 0.747 +/- 0.01). Quantitative involution measures showed anticipated associations with BBD histology, breast cancer risk, breast density, menopausal status, and breast cancer risk prediction scores (p < 0.05). Our work demonstrates the potential to improve risk prediction for women with BBD biopsies by applying CNN approaches to generate automated quantitative evaluation of TDLU involution.
Published: 2022
Full Text: View/download PDF

7. Common variants in breast cancer risk loci predispose to distinct tumor subtypes

Author: Ahearn, Thomas U., Zhang, Haoyu, Michailidou, Kyriaki, Milne, Roger L., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Lush, Michael, Wang, Qin, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Augustinsson, Annelie, Baten, Adinda, Becher, Heiko, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brooks-Wilson, Angela, Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Collee, J. Margriet, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Dork, Thilo, Dwek, Miriam, Eccles, Diana M., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kauppila, Saila, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kubelka-Sabit, Katerina, Kurian, Allison W., Kyriacou, Kyriacos, Lambrechts, Diether, Lee, Derrick G., Lindblom, Annika, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, Lo, Wing-Yee, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, McLean, Catriona, Meindl, Alfons, Menon, Usha, Nevanlinna, Heli, Newman, William G., Nodora, Jesse, Offit, Kenneth, Olsson, Hakan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa, V, Peto, Julian, Pita, Guillermo, Plaseska-Karanfilska, Dijana, Prentice, Ross, Punie, Kevin, Pylkas, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Schottker, Ben, Sherman, Mark E., Shu, Xiao-Ou, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teras, Lauren R., Terry, Mary Beth, Torres, Diana, Troester, Melissa A., Vachon, Celine M., van Deurzen, Carolien H. M., van Veen, Elke M., Wagner, Philippe, Weinberg, Clarice R., Wendt, Camilla, Wesseling, Jelle, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Couch, Fergus J., Simard, Jacques, Kraft, Peter, Easton, Douglas F., Pharoah, Paul D. P., Schmidt, Marjanka K., Garcia-Closas, Montserrat, Chatterjee, Nilanjan, Ahearn, Thomas U., Zhang, Haoyu, Michailidou, Kyriaki, Milne, Roger L., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Lush, Michael, Wang, Qin, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Augustinsson, Annelie, Baten, Adinda, Becher, Heiko, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brooks-Wilson, Angela, Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Collee, J. Margriet, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Dork, Thilo, Dwek, Miriam, Eccles, Diana M., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kauppila, Saila, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kubelka-Sabit, Katerina, Kurian, Allison W., Kyriacou, Kyriacos, Lambrechts, Diether, Lee, Derrick G., Lindblom, Annika, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, Lo, Wing-Yee, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, McLean, Catriona, Meindl, Alfons, Menon, Usha, Nevanlinna, Heli, Newman, William G., Nodora, Jesse, Offit, Kenneth, Olsson, Hakan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa, V, Peto, Julian, Pita, Guillermo, Plaseska-Karanfilska, Dijana, Prentice, Ross, Punie, Kevin, Pylkas, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Schottker, Ben, Sherman, Mark E., Shu, Xiao-Ou, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teras, Lauren R., Terry, Mary Beth, Torres, Diana, Troester, Melissa A., Vachon, Celine M., van Deurzen, Carolien H. M., van Veen, Elke M., Wagner, Philippe, Weinberg, Clarice R., Wendt, Camilla, Wesseling, Jelle, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Couch, Fergus J., Simard, Jacques, Kraft, Peter, Easton, Douglas F., Pharoah, Paul D. P., Schmidt, Marjanka K., Garcia-Closas, Montserrat, and Chatterjee, Nilanjan
Abstract: Background Genome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear. Methods Among 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes. Results Eighty-five of 173 variants were associated with at least one tumor feature (false discovery rate < 5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at p < 0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions. Conclusion This report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.
Published: 2022
Full Text: View/download PDF

8. Automated quantification of levels of breast terminal duct lobular (TDLU) involution using deep learning

Author: de Bel, Thomas, Litjens, Geert, Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Radisky, Derek C., Vierkant, Robert A., Broderick, Brendan, Hoskin, Tanya L., Winham, Stacey J., Frost, Marlene H., Visscher, Daniel W., Allers, Teresa, Degnim, Amy C., Sherman, Mark E., van der Laak, Jeroen, de Bel, Thomas, Litjens, Geert, Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Radisky, Derek C., Vierkant, Robert A., Broderick, Brendan, Hoskin, Tanya L., Winham, Stacey J., Frost, Marlene H., Visscher, Daniel W., Allers, Teresa, Degnim, Amy C., Sherman, Mark E., and van der Laak, Jeroen
Abstract: Convolutional neural networks (CNNs) offer the potential to generate comprehensive quantitative analysis of histologic features. Diagnostic reporting of benign breast disease (BBD) biopsies is usually limited to subjective assessment of the most severe lesion in a sample, while ignoring the vast majority of tissue features, including involution of background terminal duct lobular units (TDLUs), the structures from which breast cancers arise. Studies indicate that increased levels of age-related TDLU involution in BBD biopsies predict lower breast cancer risk, and therefore its assessment may have potential value in risk assessment and management. However, assessment of TDLU involution is time-consuming and difficult to standardize and quantitate. Accordingly, we developed a CNN to enable automated quantitative measurement of TDLU involution and tested its performance in 174 specimens selected from the pathology archives at Mayo Clinic, Rochester, MN. The CNN was trained and tested on a subset of 33 biopsies, delineating important tissue types. Nine quantitative features were extracted from delineated TDLU regions. Our CNN reached an overall dice-score of 0.871 (+/- 0.049) for tissue classes versus reference standard annotation. Consensus of four reviewers scoring 705 images for TDLU involution demonstrated substantial agreement with the CNN method (unweighted kappa = 0.747 +/- 0.01). Quantitative involution measures showed anticipated associations with BBD histology, breast cancer risk, breast density, menopausal status, and breast cancer risk prediction scores (p < 0.05). Our work demonstrates the potential to improve risk prediction for women with BBD biopsies by applying CNN approaches to generate automated quantitative evaluation of TDLU involution.
Published: 2022
Full Text: View/download PDF

9. Common variants in breast cancer risk loci predispose to distinct tumor subtypes

Author: Ahearn, Thomas U., Zhang, Haoyu, Michailidou, Kyriaki, Milne, Roger L., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Lush, Michael, Wang, Qin, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Augustinsson, Annelie, Baten, Adinda, Becher, Heiko, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brooks-Wilson, Angela, Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Collee, J. Margriet, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Dork, Thilo, Dwek, Miriam, Eccles, Diana M., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kauppila, Saila, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kubelka-Sabit, Katerina, Kurian, Allison W., Kyriacou, Kyriacos, Lambrechts, Diether, Lee, Derrick G., Lindblom, Annika, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, Lo, Wing-Yee, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, McLean, Catriona, Meindl, Alfons, Menon, Usha, Nevanlinna, Heli, Newman, William G., Nodora, Jesse, Offit, Kenneth, Olsson, Hakan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa, V, Peto, Julian, Pita, Guillermo, Plaseska-Karanfilska, Dijana, Prentice, Ross, Punie, Kevin, Pylkas, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Schottker, Ben, Sherman, Mark E., Shu, Xiao-Ou, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teras, Lauren R., Terry, Mary Beth, Torres, Diana, Troester, Melissa A., Vachon, Celine M., van Deurzen, Carolien H. M., van Veen, Elke M., Wagner, Philippe, Weinberg, Clarice R., Wendt, Camilla, Wesseling, Jelle, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Couch, Fergus J., Simard, Jacques, Kraft, Peter, Easton, Douglas F., Pharoah, Paul D. P., Schmidt, Marjanka K., Garcia-Closas, Montserrat, Chatterjee, Nilanjan, Ahearn, Thomas U., Zhang, Haoyu, Michailidou, Kyriaki, Milne, Roger L., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Lush, Michael, Wang, Qin, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Augustinsson, Annelie, Baten, Adinda, Becher, Heiko, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brooks-Wilson, Angela, Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Collee, J. Margriet, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Dork, Thilo, Dwek, Miriam, Eccles, Diana M., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kauppila, Saila, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kubelka-Sabit, Katerina, Kurian, Allison W., Kyriacou, Kyriacos, Lambrechts, Diether, Lee, Derrick G., Lindblom, Annika, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, Lo, Wing-Yee, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, McLean, Catriona, Meindl, Alfons, Menon, Usha, Nevanlinna, Heli, Newman, William G., Nodora, Jesse, Offit, Kenneth, Olsson, Hakan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa, V, Peto, Julian, Pita, Guillermo, Plaseska-Karanfilska, Dijana, Prentice, Ross, Punie, Kevin, Pylkas, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Schottker, Ben, Sherman, Mark E., Shu, Xiao-Ou, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teras, Lauren R., Terry, Mary Beth, Torres, Diana, Troester, Melissa A., Vachon, Celine M., van Deurzen, Carolien H. M., van Veen, Elke M., Wagner, Philippe, Weinberg, Clarice R., Wendt, Camilla, Wesseling, Jelle, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Couch, Fergus J., Simard, Jacques, Kraft, Peter, Easton, Douglas F., Pharoah, Paul D. P., Schmidt, Marjanka K., Garcia-Closas, Montserrat, and Chatterjee, Nilanjan
Abstract: Background Genome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear. Methods Among 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes. Results Eighty-five of 173 variants were associated with at least one tumor feature (false discovery rate < 5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at p < 0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions. Conclusion This report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.
Published: 2022
Full Text: View/download PDF

10. Towards defining morphologic parameters of normal parous and nulliparous breast tissues by artificial intelligence

Author: Ogony, Joshua, Bel, T. de, Radisky, D.C., Kachergus, Jennifer, Thompson, E.A., Degnim, A.C., Laak, J.A.W.M. van der, Sherman, Mark E., Ogony, Joshua, Bel, T. de, Radisky, D.C., Kachergus, Jennifer, Thompson, E.A., Degnim, A.C., Laak, J.A.W.M. van der, and Sherman, Mark E.
Abstract: Contains fulltext : 252269.pdf (Publisher’s version ) (Open Access)
Published: 2022

11. Automated quantification of levels of breast terminal duct lobular (TDLU) involution using deep learning

Author: Bel, T. de, Litjens, G.J., Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Sherman, Mark E., Laak, J.A.W.M. van der, Bel, T. de, Litjens, G.J., Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Sherman, Mark E., and Laak, J.A.W.M. van der
Abstract: Contains fulltext : 245928.pdf (Publisher’s version ) (Open Access)
Published: 2022

12. Towards defining morphologic parameters of normal parous and nulliparous breast tissues by artificial intelligence

Author: Ogony, Joshua, Bel, T. de, Radisky, D.C., Kachergus, Jennifer, Thompson, E.A., Degnim, A.C., Laak, J.A.W.M. van der, Sherman, Mark E., Ogony, Joshua, Bel, T. de, Radisky, D.C., Kachergus, Jennifer, Thompson, E.A., Degnim, A.C., Laak, J.A.W.M. van der, and Sherman, Mark E.
Abstract: Contains fulltext : 252269.pdf (Publisher’s version ) (Open Access)
Published: 2022

13. Towards defining morphologic parameters of normal parous and nulliparous breast tissues by artificial intelligence

Author: Ogony, Joshua, de Bel, Thomas, Radisky, Derek C., Kachergus, Jennifer, Thompson, E. Aubrey, Degnim, Amy C., Ruddy, Kathryn J., Hilton, Tracy, Stallings-Mann, Melody, Vachon, Celine, Hoskin, Tanya L., Heckman, Michael G., Vierkant, Robert A., White, Launia J., Moore, Raymond M., Carter, Jodi, Jensen, Matthew, Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Winham, Stacey J., van der Laak, Jeroen, Sherman, Mark E., Ogony, Joshua, de Bel, Thomas, Radisky, Derek C., Kachergus, Jennifer, Thompson, E. Aubrey, Degnim, Amy C., Ruddy, Kathryn J., Hilton, Tracy, Stallings-Mann, Melody, Vachon, Celine, Hoskin, Tanya L., Heckman, Michael G., Vierkant, Robert A., White, Launia J., Moore, Raymond M., Carter, Jodi, Jensen, Matthew, Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Winham, Stacey J., van der Laak, Jeroen, and Sherman, Mark E.
Abstract: Background Breast terminal duct lobular units (TDLUs), the source of most breast cancer (BC) precursors, are shaped by age-related involution, a gradual process, and postpartum involution (PPI), a dramatic inflammatory process that restores baseline microanatomy after weaning. Dysregulated PPI is implicated in the pathogenesis of postpartum BCs. We propose that assessment of TDLUs in the postpartum period may have value in risk estimation, but characteristics of these tissues in relation to epidemiological factors are incompletely described. Methods Using validated Artificial Intelligence and morphometric methods, we analyzed digitized images of tissue sections of normal breast tissues stained with hematoxylin and eosin from donors <= 45 years from the Komen Tissue Bank (180 parous and 545 nulliparous). Metrics assessed by AI, included: TDLU count; adipose tissue fraction; mean acini count/TDLU; mean dilated acini; mean average acini area; mean "capillary" area; mean epithelial area; mean ratio of epithelial area versus intralobular stroma; mean mononuclear cell count (surrogate of immune cells); mean fat area proximate to TDLUs and TDLU area. We compared epidemiologic characteristics collected via questionnaire by parity status and race, using a Wilcoxon rank sum test or Fishers exact test. Histologic features were compared between nulliparous and parous women (overall and by time between last birth and donation [recent birth: <= 5 years versus remote birth: > 5 years]) using multivariable regression models. Results Normal breast tissues of parous women contained significantly higher TDLU counts and acini counts, more frequent dilated acini, higher mononuclear cell counts in TDLUs and smaller acini area per TDLU than nulliparas (all multivariable analyses p < 0.001). Differences in TDLU counts and average acini size persisted for > 5 years postpartum, whereas increases in immune cells were most marked <= 5 years of a birth., Funding Agencies|National Institutes of Health [CA RO1 CA229811, R01 CA262393]; Mayo Clinic Comprehensive Cancer Center [P30CA15083-45]
Published: 2022
Full Text: View/download PDF

14. Automated quantification of levels of breast terminal duct lobular (TDLU) involution using deep learning

Author: de Bel, Thomas, Litjens, Geert, Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Radisky, Derek C., Vierkant, Robert A., Broderick, Brendan, Hoskin, Tanya L., Winham, Stacey J., Frost, Marlene H., Visscher, Daniel W., Allers, Teresa, Degnim, Amy C., Sherman, Mark E., van der Laak, Jeroen, de Bel, Thomas, Litjens, Geert, Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Radisky, Derek C., Vierkant, Robert A., Broderick, Brendan, Hoskin, Tanya L., Winham, Stacey J., Frost, Marlene H., Visscher, Daniel W., Allers, Teresa, Degnim, Amy C., Sherman, Mark E., and van der Laak, Jeroen
Abstract: Convolutional neural networks (CNNs) offer the potential to generate comprehensive quantitative analysis of histologic features. Diagnostic reporting of benign breast disease (BBD) biopsies is usually limited to subjective assessment of the most severe lesion in a sample, while ignoring the vast majority of tissue features, including involution of background terminal duct lobular units (TDLUs), the structures from which breast cancers arise. Studies indicate that increased levels of age-related TDLU involution in BBD biopsies predict lower breast cancer risk, and therefore its assessment may have potential value in risk assessment and management. However, assessment of TDLU involution is time-consuming and difficult to standardize and quantitate. Accordingly, we developed a CNN to enable automated quantitative measurement of TDLU involution and tested its performance in 174 specimens selected from the pathology archives at Mayo Clinic, Rochester, MN. The CNN was trained and tested on a subset of 33 biopsies, delineating important tissue types. Nine quantitative features were extracted from delineated TDLU regions. Our CNN reached an overall dice-score of 0.871 (+/- 0.049) for tissue classes versus reference standard annotation. Consensus of four reviewers scoring 705 images for TDLU involution demonstrated substantial agreement with the CNN method (unweighted kappa = 0.747 +/- 0.01). Quantitative involution measures showed anticipated associations with BBD histology, breast cancer risk, breast density, menopausal status, and breast cancer risk prediction scores (p < 0.05). Our work demonstrates the potential to improve risk prediction for women with BBD biopsies by applying CNN approaches to generate automated quantitative evaluation of TDLU involution.
Published: 2022
Full Text: View/download PDF

15. Common variants in breast cancer risk loci predispose to distinct tumor subtypes

Author: Ahearn, Thomas U., Zhang, Haoyu, Michailidou, Kyriaki, Milne, Roger L., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Lush, Michael, Wang, Qin, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Augustinsson, Annelie, Baten, Adinda, Becher, Heiko, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brooks-Wilson, Angela, Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Collee, J. Margriet, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Dork, Thilo, Dwek, Miriam, Eccles, Diana M., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kauppila, Saila, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kubelka-Sabit, Katerina, Kurian, Allison W., Kyriacou, Kyriacos, Lambrechts, Diether, Lee, Derrick G., Lindblom, Annika, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, Lo, Wing-Yee, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, McLean, Catriona, Meindl, Alfons, Menon, Usha, Nevanlinna, Heli, Newman, William G., Nodora, Jesse, Offit, Kenneth, Olsson, Hakan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa, V, Peto, Julian, Pita, Guillermo, Plaseska-Karanfilska, Dijana, Prentice, Ross, Punie, Kevin, Pylkas, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Schottker, Ben, Sherman, Mark E., Shu, Xiao-Ou, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teras, Lauren R., Terry, Mary Beth, Torres, Diana, Troester, Melissa A., Vachon, Celine M., van Deurzen, Carolien H. M., van Veen, Elke M., Wagner, Philippe, Weinberg, Clarice R., Wendt, Camilla, Wesseling, Jelle, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Couch, Fergus J., Simard, Jacques, Kraft, Peter, Easton, Douglas F., Pharoah, Paul D. P., Schmidt, Marjanka K., Garcia-Closas, Montserrat, Chatterjee, Nilanjan, Ahearn, Thomas U., Zhang, Haoyu, Michailidou, Kyriaki, Milne, Roger L., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Lush, Michael, Wang, Qin, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Augustinsson, Annelie, Baten, Adinda, Becher, Heiko, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brooks-Wilson, Angela, Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Collee, J. Margriet, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Dork, Thilo, Dwek, Miriam, Eccles, Diana M., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kauppila, Saila, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kubelka-Sabit, Katerina, Kurian, Allison W., Kyriacou, Kyriacos, Lambrechts, Diether, Lee, Derrick G., Lindblom, Annika, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, Lo, Wing-Yee, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, McLean, Catriona, Meindl, Alfons, Menon, Usha, Nevanlinna, Heli, Newman, William G., Nodora, Jesse, Offit, Kenneth, Olsson, Hakan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa, V, Peto, Julian, Pita, Guillermo, Plaseska-Karanfilska, Dijana, Prentice, Ross, Punie, Kevin, Pylkas, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Schottker, Ben, Sherman, Mark E., Shu, Xiao-Ou, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teras, Lauren R., Terry, Mary Beth, Torres, Diana, Troester, Melissa A., Vachon, Celine M., van Deurzen, Carolien H. M., van Veen, Elke M., Wagner, Philippe, Weinberg, Clarice R., Wendt, Camilla, Wesseling, Jelle, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Couch, Fergus J., Simard, Jacques, Kraft, Peter, Easton, Douglas F., Pharoah, Paul D. P., Schmidt, Marjanka K., Garcia-Closas, Montserrat, and Chatterjee, Nilanjan
Abstract: Background Genome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear. Methods Among 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes. Results Eighty-five of 173 variants were associated with at least one tumor feature (false discovery rate < 5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at p < 0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions. Conclusion This report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.
Published: 2022
Full Text: View/download PDF

16. Common variants in breast cancer risk loci predispose to distinct tumor subtypes

Author: Ahearn, Thomas U., Zhang, Haoyu, Michailidou, Kyriaki, Milne, Roger L., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Lush, Michael, Wang, Qin, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Augustinsson, Annelie, Baten, Adinda, Becher, Heiko, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brooks-Wilson, Angela, Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Collee, J. Margriet, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Dork, Thilo, Dwek, Miriam, Eccles, Diana M., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kauppila, Saila, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kubelka-Sabit, Katerina, Kurian, Allison W., Kyriacou, Kyriacos, Lambrechts, Diether, Lee, Derrick G., Lindblom, Annika, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, Lo, Wing-Yee, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, McLean, Catriona, Meindl, Alfons, Menon, Usha, Nevanlinna, Heli, Newman, William G., Nodora, Jesse, Offit, Kenneth, Olsson, Hakan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa, V, Peto, Julian, Pita, Guillermo, Plaseska-Karanfilska, Dijana, Prentice, Ross, Punie, Kevin, Pylkas, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Schottker, Ben, Sherman, Mark E., Shu, Xiao-Ou, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teras, Lauren R., Terry, Mary Beth, Torres, Diana, Troester, Melissa A., Vachon, Celine M., van Deurzen, Carolien H. M., van Veen, Elke M., Wagner, Philippe, Weinberg, Clarice R., Wendt, Camilla, Wesseling, Jelle, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Couch, Fergus J., Simard, Jacques, Kraft, Peter, Easton, Douglas F., Pharoah, Paul D. P., Schmidt, Marjanka K., Garcia-Closas, Montserrat, Chatterjee, Nilanjan, Ahearn, Thomas U., Zhang, Haoyu, Michailidou, Kyriaki, Milne, Roger L., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Lush, Michael, Wang, Qin, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Augustinsson, Annelie, Baten, Adinda, Becher, Heiko, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brooks-Wilson, Angela, Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Collee, J. Margriet, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Dork, Thilo, Dwek, Miriam, Eccles, Diana M., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kauppila, Saila, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kubelka-Sabit, Katerina, Kurian, Allison W., Kyriacou, Kyriacos, Lambrechts, Diether, Lee, Derrick G., Lindblom, Annika, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, Lo, Wing-Yee, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, McLean, Catriona, Meindl, Alfons, Menon, Usha, Nevanlinna, Heli, Newman, William G., Nodora, Jesse, Offit, Kenneth, Olsson, Hakan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa, V, Peto, Julian, Pita, Guillermo, Plaseska-Karanfilska, Dijana, Prentice, Ross, Punie, Kevin, Pylkas, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Schottker, Ben, Sherman, Mark E., Shu, Xiao-Ou, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teras, Lauren R., Terry, Mary Beth, Torres, Diana, Troester, Melissa A., Vachon, Celine M., van Deurzen, Carolien H. M., van Veen, Elke M., Wagner, Philippe, Weinberg, Clarice R., Wendt, Camilla, Wesseling, Jelle, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Couch, Fergus J., Simard, Jacques, Kraft, Peter, Easton, Douglas F., Pharoah, Paul D. P., Schmidt, Marjanka K., Garcia-Closas, Montserrat, and Chatterjee, Nilanjan
Abstract: Background Genome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear. Methods Among 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes. Results Eighty-five of 173 variants were associated with at least one tumor feature (false discovery rate < 5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at p < 0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions. Conclusion This report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.
Published: 2022

17. Towards defining morphologic parameters of normal parous and nulliparous breast tissues by artificial intelligence

Author: Ogony, Joshua, de Bel, Thomas, Radisky, Derek C., Kachergus, Jennifer, Thompson, E. Aubrey, Degnim, Amy C., Ruddy, Kathryn J., Hilton, Tracy, Stallings-Mann, Melody, Vachon, Celine, Hoskin, Tanya L., Heckman, Michael G., Vierkant, Robert A., White, Launia J., Moore, Raymond M., Carter, Jodi, Jensen, Matthew, Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Winham, Stacey J., van der Laak, Jeroen, Sherman, Mark E., Ogony, Joshua, de Bel, Thomas, Radisky, Derek C., Kachergus, Jennifer, Thompson, E. Aubrey, Degnim, Amy C., Ruddy, Kathryn J., Hilton, Tracy, Stallings-Mann, Melody, Vachon, Celine, Hoskin, Tanya L., Heckman, Michael G., Vierkant, Robert A., White, Launia J., Moore, Raymond M., Carter, Jodi, Jensen, Matthew, Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Winham, Stacey J., van der Laak, Jeroen, and Sherman, Mark E.
Abstract: Background Breast terminal duct lobular units (TDLUs), the source of most breast cancer (BC) precursors, are shaped by age-related involution, a gradual process, and postpartum involution (PPI), a dramatic inflammatory process that restores baseline microanatomy after weaning. Dysregulated PPI is implicated in the pathogenesis of postpartum BCs. We propose that assessment of TDLUs in the postpartum period may have value in risk estimation, but characteristics of these tissues in relation to epidemiological factors are incompletely described. Methods Using validated Artificial Intelligence and morphometric methods, we analyzed digitized images of tissue sections of normal breast tissues stained with hematoxylin and eosin from donors <= 45 years from the Komen Tissue Bank (180 parous and 545 nulliparous). Metrics assessed by AI, included: TDLU count; adipose tissue fraction; mean acini count/TDLU; mean dilated acini; mean average acini area; mean "capillary" area; mean epithelial area; mean ratio of epithelial area versus intralobular stroma; mean mononuclear cell count (surrogate of immune cells); mean fat area proximate to TDLUs and TDLU area. We compared epidemiologic characteristics collected via questionnaire by parity status and race, using a Wilcoxon rank sum test or Fishers exact test. Histologic features were compared between nulliparous and parous women (overall and by time between last birth and donation [recent birth: <= 5 years versus remote birth: > 5 years]) using multivariable regression models. Results Normal breast tissues of parous women contained significantly higher TDLU counts and acini counts, more frequent dilated acini, higher mononuclear cell counts in TDLUs and smaller acini area per TDLU than nulliparas (all multivariable analyses p < 0.001). Differences in TDLU counts and average acini size persisted for > 5 years postpartum, whereas increases in immune cells were most marked <= 5 years of a birth., Funding Agencies|National Institutes of Health [CA RO1 CA229811, R01 CA262393]; Mayo Clinic Comprehensive Cancer Center [P30CA15083-45]
Published: 2022
Full Text: View/download PDF

18. Serum hormone levels and normal breast histology among premenopausal women

Author: Sherman, Mark E., de Bel, Thomas, Heckman, Michael G., White, Launia J., Ogony, Joshua, Stallings-Mann, Melody, Hilton, Tracy, Degnim, Amy C., Vierkant, Robert A., Hoskin, Tanya, Jensen, Matthew R., Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Carter, Jodi M., Winham, Stacey J., Radisky, Derek C., van der Laak, Jeroen, Sherman, Mark E., de Bel, Thomas, Heckman, Michael G., White, Launia J., Ogony, Joshua, Stallings-Mann, Melody, Hilton, Tracy, Degnim, Amy C., Vierkant, Robert A., Hoskin, Tanya, Jensen, Matthew R., Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Carter, Jodi M., Winham, Stacey J., Radisky, Derek C., and van der Laak, Jeroen
Abstract: Purpose Breast terminal duct lobular units (TDLUs) are the main source of breast cancer (BC) precursors. Higher serum concentrations of hormones and growth factors have been linked to increased TDLU numbers and to elevated BC risk, with variable effects by menopausal status. We assessed associations of circulating factors with breast histology among premenopausal women using artificial intelligence (AI) and preliminarily tested whether parity modifies associations. Methods Pathology AI analysis was performed on 316 digital images of H&E-stained sections of normal breast tissues from Komen Tissue Bank donors ages ≤ 45 years to assess 11 quantitative metrics. Associations of circulating factors with AI metrics were assessed using regression analyses, with inclusion of interaction terms to assess effect modification. Results Higher prolactin levels were related to larger TDLU area (p<0.001) and increased presence of adipose tissue proximate to TDLUs (p<0.001), with less significant positive associations for acini counts (p = 0.012), dilated acini (p = 0.043), capillary area (p = 0.014), epithelial area (p = 0.007), and mononuclear cell counts (p = 0.017). Testosterone levels were associated with increased TDLU counts (p<0.001), irrespective of parity, but associations differed by adipose tissue content. AI data for TDLU counts generally agreed with prior visual assessments. Conclusion Among premenopausal women, serum hormone levels linked to BC risk were also associated with quantitative features of normal breast tissue. These relationships were suggestively modified by parity status and tissue composition. We conclude that the microanatomic features of normal breast tissue may represent a marker of BC risk., Funding Agencies: Mayo Clinic Cancer Center [P30CA15083-45]
Published: 2022
Full Text: View/download PDF

19. Towards defining morphologic parameters of normal parous and nulliparous breast tissues by artificial intelligence

Author: Ogony, Joshua, de Bel, Thomas, Radisky, Derek C., Kachergus, Jennifer, Thompson, E. Aubrey, Degnim, Amy C., Ruddy, Kathryn J., Hilton, Tracy, Stallings-Mann, Melody, Vachon, Celine, Hoskin, Tanya L., Heckman, Michael G., Vierkant, Robert A., White, Launia J., Moore, Raymond M., Carter, Jodi, Jensen, Matthew, Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Winham, Stacey J., van der Laak, Jeroen, Sherman, Mark E., Ogony, Joshua, de Bel, Thomas, Radisky, Derek C., Kachergus, Jennifer, Thompson, E. Aubrey, Degnim, Amy C., Ruddy, Kathryn J., Hilton, Tracy, Stallings-Mann, Melody, Vachon, Celine, Hoskin, Tanya L., Heckman, Michael G., Vierkant, Robert A., White, Launia J., Moore, Raymond M., Carter, Jodi, Jensen, Matthew, Pacheco-Spann, Laura, Henry, Jill E., Storniolo, Anna Maria, Winham, Stacey J., van der Laak, Jeroen, and Sherman, Mark E.
Abstract: Background Breast terminal duct lobular units (TDLUs), the source of most breast cancer (BC) precursors, are shaped by age-related involution, a gradual process, and postpartum involution (PPI), a dramatic inflammatory process that restores baseline microanatomy after weaning. Dysregulated PPI is implicated in the pathogenesis of postpartum BCs. We propose that assessment of TDLUs in the postpartum period may have value in risk estimation, but characteristics of these tissues in relation to epidemiological factors are incompletely described. Methods Using validated Artificial Intelligence and morphometric methods, we analyzed digitized images of tissue sections of normal breast tissues stained with hematoxylin and eosin from donors <= 45 years from the Komen Tissue Bank (180 parous and 545 nulliparous). Metrics assessed by AI, included: TDLU count; adipose tissue fraction; mean acini count/TDLU; mean dilated acini; mean average acini area; mean "capillary" area; mean epithelial area; mean ratio of epithelial area versus intralobular stroma; mean mononuclear cell count (surrogate of immune cells); mean fat area proximate to TDLUs and TDLU area. We compared epidemiologic characteristics collected via questionnaire by parity status and race, using a Wilcoxon rank sum test or Fishers exact test. Histologic features were compared between nulliparous and parous women (overall and by time between last birth and donation [recent birth: <= 5 years versus remote birth: > 5 years]) using multivariable regression models. Results Normal breast tissues of parous women contained significantly higher TDLU counts and acini counts, more frequent dilated acini, higher mononuclear cell counts in TDLUs and smaller acini area per TDLU than nulliparas (all multivariable analyses p < 0.001). Differences in TDLU counts and average acini size persisted for > 5 years postpartum, whereas increases in immune cells were most marked <= 5 years of a birth., Funding Agencies|National Institutes of Health [CA RO1 CA229811, R01 CA262393]; Mayo Clinic Comprehensive Cancer Center [P30CA15083-45]
Published: 2022
Full Text: View/download PDF

20. Assessing interactions between the associations of common genetic susceptibility variants, reproductive history and body mass index with breast cancer risk in the breast cancer association consortium: a combined case-control study

Author: Milne, Roger L, Gaudet, Mia M, Spurdle, Amanda B, Fasching, Peter A, Couch, Fergus J, Benítez, Javier, Arias Pérez, José Ignacio, Zamora, M Pilar, Malats, Núria, dos Santos Silva, Isabel, Gibson, Lorna J, Fletcher, Olivia, Johnson, Nichola, Anton-Culver, Hoda, Ziogas, Argyrios, Figueroa, Jonine, Brinton, Louise, Sherman, Mark E, Lissowska, Jolanta, Hopper, John L, Dite, Gillian S, Apicella, Carmel, Southey, Melissa C, Sigurdson, Alice J, Linet, Martha S, Schonfeld, Sara J, Freedman, D Michal, Mannermaa, Arto, Kosma, Veli-Matti, Kataja, Vesa, Auvinen, Päivi, Andrulis, Irene L, Glendon, Gord, Knight, Julia A, Weerasooriya, Nayana, Cox, Angela, Reed, Malcolm WR, Cross, Simon S, Dunning, Alison M, Ahmed, Shahana, Shah, Mitul, Brauch, Hiltrud, Ko, Yon-Dschun, Brüning, Thomas, Lambrechts, Diether, Reumers, Joke, Smeets, Ann, Wang-Gohrke, Shan, Hall, Per, Czene, Kamila, Liu, Jianjun, Irwanto, Astrid K, Chenevix-Trench, Georgia, Holland, Helene, Giles, Graham G, Baglietto, Laura, Severi, Gianluca, Bojensen, Stig E, Nordestgaard, Børge G, Flyger, Henrik, John, Esther M, West, Dee W, Whittemore, Alice S, Vachon, Celine, Olson, Janet E, Fredericksen, Zachary, Kosel, Matthew, Hein, Rebecca, Vrieling, Alina, Flesch-Janys, Dieter, Heinz, Judith, Beckmann, Matthias W, Heusinger, Katharina, Ekici, Arif B, Haeberle, Lothar, Humphreys, Manjeet K, Morrison, Jonathan, Easton, Doug F, Pharoah, Paul D, García-Closas, Montserrat, Goode, Ellen L, Chang-Claude, Jenny, Milne, Roger L, Gaudet, Mia M, Spurdle, Amanda B, Fasching, Peter A, Couch, Fergus J, Benítez, Javier, Arias Pérez, José Ignacio, Zamora, M Pilar, Malats, Núria, dos Santos Silva, Isabel, Gibson, Lorna J, Fletcher, Olivia, Johnson, Nichola, Anton-Culver, Hoda, Ziogas, Argyrios, Figueroa, Jonine, Brinton, Louise, Sherman, Mark E, Lissowska, Jolanta, Hopper, John L, Dite, Gillian S, Apicella, Carmel, Southey, Melissa C, Sigurdson, Alice J, Linet, Martha S, Schonfeld, Sara J, Freedman, D Michal, Mannermaa, Arto, Kosma, Veli-Matti, Kataja, Vesa, Auvinen, Päivi, Andrulis, Irene L, Glendon, Gord, Knight, Julia A, Weerasooriya, Nayana, Cox, Angela, Reed, Malcolm WR, Cross, Simon S, Dunning, Alison M, Ahmed, Shahana, Shah, Mitul, Brauch, Hiltrud, Ko, Yon-Dschun, Brüning, Thomas, Lambrechts, Diether, Reumers, Joke, Smeets, Ann, Wang-Gohrke, Shan, Hall, Per, Czene, Kamila, Liu, Jianjun, Irwanto, Astrid K, Chenevix-Trench, Georgia, Holland, Helene, Giles, Graham G, Baglietto, Laura, Severi, Gianluca, Bojensen, Stig E, Nordestgaard, Børge G, Flyger, Henrik, John, Esther M, West, Dee W, Whittemore, Alice S, Vachon, Celine, Olson, Janet E, Fredericksen, Zachary, Kosel, Matthew, Hein, Rebecca, Vrieling, Alina, Flesch-Janys, Dieter, Heinz, Judith, Beckmann, Matthias W, Heusinger, Katharina, Ekici, Arif B, Haeberle, Lothar, Humphreys, Manjeet K, Morrison, Jonathan, Easton, Doug F, Pharoah, Paul D, García-Closas, Montserrat, Goode, Ellen L, and Chang-Claude, Jenny
Abstract: Introduction: Several common breast cancer genetic susceptibility variants have recently been identified. We aimed to determine how these variants combine with a subset of other known risk factors to influence breast cancer risk in white women of European ancestry using case-control studies participating in the Breast Cancer Association Consortium.Methods: We evaluated two-way interactions between each of age at menarche, ever having had a live birth, number of live births, age at first birth and body mass index (BMI) and each of 12 single nucleotide polymorphisms (SNPs) (10q26-rs2981582 (FGFR2), 8q24-rs13281615, 11p15-rs3817198 (LSP1), 5q11-rs889312 (MAP3K1), 16q12-rs3803662 (TOX3), 2q35-rs13387042, 5p12-rs10941679 (MRPS30), 17q23-rs6504950 (COX11), 3p24-rs4973768 (SLC4A7), CASP8-rs17468277, TGFB1-rs1982073 and ESR1-rs3020314). Interactions were tested for by fitting logistic regression models including per-allele and linear trend main effects for SNPs and risk factors, respectively, and single-parameter interaction terms for linear departure from independent multiplicative effects.Results: These analyses were applied to data for up to 26,349 invasive breast cancer cases and up to 32,208 controls from 21 case-control studies. No statistical evidence of interaction was observed beyond that expected by chance. Analyses were repeated using data from 11 population-based studies, and results were very similar.Conclusions: The relative risks for breast cancer associated with the common susceptibility variants identified to date do not appear to vary across women with different reproductive histories or body mass index (BMI). The assumption of multiplicative combined effects for these established genetic and other risk factors in risk prediction models appears justified. © 2010 Milne et al.; licensee BioMed Central Ltd.
Published: 2022

21. Common variants in breast cancer risk loci predispose to distinct tumor subtypes

Author: Ahearn, Thomas U., Zhang, Haoyu, Michailidou, Kyriaki, Milne, Roger L., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Lush, Michael, Wang, Qin, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Augustinsson, Annelie, Baten, Adinda, Becher, Heiko, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brooks-Wilson, Angela, Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Collee, J. Margriet, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Dork, Thilo, Dwek, Miriam, Eccles, Diana M., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kauppila, Saila, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kubelka-Sabit, Katerina, Kurian, Allison W., Kyriacou, Kyriacos, Lambrechts, Diether, Lee, Derrick G., Lindblom, Annika, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, Lo, Wing-Yee, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, McLean, Catriona, Meindl, Alfons, Menon, Usha, Nevanlinna, Heli, Newman, William G., Nodora, Jesse, Offit, Kenneth, Olsson, Hakan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa, V, Peto, Julian, Pita, Guillermo, Plaseska-Karanfilska, Dijana, Prentice, Ross, Punie, Kevin, Pylkas, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Schottker, Ben, Sherman, Mark E., Shu, Xiao-Ou, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teras, Lauren R., Terry, Mary Beth, Torres, Diana, Troester, Melissa A., Vachon, Celine M., van Deurzen, Carolien H. M., van Veen, Elke M., Wagner, Philippe, Weinberg, Clarice R., Wendt, Camilla, Wesseling, Jelle, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Couch, Fergus J., Simard, Jacques, Kraft, Peter, Easton, Douglas F., Pharoah, Paul D. P., Schmidt, Marjanka K., Garcia-Closas, Montserrat, Chatterjee, Nilanjan, Ahearn, Thomas U., Zhang, Haoyu, Michailidou, Kyriaki, Milne, Roger L., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Lush, Michael, Wang, Qin, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Augustinsson, Annelie, Baten, Adinda, Becher, Heiko, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brooks-Wilson, Angela, Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Collee, J. Margriet, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Dork, Thilo, Dwek, Miriam, Eccles, Diana M., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Guenel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kauppila, Saila, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kubelka-Sabit, Katerina, Kurian, Allison W., Kyriacou, Kyriacos, Lambrechts, Diether, Lee, Derrick G., Lindblom, Annika, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, Lo, Wing-Yee, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martinez, Maria Elena, McLean, Catriona, Meindl, Alfons, Menon, Usha, Nevanlinna, Heli, Newman, William G., Nodora, Jesse, Offit, Kenneth, Olsson, Hakan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa, V, Peto, Julian, Pita, Guillermo, Plaseska-Karanfilska, Dijana, Prentice, Ross, Punie, Kevin, Pylkas, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Schottker, Ben, Sherman, Mark E., Shu, Xiao-Ou, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teras, Lauren R., Terry, Mary Beth, Torres, Diana, Troester, Melissa A., Vachon, Celine M., van Deurzen, Carolien H. M., van Veen, Elke M., Wagner, Philippe, Weinberg, Clarice R., Wendt, Camilla, Wesseling, Jelle, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Couch, Fergus J., Simard, Jacques, Kraft, Peter, Easton, Douglas F., Pharoah, Paul D. P., Schmidt, Marjanka K., Garcia-Closas, Montserrat, and Chatterjee, Nilanjan
Abstract: Background Genome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear. Methods Among 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes. Results Eighty-five of 173 variants were associated with at least one tumor feature (false discovery rate < 5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at p < 0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions. Conclusion This report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.
Published: 2022
Full Text: View/download PDF

22. Automated quantification of levels of breast terminal duct lobular (TDLU) involution using deep learning

Author: de Bel, Thomas, Litjens, Geert, Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Radisky, Derek C., Vierkant, Robert A., Broderick, Brendan, Hoskin, Tanya L., Winham, Stacey J., Frost, Marlene H., Visscher, Daniel W., Allers, Teresa, Degnim, Amy C., Sherman, Mark E., van der Laak, Jeroen, de Bel, Thomas, Litjens, Geert, Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Radisky, Derek C., Vierkant, Robert A., Broderick, Brendan, Hoskin, Tanya L., Winham, Stacey J., Frost, Marlene H., Visscher, Daniel W., Allers, Teresa, Degnim, Amy C., Sherman, Mark E., and van der Laak, Jeroen
Abstract: Convolutional neural networks (CNNs) offer the potential to generate comprehensive quantitative analysis of histologic features. Diagnostic reporting of benign breast disease (BBD) biopsies is usually limited to subjective assessment of the most severe lesion in a sample, while ignoring the vast majority of tissue features, including involution of background terminal duct lobular units (TDLUs), the structures from which breast cancers arise. Studies indicate that increased levels of age-related TDLU involution in BBD biopsies predict lower breast cancer risk, and therefore its assessment may have potential value in risk assessment and management. However, assessment of TDLU involution is time-consuming and difficult to standardize and quantitate. Accordingly, we developed a CNN to enable automated quantitative measurement of TDLU involution and tested its performance in 174 specimens selected from the pathology archives at Mayo Clinic, Rochester, MN. The CNN was trained and tested on a subset of 33 biopsies, delineating important tissue types. Nine quantitative features were extracted from delineated TDLU regions. Our CNN reached an overall dice-score of 0.871 (+/- 0.049) for tissue classes versus reference standard annotation. Consensus of four reviewers scoring 705 images for TDLU involution demonstrated substantial agreement with the CNN method (unweighted kappa = 0.747 +/- 0.01). Quantitative involution measures showed anticipated associations with BBD histology, breast cancer risk, breast density, menopausal status, and breast cancer risk prediction scores (p < 0.05). Our work demonstrates the potential to improve risk prediction for women with BBD biopsies by applying CNN approaches to generate automated quantitative evaluation of TDLU involution.
Published: 2022
Full Text: View/download PDF

23. Automated quantification of levels of breast terminal duct lobular (TDLU) involution using deep learning

Author: de Bel, Thomas, Litjens, Geert, Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Radisky, Derek C., Vierkant, Robert A., Broderick, Brendan, Hoskin, Tanya L., Winham, Stacey J., Frost, Marlene H., Visscher, Daniel W., Allers, Teresa, Degnim, Amy C., Sherman, Mark E., van der Laak, Jeroen, de Bel, Thomas, Litjens, Geert, Ogony, Joshua, Stallings-Mann, Melody, Carter, Jodi M., Hilton, Tracy, Radisky, Derek C., Vierkant, Robert A., Broderick, Brendan, Hoskin, Tanya L., Winham, Stacey J., Frost, Marlene H., Visscher, Daniel W., Allers, Teresa, Degnim, Amy C., Sherman, Mark E., and van der Laak, Jeroen
Abstract: Convolutional neural networks (CNNs) offer the potential to generate comprehensive quantitative analysis of histologic features. Diagnostic reporting of benign breast disease (BBD) biopsies is usually limited to subjective assessment of the most severe lesion in a sample, while ignoring the vast majority of tissue features, including involution of background terminal duct lobular units (TDLUs), the structures from which breast cancers arise. Studies indicate that increased levels of age-related TDLU involution in BBD biopsies predict lower breast cancer risk, and therefore its assessment may have potential value in risk assessment and management. However, assessment of TDLU involution is time-consuming and difficult to standardize and quantitate. Accordingly, we developed a CNN to enable automated quantitative measurement of TDLU involution and tested its performance in 174 specimens selected from the pathology archives at Mayo Clinic, Rochester, MN. The CNN was trained and tested on a subset of 33 biopsies, delineating important tissue types. Nine quantitative features were extracted from delineated TDLU regions. Our CNN reached an overall dice-score of 0.871 (+/- 0.049) for tissue classes versus reference standard annotation. Consensus of four reviewers scoring 705 images for TDLU involution demonstrated substantial agreement with the CNN method (unweighted kappa = 0.747 +/- 0.01). Quantitative involution measures showed anticipated associations with BBD histology, breast cancer risk, breast density, menopausal status, and breast cancer risk prediction scores (p < 0.05). Our work demonstrates the potential to improve risk prediction for women with BBD biopsies by applying CNN approaches to generate automated quantitative evaluation of TDLU involution.
Published: 2022
Full Text: View/download PDF

24. Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses

Author: Zhan, Haoyu, Ahearn, Thomas U., Lecarpentier, Julie, Barnes, Daniel, Beesley, Jonathan, Qi, Guanghao, Hang, Xia, O'Mara, Tracy A., Zhao, Ni, Bolla, Manjeet K., Dunning, Alison M., Dennis, Joe, Wang, Qin, Abu Ful, Zumuruda, Aittomaki, Kristiina, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Arun, Banu K., Auer, Paul L., Azzollini, Jacopo, Barrowdale, Daniel, Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bialkowska, Katarzyna, Blanco, Ana, Blomqvist, Carl, Bogdanova, Natalia, V, Bojesen, Stig E., Bonanni, Bernardo, Bondavalli, Davide, Borg, Ake, Brauch, Hiltrud, Brenner, Hermann, Briceno, Ignacio, Broeks, Annegien, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Byers, Helen, Caldes, Trinidad, Caligo, Maria A., Calvello, Mariarosaria, Campa, Daniele, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Christiaens, Melissa, Christiansen, Hans, Chung, Wendy K., Claes, Kathleen B. M., Clarke, Christine L., Cornelissen, Sten, Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Diez, Orland, Domchek, Susan M., Doerk, Thilo, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Foretova, Lenka, Fostira, Florentia, Friedman, Eitan, Frost, Debra, Gago-Dominguez, Manuela, Gapstur, Susan M., Garber, Judy, Garcia-Saenz, Jose A., Gaudet, Mia M., Gayther, Simon A., Giles, Graham G., Godwin, Andrew K., Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Greene, Mark H., Gronwald, Jacek, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hake, Christopher R., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Hillemanns, Peter, Hogervorst, Frans B. L., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Huebner, Hanna, Hulick, Peter J., Imyanitov, Evgeny N., Isaacs, Claudine, Izatt, Louise, Jager, Agnes, Jakimovska, Milena, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Janni, Wolfgang, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kapoor, Pooja Middha, Karlan, Beth Y., Keeman, Renske, Khan, Sofia, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Konstantopoulou, Irene, Koppert, Linetta B., Koutros, Stella, Kristensen, Vessela N., Laenkholm, Anne-Vibeke, Lambrechts, Diether, Larsson, Susanna C., Laurent-Puig, Pierre, Lazaro, Conxi, Lazarova, Emilija, Lejbkowicz, Flavio, Leslie, Goska, Lesueur, Fabienne, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loud, Jennifer T., Lubinski, Jan, Lukomska, Alicja, Maclnnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Maria Elena, Matricardi, Laura, McGuffog, Lesley, McLean, Catriona, Mebirouk, Noura, Meindl, Alfons, Menon, Usha, Miller, Austin, Mingazheva, Elvira, Montagna, Marco, Mulligan, Anna Marie, Mulot, Claire, Muranen, Taru A., Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Newman, William G., Nielsens, Finn C., Nikitina-Zake, Liene, Nodora, Jesse, Offit, Kenneth, Olah, Edith, Olopade, Olufunmilayo, I, Olsson, Hakan, Orr, Nick, Papi, Laura, Papp, Janos, Park-Simon, Tjoung-Won, Parsons, Michael T., Peissel, Bernard, Peixoto, Ana, Peshkin, Beth, Peterlongo, Paolo, Peto, Julian, Phillips, Kelly-Anne, Piedmonte, Marion, Plaseska-Karanfilska, Dijana, Prajzendanc, Karolina, Prentice, Ross, Prokofyeva, Darya, Rack, Brigitte, Radice, Paolo, Ramus, Susan J., Rantala, Johanna, Rashid, Muhammad U., Rennert, Gad, Rennert, Hedy S., Risch, Harvey A., Romero, Atocha, Rookus, Matti A., Ruebner, Matthias, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Scheuner, Maren T., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schoettker, Ben, Schuermann, Peter, Senter, Leigha, Sharma, Priyanka, Sherman, Mark E., Shu, Xiao-Ou, Singer, Christian F., Smichkoska, Snezhana, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Stone, Jennifer, Stoppa-Lyonnet, Dominique, Swerdlow, Anthony J., Szabo, Csilla, I, Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teixeira, Manuel R., Terry, MaryBeth, Thomassen, Mads, Thull, Darcy L., Tischkowitz, Marc, Toland, Amanda E., Tollenaar, Rob A. E. M., Tomlinson, Ian, Torres, Diana, Troester, Melissa A., Truong, Therese, Tung, Nadine, Untch, Michael, Vachon, Celine M., van den Ouweland, Ans M. W., van der Kolk, Lizet E., van Veen, Elke M., vanRensburg, Elizabeth J., Vega, Ana, Wappenschmidt, Barbara, Weinberg, Clarice R., Weitzel, Jeffrey N., Wildiers, Hans, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zheng, Wei, Zorn, Kristin K., Milne, Roger L., Kraft, Peter, Simard, Jacques, Pharoah, Paul D. P., Michailidou, Kyriaki, Antoniou, Antonis C., Schmidt, Marjanka K., Chenevix-Trench, Georgia, Easton, Douglas F., Chatterjee, Nilanjan, Garcia-Closas, Montserrat, Zhan, Haoyu, Ahearn, Thomas U., Lecarpentier, Julie, Barnes, Daniel, Beesley, Jonathan, Qi, Guanghao, Hang, Xia, O'Mara, Tracy A., Zhao, Ni, Bolla, Manjeet K., Dunning, Alison M., Dennis, Joe, Wang, Qin, Abu Ful, Zumuruda, Aittomaki, Kristiina, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Arun, Banu K., Auer, Paul L., Azzollini, Jacopo, Barrowdale, Daniel, Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bialkowska, Katarzyna, Blanco, Ana, Blomqvist, Carl, Bogdanova, Natalia, V, Bojesen, Stig E., Bonanni, Bernardo, Bondavalli, Davide, Borg, Ake, Brauch, Hiltrud, Brenner, Hermann, Briceno, Ignacio, Broeks, Annegien, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Byers, Helen, Caldes, Trinidad, Caligo, Maria A., Calvello, Mariarosaria, Campa, Daniele, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Christiaens, Melissa, Christiansen, Hans, Chung, Wendy K., Claes, Kathleen B. M., Clarke, Christine L., Cornelissen, Sten, Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Diez, Orland, Domchek, Susan M., Doerk, Thilo, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Foretova, Lenka, Fostira, Florentia, Friedman, Eitan, Frost, Debra, Gago-Dominguez, Manuela, Gapstur, Susan M., Garber, Judy, Garcia-Saenz, Jose A., Gaudet, Mia M., Gayther, Simon A., Giles, Graham G., Godwin, Andrew K., Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Greene, Mark H., Gronwald, Jacek, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hake, Christopher R., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Hillemanns, Peter, Hogervorst, Frans B. L., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Huebner, Hanna, Hulick, Peter J., Imyanitov, Evgeny N., Isaacs, Claudine, Izatt, Louise, Jager, Agnes, Jakimovska, Milena, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Janni, Wolfgang, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kapoor, Pooja Middha, Karlan, Beth Y., Keeman, Renske, Khan, Sofia, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Konstantopoulou, Irene, Koppert, Linetta B., Koutros, Stella, Kristensen, Vessela N., Laenkholm, Anne-Vibeke, Lambrechts, Diether, Larsson, Susanna C., Laurent-Puig, Pierre, Lazaro, Conxi, Lazarova, Emilija, Lejbkowicz, Flavio, Leslie, Goska, Lesueur, Fabienne, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loud, Jennifer T., Lubinski, Jan, Lukomska, Alicja, Maclnnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Maria Elena, Matricardi, Laura, McGuffog, Lesley, McLean, Catriona, Mebirouk, Noura, Meindl, Alfons, Menon, Usha, Miller, Austin, Mingazheva, Elvira, Montagna, Marco, Mulligan, Anna Marie, Mulot, Claire, Muranen, Taru A., Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Newman, William G., Nielsens, Finn C., Nikitina-Zake, Liene, Nodora, Jesse, Offit, Kenneth, Olah, Edith, Olopade, Olufunmilayo, I, Olsson, Hakan, Orr, Nick, Papi, Laura, Papp, Janos, Park-Simon, Tjoung-Won, Parsons, Michael T., Peissel, Bernard, Peixoto, Ana, Peshkin, Beth, Peterlongo, Paolo, Peto, Julian, Phillips, Kelly-Anne, Piedmonte, Marion, Plaseska-Karanfilska, Dijana, Prajzendanc, Karolina, Prentice, Ross, Prokofyeva, Darya, Rack, Brigitte, Radice, Paolo, Ramus, Susan J., Rantala, Johanna, Rashid, Muhammad U., Rennert, Gad, Rennert, Hedy S., Risch, Harvey A., Romero, Atocha, Rookus, Matti A., Ruebner, Matthias, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Scheuner, Maren T., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schoettker, Ben, Schuermann, Peter, Senter, Leigha, Sharma, Priyanka, Sherman, Mark E., Shu, Xiao-Ou, Singer, Christian F., Smichkoska, Snezhana, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Stone, Jennifer, Stoppa-Lyonnet, Dominique, Swerdlow, Anthony J., Szabo, Csilla, I, Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teixeira, Manuel R., Terry, MaryBeth, Thomassen, Mads, Thull, Darcy L., Tischkowitz, Marc, Toland, Amanda E., Tollenaar, Rob A. E. M., Tomlinson, Ian, Torres, Diana, Troester, Melissa A., Truong, Therese, Tung, Nadine, Untch, Michael, Vachon, Celine M., van den Ouweland, Ans M. W., van der Kolk, Lizet E., van Veen, Elke M., vanRensburg, Elizabeth J., Vega, Ana, Wappenschmidt, Barbara, Weinberg, Clarice R., Weitzel, Jeffrey N., Wildiers, Hans, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zheng, Wei, Zorn, Kristin K., Milne, Roger L., Kraft, Peter, Simard, Jacques, Pharoah, Paul D. P., Michailidou, Kyriaki, Antoniou, Antonis C., Schmidt, Marjanka K., Chenevix-Trench, Georgia, Easton, Douglas F., Chatterjee, Nilanjan, and Garcia-Closas, Montserrat
Abstract: Genome-wide analysis identifies 32 loci associated with breast cancer susceptibility, accounting for estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade. Breast cancer susceptibility variants frequently show heterogeneity in associations by tumor subtype(1-3). To identify novel loci, we performed a genome-wide association study including 133,384 breast cancer cases and 113,789 controls, plus 18,908 BRCA1 mutation carriers (9,414 with breast cancer) of European ancestry, using both standard and novel methodologies that account for underlying tumor heterogeneity by estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade. We identified 32 novel susceptibility loci (P < 5.0 x 10(-8)), 15 of which showed evidence for associations with at least one tumor feature (false discovery rate < 0.05). Five loci showed associations (P < 0.05) in opposite directions between luminal and non-luminal subtypes. In silico analyses showed that these five loci contained cell-specific enhancers that differed between normal luminal and basal mammary cells. The genetic correlations between five intrinsic-like subtypes ranged from 0.35 to 0.80. The proportion of genome-wide chip heritability explained by all known susceptibility loci was 54.2% for luminal A-like disease and 37.6% for triple-negative disease. The odds ratios of polygenic risk scores, which included 330 variants, for the highest 1% of quantiles compared with middle quantiles were 5.63 and 3.02 for luminal A-like and triple-negative disease, respectively. These findings provide an improved understanding of genetic predisposition to breast cancer subtypes and will inform the development of subtype-specific polygenic risk scores.
Published: 2020
Full Text: View/download PDF

25. Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE).

Author: Talhouk, Aline, Talhouk, Aline, George, Joshy, Wang, Chen, Budden, Timothy, Tan, Tuan Zea, Chiu, Derek S, Kommoss, Stefan, Leong, Huei San, Chen, Stephanie, Intermaggio, Maria P, Gilks, Blake, Nazeran, Tayyebeh M, Volchek, Mila, Elatre, Wafaa, Bentley, Rex C, Senz, Janine, Lum, Amy, Chow, Veronica, Sudderuddin, Hanwei, Mackenzie, Robertson, Leong, Samuel CY, Liu, Geyi, Johnson, Dustin, Chen, Billy, Group, Aocs, Alsop, Jennifer, Banerjee, Susana N, Behrens, Sabine, Bodelon, Clara, Brand, Alison H, Brinton, Louise, Carney, Michael E, Chiew, Yoke-Eng, Cushing-Haugen, Kara L, Cybulski, Cezary, Ennis, Darren, Fereday, Sian, Fortner, Renée T, García-Donas, Jesús, Gentry-Maharaj, Aleksandra, Glasspool, Rosalind, Goranova, Teodora, Greene, Casey S, Haluska, Paul, Harris, Holly R, Hendley, Joy, Hernandez, Brenda Y, Herpel, Esther, Jimenez-Linan, Mercedes, Karpinskyj, Chloe, Kaufmann, Scott H, Keeney, Gary L, Kennedy, Catherine J, Köbel, Martin, Koziak, Jennifer M, Larson, Melissa C, Lester, Jenny, Lewsley, Liz-Anne, Lissowska, Jolanta, Lubiński, Jan, Luk, Hugh, Macintyre, Geoff, Mahner, Sven, McNeish, Iain A, Menkiszak, Janusz, Nevins, Nikilyn, Osorio, Ana, Oszurek, Oleg, Palacios, José, Hinsley, Samantha, Pearce, Celeste L, Pike, Malcolm C, Piskorz, Anna M, Ray-Coquard, Isabelle, Rhenius, Valerie, Rodriguez-Antona, Cristina, Sharma, Raghwa, Sherman, Mark E, De Silva, Dilrini, Singh, Naveena, Sinn, Peter, Slamon, Dennis, Song, Honglin, Steed, Helen, Stronach, Euan A, Thompson, Pamela J, Tołoczko, Aleksandra, Trabert, Britton, Traficante, Nadia, Tseng, Chiu-Chen, Widschwendter, Martin, Wilkens, Lynne R, Winham, Stacey J, Winterhoff, Boris, Beeghly-Fadiel, Alicia, Benitez, Javier, Berchuck, Andrew, Brenton, James D, Brown, Robert, Chang-Claude, Jenny, Talhouk, Aline, Talhouk, Aline, George, Joshy, Wang, Chen, Budden, Timothy, Tan, Tuan Zea, Chiu, Derek S, Kommoss, Stefan, Leong, Huei San, Chen, Stephanie, Intermaggio, Maria P, Gilks, Blake, Nazeran, Tayyebeh M, Volchek, Mila, Elatre, Wafaa, Bentley, Rex C, Senz, Janine, Lum, Amy, Chow, Veronica, Sudderuddin, Hanwei, Mackenzie, Robertson, Leong, Samuel CY, Liu, Geyi, Johnson, Dustin, Chen, Billy, Group, Aocs, Alsop, Jennifer, Banerjee, Susana N, Behrens, Sabine, Bodelon, Clara, Brand, Alison H, Brinton, Louise, Carney, Michael E, Chiew, Yoke-Eng, Cushing-Haugen, Kara L, Cybulski, Cezary, Ennis, Darren, Fereday, Sian, Fortner, Renée T, García-Donas, Jesús, Gentry-Maharaj, Aleksandra, Glasspool, Rosalind, Goranova, Teodora, Greene, Casey S, Haluska, Paul, Harris, Holly R, Hendley, Joy, Hernandez, Brenda Y, Herpel, Esther, Jimenez-Linan, Mercedes, Karpinskyj, Chloe, Kaufmann, Scott H, Keeney, Gary L, Kennedy, Catherine J, Köbel, Martin, Koziak, Jennifer M, Larson, Melissa C, Lester, Jenny, Lewsley, Liz-Anne, Lissowska, Jolanta, Lubiński, Jan, Luk, Hugh, Macintyre, Geoff, Mahner, Sven, McNeish, Iain A, Menkiszak, Janusz, Nevins, Nikilyn, Osorio, Ana, Oszurek, Oleg, Palacios, José, Hinsley, Samantha, Pearce, Celeste L, Pike, Malcolm C, Piskorz, Anna M, Ray-Coquard, Isabelle, Rhenius, Valerie, Rodriguez-Antona, Cristina, Sharma, Raghwa, Sherman, Mark E, De Silva, Dilrini, Singh, Naveena, Sinn, Peter, Slamon, Dennis, Song, Honglin, Steed, Helen, Stronach, Euan A, Thompson, Pamela J, Tołoczko, Aleksandra, Trabert, Britton, Traficante, Nadia, Tseng, Chiu-Chen, Widschwendter, Martin, Wilkens, Lynne R, Winham, Stacey J, Winterhoff, Boris, Beeghly-Fadiel, Alicia, Benitez, Javier, Berchuck, Andrew, Brenton, James D, Brown, Robert, and Chang-Claude, Jenny
Abstract: PurposeGene expression-based molecular subtypes of high-grade serous tubo-ovarian cancer (HGSOC), demonstrated across multiple studies, may provide improved stratification for molecularly targeted trials. However, evaluation of clinical utility has been hindered by nonstandardized methods, which are not applicable in a clinical setting. We sought to generate a clinical grade minimal gene set assay for classification of individual tumor specimens into HGSOC subtypes and confirm previously reported subtype-associated features.Experimental designAdopting two independent approaches, we derived and internally validated algorithms for subtype prediction using published gene expression data from 1,650 tumors. We applied resulting models to NanoString data on 3,829 HGSOCs from the Ovarian Tumor Tissue Analysis consortium. We further developed, confirmed, and validated a reduced, minimal gene set predictor, with methods suitable for a single-patient setting.ResultsGene expression data were used to derive the predictor of high-grade serous ovarian carcinoma molecular subtype (PrOTYPE) assay. We established a de facto standard as a consensus of two parallel approaches. PrOTYPE subtypes are significantly associated with age, stage, residual disease, tumor-infiltrating lymphocytes, and outcome. The locked-down clinical grade PrOTYPE test includes a model with 55 genes that predicted gene expression subtype with >95% accuracy that was maintained in all analytic and biological validations.ConclusionsWe validated the PrOTYPE assay following the Institute of Medicine guidelines for the development of omics-based tests. This fully defined and locked-down clinical grade assay will enable trial design with molecular subtype stratification and allow for objective assessment of the predictive value of HGSOC molecular subtypes in precision medicine applications.See related commentary by McMullen et al., p. 5271.
Published: 2020

26. Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses

Author: Zhan, Haoyu, Ahearn, Thomas U., Lecarpentier, Julie, Barnes, Daniel, Beesley, Jonathan, Qi, Guanghao, Jiang, Xia, O'Mara, Tracy A., Zhao, Ni, Bolla, Manjeet K., Dunning, Alison M., Dennis, Joe, Wang, Qin, Abu Ful, Zumuruda, Aittomaki, Kristiina, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Arun, Banu K., Auer, Paul L., Azzollini, Jacopo, Barrowdale, Daniel, Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bialkowska, Katarzyna, Blanco, Ana, Blomqvist, Carl, Bogdanova, Natalia, V, Bojesen, Stig E., Bonanni, Bernardo, Bondavalli, Davide, Borg, Ake, Brauch, Hiltrud, Brenner, Hermann, Briceno, Ignacio, Broeks, Annegien, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Byers, Helen, Caldes, Trinidad, Caligo, Maria A., Calvello, Mariarosaria, Campa, Daniele, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Christiaens, Melissa, Christiansen, Hans, Chung, Wendy K., Claes, Kathleen B. M., Clarke, Christine L., Cornelissen, Sten, Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Diez, Orland, Domchek, Susan M., Doerk, Thilo, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Foretova, Lenka, Fostira, Florentia, Friedman, Eitan, Frost, Debra, Gago-Dominguez, Manuela, Gapstur, Susan M., Garber, Judy, Garcia-Saenz, Jose A., Gaudet, Mia M., Gayther, Simon A., Giles, Graham G., Godwin, Andrew K., Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Greene, Mark H., Gronwald, Jacek, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hake, Christopher R., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Hillemanns, Peter, Hogervorst, Frans B. L., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Huebner, Hanna, Hulick, Peter J., Imyanitov, Evgeny N., Isaacs, Claudine, Izatt, Louise, Jager, Agnes, Jakimovska, Milena, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Janni, Wolfgang, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kapoor, Pooja Middha, Karlan, Beth Y., Keeman, Renske, Khan, Sofia, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Konstantopoulou, Irene, Koppert, Linetta B., Koutros, Stella, Kristensen, Vessela N., Laenkholm, Anne-Vibeke, Lambrechts, Diether, Larsson, Susanna C., Laurent-Puig, Pierre, Lazaro, Conxi, Lazarova, Emilija, Lejbkowicz, Flavio, Leslie, Goska, Lesueur, Fabienne, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loud, Jennifer T., Lubinski, Jan, Lukomska, Alicja, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Maria Elena, Matricardi, Laura, McGuffog, Lesley, McLean, Catriona, Mebirouk, Noura, Meindl, Alfons, Menon, Usha, Miller, Austin, Mingazheva, Elvira, Montagna, Marco, Mulligan, Anna Marie, Mulot, Claire, Muranen, Taru A., Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Newman, William G., Nielsens, Finn C., Nikitina-Zake, Liene, Nodora, Jesse, Offit, Kenneth, Olah, Edith, Olopade, Olufunmilayo, I, Olsson, Hakan, Orr, Nick, Papi, Laura, Papp, Janos, Park-Simon, Tjoung-Won, Parsons, Michael T., Peissel, Bernard, Peixoto, Ana, Peshkin, Beth, Peterlongo, Paolo, Peto, Julian, Phillips, Kelly-Anne, Piedmonte, Marion, Plaseska-Karanfilska, Dijana, Prajzendanc, Karolina, Prentice, Ross, Prokofyeva, Darya, Rack, Brigitte, Radice, Paolo, Ramus, Susan J., Rantala, Johanna, Rashid, Muhammad U., Rennert, Gad, Rennert, Hedy S., Risch, Harvey A., Romero, Atocha, Rookus, Matti A., Ruebner, Matthias, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Scheuner, Maren T., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schoettker, Ben, Schuermann, Peter, Senter, Leigha, Sharma, Priyanka, Sherman, Mark E., Shu, Xiao-Ou, Singer, Christian F., Smichkoska, Snezhana, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Stone, Jennifer, Stoppa-Lyonnet, Dominique, Swerdlow, Anthony J., Szabo, Csilla, I, Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teixeira, Manuel R., Terry, MaryBeth, Thomassen, Mads, Thull, Darcy L., Tischkowitz, Marc, Toland, Amanda E., Tollenaar, Rob A. E. M., Tomlinson, Ian, Torres, Diana, Troester, Melissa A., Truong, Therese, Tung, Nadine, Untch, Michael, Vachon, Celine M., van den Ouweland, Ans M. W., van der Kolk, Lizet E., van Veen, Elke M., vanRensburg, Elizabeth J., Vega, Ana, Wappenschmidt, Barbara, Weinberg, Clarice R., Weitzel, Jeffrey N., Wildiers, Hans, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zheng, Wei, Zorn, Kristin K., Milne, Roger L., Kraft, Peter, Simard, Jacques, Pharoah, Paul D. P., Michailidou, Kyriaki, Antoniou, Antonis C., Schmidt, Marjanka K., Chenevix-Trench, Georgia, Easton, Douglas F., Chatterjee, Nilanjan, Garcia-Closas, Montserrat, Zhan, Haoyu, Ahearn, Thomas U., Lecarpentier, Julie, Barnes, Daniel, Beesley, Jonathan, Qi, Guanghao, Jiang, Xia, O'Mara, Tracy A., Zhao, Ni, Bolla, Manjeet K., Dunning, Alison M., Dennis, Joe, Wang, Qin, Abu Ful, Zumuruda, Aittomaki, Kristiina, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Arun, Banu K., Auer, Paul L., Azzollini, Jacopo, Barrowdale, Daniel, Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bialkowska, Katarzyna, Blanco, Ana, Blomqvist, Carl, Bogdanova, Natalia, V, Bojesen, Stig E., Bonanni, Bernardo, Bondavalli, Davide, Borg, Ake, Brauch, Hiltrud, Brenner, Hermann, Briceno, Ignacio, Broeks, Annegien, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Byers, Helen, Caldes, Trinidad, Caligo, Maria A., Calvello, Mariarosaria, Campa, Daniele, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Christiaens, Melissa, Christiansen, Hans, Chung, Wendy K., Claes, Kathleen B. M., Clarke, Christine L., Cornelissen, Sten, Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Diez, Orland, Domchek, Susan M., Doerk, Thilo, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Foretova, Lenka, Fostira, Florentia, Friedman, Eitan, Frost, Debra, Gago-Dominguez, Manuela, Gapstur, Susan M., Garber, Judy, Garcia-Saenz, Jose A., Gaudet, Mia M., Gayther, Simon A., Giles, Graham G., Godwin, Andrew K., Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Greene, Mark H., Gronwald, Jacek, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hake, Christopher R., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Hillemanns, Peter, Hogervorst, Frans B. L., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Huebner, Hanna, Hulick, Peter J., Imyanitov, Evgeny N., Isaacs, Claudine, Izatt, Louise, Jager, Agnes, Jakimovska, Milena, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Janni, Wolfgang, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kapoor, Pooja Middha, Karlan, Beth Y., Keeman, Renske, Khan, Sofia, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Konstantopoulou, Irene, Koppert, Linetta B., Koutros, Stella, Kristensen, Vessela N., Laenkholm, Anne-Vibeke, Lambrechts, Diether, Larsson, Susanna C., Laurent-Puig, Pierre, Lazaro, Conxi, Lazarova, Emilija, Lejbkowicz, Flavio, Leslie, Goska, Lesueur, Fabienne, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loud, Jennifer T., Lubinski, Jan, Lukomska, Alicja, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Maria Elena, Matricardi, Laura, McGuffog, Lesley, McLean, Catriona, Mebirouk, Noura, Meindl, Alfons, Menon, Usha, Miller, Austin, Mingazheva, Elvira, Montagna, Marco, Mulligan, Anna Marie, Mulot, Claire, Muranen, Taru A., Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Newman, William G., Nielsens, Finn C., Nikitina-Zake, Liene, Nodora, Jesse, Offit, Kenneth, Olah, Edith, Olopade, Olufunmilayo, I, Olsson, Hakan, Orr, Nick, Papi, Laura, Papp, Janos, Park-Simon, Tjoung-Won, Parsons, Michael T., Peissel, Bernard, Peixoto, Ana, Peshkin, Beth, Peterlongo, Paolo, Peto, Julian, Phillips, Kelly-Anne, Piedmonte, Marion, Plaseska-Karanfilska, Dijana, Prajzendanc, Karolina, Prentice, Ross, Prokofyeva, Darya, Rack, Brigitte, Radice, Paolo, Ramus, Susan J., Rantala, Johanna, Rashid, Muhammad U., Rennert, Gad, Rennert, Hedy S., Risch, Harvey A., Romero, Atocha, Rookus, Matti A., Ruebner, Matthias, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Scheuner, Maren T., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schoettker, Ben, Schuermann, Peter, Senter, Leigha, Sharma, Priyanka, Sherman, Mark E., Shu, Xiao-Ou, Singer, Christian F., Smichkoska, Snezhana, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Stone, Jennifer, Stoppa-Lyonnet, Dominique, Swerdlow, Anthony J., Szabo, Csilla, I, Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teixeira, Manuel R., Terry, MaryBeth, Thomassen, Mads, Thull, Darcy L., Tischkowitz, Marc, Toland, Amanda E., Tollenaar, Rob A. E. M., Tomlinson, Ian, Torres, Diana, Troester, Melissa A., Truong, Therese, Tung, Nadine, Untch, Michael, Vachon, Celine M., van den Ouweland, Ans M. W., van der Kolk, Lizet E., van Veen, Elke M., vanRensburg, Elizabeth J., Vega, Ana, Wappenschmidt, Barbara, Weinberg, Clarice R., Weitzel, Jeffrey N., Wildiers, Hans, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zheng, Wei, Zorn, Kristin K., Milne, Roger L., Kraft, Peter, Simard, Jacques, Pharoah, Paul D. P., Michailidou, Kyriaki, Antoniou, Antonis C., Schmidt, Marjanka K., Chenevix-Trench, Georgia, Easton, Douglas F., Chatterjee, Nilanjan, and Garcia-Closas, Montserrat
Abstract: Genome-wide analysis identifies 32 loci associated with breast cancer susceptibility, accounting for estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade. Breast cancer susceptibility variants frequently show heterogeneity in associations by tumor subtype(1-3). To identify novel loci, we performed a genome-wide association study including 133,384 breast cancer cases and 113,789 controls, plus 18,908 BRCA1 mutation carriers (9,414 with breast cancer) of European ancestry, using both standard and novel methodologies that account for underlying tumor heterogeneity by estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade. We identified 32 novel susceptibility loci (P < 5.0 x 10(-8)), 15 of which showed evidence for associations with at least one tumor feature (false discovery rate < 0.05). Five loci showed associations (P < 0.05) in opposite directions between luminal and non-luminal subtypes. In silico analyses showed that these five loci contained cell-specific enhancers that differed between normal luminal and basal mammary cells. The genetic correlations between five intrinsic-like subtypes ranged from 0.35 to 0.80. The proportion of genome-wide chip heritability explained by all known susceptibility loci was 54.2% for luminal A-like disease and 37.6% for triple-negative disease. The odds ratios of polygenic risk scores, which included 330 variants, for the highest 1% of quantiles compared with middle quantiles were 5.63 and 3.02 for luminal A-like and triple-negative disease, respectively. These findings provide an improved understanding of genetic predisposition to breast cancer subtypes and will inform the development of subtype-specific polygenic risk scores.
Published: 2020

27. Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE).

Author: Talhouk, Aline, Talhouk, Aline, George, Joshy, Wang, Chen, Budden, Timothy, Tan, Tuan Zea, Chiu, Derek S, Kommoss, Stefan, Leong, Huei San, Chen, Stephanie, Intermaggio, Maria P, Gilks, Blake, Nazeran, Tayyebeh M, Volchek, Mila, Elatre, Wafaa, Bentley, Rex C, Senz, Janine, Lum, Amy, Chow, Veronica, Sudderuddin, Hanwei, Mackenzie, Robertson, Leong, Samuel CY, Liu, Geyi, Johnson, Dustin, Chen, Billy, Group, Aocs, Alsop, Jennifer, Banerjee, Susana N, Behrens, Sabine, Bodelon, Clara, Brand, Alison H, Brinton, Louise, Carney, Michael E, Chiew, Yoke-Eng, Cushing-Haugen, Kara L, Cybulski, Cezary, Ennis, Darren, Fereday, Sian, Fortner, Renée T, García-Donas, Jesús, Gentry-Maharaj, Aleksandra, Glasspool, Rosalind, Goranova, Teodora, Greene, Casey S, Haluska, Paul, Harris, Holly R, Hendley, Joy, Hernandez, Brenda Y, Herpel, Esther, Jimenez-Linan, Mercedes, Karpinskyj, Chloe, Kaufmann, Scott H, Keeney, Gary L, Kennedy, Catherine J, Köbel, Martin, Koziak, Jennifer M, Larson, Melissa C, Lester, Jenny, Lewsley, Liz-Anne, Lissowska, Jolanta, Lubiński, Jan, Luk, Hugh, Macintyre, Geoff, Mahner, Sven, McNeish, Iain A, Menkiszak, Janusz, Nevins, Nikilyn, Osorio, Ana, Oszurek, Oleg, Palacios, José, Hinsley, Samantha, Pearce, Celeste L, Pike, Malcolm C, Piskorz, Anna M, Ray-Coquard, Isabelle, Rhenius, Valerie, Rodriguez-Antona, Cristina, Sharma, Raghwa, Sherman, Mark E, De Silva, Dilrini, Singh, Naveena, Sinn, Peter, Slamon, Dennis, Song, Honglin, Steed, Helen, Stronach, Euan A, Thompson, Pamela J, Tołoczko, Aleksandra, Trabert, Britton, Traficante, Nadia, Tseng, Chiu-Chen, Widschwendter, Martin, Wilkens, Lynne R, Winham, Stacey J, Winterhoff, Boris, Beeghly-Fadiel, Alicia, Benitez, Javier, Berchuck, Andrew, Brenton, James D, Brown, Robert, Chang-Claude, Jenny, Talhouk, Aline, Talhouk, Aline, George, Joshy, Wang, Chen, Budden, Timothy, Tan, Tuan Zea, Chiu, Derek S, Kommoss, Stefan, Leong, Huei San, Chen, Stephanie, Intermaggio, Maria P, Gilks, Blake, Nazeran, Tayyebeh M, Volchek, Mila, Elatre, Wafaa, Bentley, Rex C, Senz, Janine, Lum, Amy, Chow, Veronica, Sudderuddin, Hanwei, Mackenzie, Robertson, Leong, Samuel CY, Liu, Geyi, Johnson, Dustin, Chen, Billy, Group, Aocs, Alsop, Jennifer, Banerjee, Susana N, Behrens, Sabine, Bodelon, Clara, Brand, Alison H, Brinton, Louise, Carney, Michael E, Chiew, Yoke-Eng, Cushing-Haugen, Kara L, Cybulski, Cezary, Ennis, Darren, Fereday, Sian, Fortner, Renée T, García-Donas, Jesús, Gentry-Maharaj, Aleksandra, Glasspool, Rosalind, Goranova, Teodora, Greene, Casey S, Haluska, Paul, Harris, Holly R, Hendley, Joy, Hernandez, Brenda Y, Herpel, Esther, Jimenez-Linan, Mercedes, Karpinskyj, Chloe, Kaufmann, Scott H, Keeney, Gary L, Kennedy, Catherine J, Köbel, Martin, Koziak, Jennifer M, Larson, Melissa C, Lester, Jenny, Lewsley, Liz-Anne, Lissowska, Jolanta, Lubiński, Jan, Luk, Hugh, Macintyre, Geoff, Mahner, Sven, McNeish, Iain A, Menkiszak, Janusz, Nevins, Nikilyn, Osorio, Ana, Oszurek, Oleg, Palacios, José, Hinsley, Samantha, Pearce, Celeste L, Pike, Malcolm C, Piskorz, Anna M, Ray-Coquard, Isabelle, Rhenius, Valerie, Rodriguez-Antona, Cristina, Sharma, Raghwa, Sherman, Mark E, De Silva, Dilrini, Singh, Naveena, Sinn, Peter, Slamon, Dennis, Song, Honglin, Steed, Helen, Stronach, Euan A, Thompson, Pamela J, Tołoczko, Aleksandra, Trabert, Britton, Traficante, Nadia, Tseng, Chiu-Chen, Widschwendter, Martin, Wilkens, Lynne R, Winham, Stacey J, Winterhoff, Boris, Beeghly-Fadiel, Alicia, Benitez, Javier, Berchuck, Andrew, Brenton, James D, Brown, Robert, and Chang-Claude, Jenny
Abstract: PurposeGene expression-based molecular subtypes of high-grade serous tubo-ovarian cancer (HGSOC), demonstrated across multiple studies, may provide improved stratification for molecularly targeted trials. However, evaluation of clinical utility has been hindered by nonstandardized methods, which are not applicable in a clinical setting. We sought to generate a clinical grade minimal gene set assay for classification of individual tumor specimens into HGSOC subtypes and confirm previously reported subtype-associated features.Experimental designAdopting two independent approaches, we derived and internally validated algorithms for subtype prediction using published gene expression data from 1,650 tumors. We applied resulting models to NanoString data on 3,829 HGSOCs from the Ovarian Tumor Tissue Analysis consortium. We further developed, confirmed, and validated a reduced, minimal gene set predictor, with methods suitable for a single-patient setting.ResultsGene expression data were used to derive the predictor of high-grade serous ovarian carcinoma molecular subtype (PrOTYPE) assay. We established a de facto standard as a consensus of two parallel approaches. PrOTYPE subtypes are significantly associated with age, stage, residual disease, tumor-infiltrating lymphocytes, and outcome. The locked-down clinical grade PrOTYPE test includes a model with 55 genes that predicted gene expression subtype with >95% accuracy that was maintained in all analytic and biological validations.ConclusionsWe validated the PrOTYPE assay following the Institute of Medicine guidelines for the development of omics-based tests. This fully defined and locked-down clinical grade assay will enable trial design with molecular subtype stratification and allow for objective assessment of the predictive value of HGSOC molecular subtypes in precision medicine applications.See related commentary by McMullen et al., p. 5271.
Published: 2020

28. Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses

Author: Zhan, Haoyu, Ahearn, Thomas U., Lecarpentier, Julie, Barnes, Daniel, Beesley, Jonathan, Qi, Guanghao, Jiang, Xia, O'Mara, Tracy A., Zhao, Ni, Bolla, Manjeet K., Dunning, Alison M., Dennis, Joe, Wang, Qin, Abu Ful, Zumuruda, Aittomaki, Kristiina, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Arun, Banu K., Auer, Paul L., Azzollini, Jacopo, Barrowdale, Daniel, Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bialkowska, Katarzyna, Blanco, Ana, Blomqvist, Carl, Bogdanova, Natalia, V, Bojesen, Stig E., Bonanni, Bernardo, Bondavalli, Davide, Borg, Ake, Brauch, Hiltrud, Brenner, Hermann, Briceno, Ignacio, Broeks, Annegien, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Byers, Helen, Caldes, Trinidad, Caligo, Maria A., Calvello, Mariarosaria, Campa, Daniele, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Christiaens, Melissa, Christiansen, Hans, Chung, Wendy K., Claes, Kathleen B. M., Clarke, Christine L., Cornelissen, Sten, Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Diez, Orland, Domchek, Susan M., Doerk, Thilo, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Foretova, Lenka, Fostira, Florentia, Friedman, Eitan, Frost, Debra, Gago-Dominguez, Manuela, Gapstur, Susan M., Garber, Judy, Garcia-Saenz, Jose A., Gaudet, Mia M., Gayther, Simon A., Giles, Graham G., Godwin, Andrew K., Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Greene, Mark H., Gronwald, Jacek, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hake, Christopher R., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Hillemanns, Peter, Hogervorst, Frans B. L., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Huebner, Hanna, Hulick, Peter J., Imyanitov, Evgeny N., Isaacs, Claudine, Izatt, Louise, Jager, Agnes, Jakimovska, Milena, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Janni, Wolfgang, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kapoor, Pooja Middha, Karlan, Beth Y., Keeman, Renske, Khan, Sofia, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Konstantopoulou, Irene, Koppert, Linetta B., Koutros, Stella, Kristensen, Vessela N., Laenkholm, Anne-Vibeke, Lambrechts, Diether, Larsson, Susanna C., Laurent-Puig, Pierre, Lazaro, Conxi, Lazarova, Emilija, Lejbkowicz, Flavio, Leslie, Goska, Lesueur, Fabienne, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loud, Jennifer T., Lubinski, Jan, Lukomska, Alicja, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Maria Elena, Matricardi, Laura, McGuffog, Lesley, McLean, Catriona, Mebirouk, Noura, Meindl, Alfons, Menon, Usha, Miller, Austin, Mingazheva, Elvira, Montagna, Marco, Mulligan, Anna Marie, Mulot, Claire, Muranen, Taru A., Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Newman, William G., Nielsens, Finn C., Nikitina-Zake, Liene, Nodora, Jesse, Offit, Kenneth, Olah, Edith, Olopade, Olufunmilayo, I, Olsson, Hakan, Orr, Nick, Papi, Laura, Papp, Janos, Park-Simon, Tjoung-Won, Parsons, Michael T., Peissel, Bernard, Peixoto, Ana, Peshkin, Beth, Peterlongo, Paolo, Peto, Julian, Phillips, Kelly-Anne, Piedmonte, Marion, Plaseska-Karanfilska, Dijana, Prajzendanc, Karolina, Prentice, Ross, Prokofyeva, Darya, Rack, Brigitte, Radice, Paolo, Ramus, Susan J., Rantala, Johanna, Rashid, Muhammad U., Rennert, Gad, Rennert, Hedy S., Risch, Harvey A., Romero, Atocha, Rookus, Matti A., Ruebner, Matthias, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Scheuner, Maren T., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schoettker, Ben, Schuermann, Peter, Senter, Leigha, Sharma, Priyanka, Sherman, Mark E., Shu, Xiao-Ou, Singer, Christian F., Smichkoska, Snezhana, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Stone, Jennifer, Stoppa-Lyonnet, Dominique, Swerdlow, Anthony J., Szabo, Csilla, I, Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teixeira, Manuel R., Terry, MaryBeth, Thomassen, Mads, Thull, Darcy L., Tischkowitz, Marc, Toland, Amanda E., Tollenaar, Rob A. E. M., Tomlinson, Ian, Torres, Diana, Troester, Melissa A., Truong, Therese, Tung, Nadine, Untch, Michael, Vachon, Celine M., van den Ouweland, Ans M. W., van der Kolk, Lizet E., van Veen, Elke M., vanRensburg, Elizabeth J., Vega, Ana, Wappenschmidt, Barbara, Weinberg, Clarice R., Weitzel, Jeffrey N., Wildiers, Hans, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zheng, Wei, Zorn, Kristin K., Milne, Roger L., Kraft, Peter, Simard, Jacques, Pharoah, Paul D. P., Michailidou, Kyriaki, Antoniou, Antonis C., Schmidt, Marjanka K., Chenevix-Trench, Georgia, Easton, Douglas F., Chatterjee, Nilanjan, Garcia-Closas, Montserrat, Zhan, Haoyu, Ahearn, Thomas U., Lecarpentier, Julie, Barnes, Daniel, Beesley, Jonathan, Qi, Guanghao, Jiang, Xia, O'Mara, Tracy A., Zhao, Ni, Bolla, Manjeet K., Dunning, Alison M., Dennis, Joe, Wang, Qin, Abu Ful, Zumuruda, Aittomaki, Kristiina, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Arun, Banu K., Auer, Paul L., Azzollini, Jacopo, Barrowdale, Daniel, Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bialkowska, Katarzyna, Blanco, Ana, Blomqvist, Carl, Bogdanova, Natalia, V, Bojesen, Stig E., Bonanni, Bernardo, Bondavalli, Davide, Borg, Ake, Brauch, Hiltrud, Brenner, Hermann, Briceno, Ignacio, Broeks, Annegien, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Buys, Saundra S., Byers, Helen, Caldes, Trinidad, Caligo, Maria A., Calvello, Mariarosaria, Campa, Daniele, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Christiaens, Melissa, Christiansen, Hans, Chung, Wendy K., Claes, Kathleen B. M., Clarke, Christine L., Cornelissen, Sten, Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Diez, Orland, Domchek, Susan M., Doerk, Thilo, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Foretova, Lenka, Fostira, Florentia, Friedman, Eitan, Frost, Debra, Gago-Dominguez, Manuela, Gapstur, Susan M., Garber, Judy, Garcia-Saenz, Jose A., Gaudet, Mia M., Gayther, Simon A., Giles, Graham G., Godwin, Andrew K., Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Greene, Mark H., Gronwald, Jacek, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hake, Christopher R., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Hillemanns, Peter, Hogervorst, Frans B. L., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Huebner, Hanna, Hulick, Peter J., Imyanitov, Evgeny N., Isaacs, Claudine, Izatt, Louise, Jager, Agnes, Jakimovska, Milena, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Janni, Wolfgang, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kapoor, Pooja Middha, Karlan, Beth Y., Keeman, Renske, Khan, Sofia, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Konstantopoulou, Irene, Koppert, Linetta B., Koutros, Stella, Kristensen, Vessela N., Laenkholm, Anne-Vibeke, Lambrechts, Diether, Larsson, Susanna C., Laurent-Puig, Pierre, Lazaro, Conxi, Lazarova, Emilija, Lejbkowicz, Flavio, Leslie, Goska, Lesueur, Fabienne, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loud, Jennifer T., Lubinski, Jan, Lukomska, Alicja, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Maria Elena, Matricardi, Laura, McGuffog, Lesley, McLean, Catriona, Mebirouk, Noura, Meindl, Alfons, Menon, Usha, Miller, Austin, Mingazheva, Elvira, Montagna, Marco, Mulligan, Anna Marie, Mulot, Claire, Muranen, Taru A., Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Newman, William G., Nielsens, Finn C., Nikitina-Zake, Liene, Nodora, Jesse, Offit, Kenneth, Olah, Edith, Olopade, Olufunmilayo, I, Olsson, Hakan, Orr, Nick, Papi, Laura, Papp, Janos, Park-Simon, Tjoung-Won, Parsons, Michael T., Peissel, Bernard, Peixoto, Ana, Peshkin, Beth, Peterlongo, Paolo, Peto, Julian, Phillips, Kelly-Anne, Piedmonte, Marion, Plaseska-Karanfilska, Dijana, Prajzendanc, Karolina, Prentice, Ross, Prokofyeva, Darya, Rack, Brigitte, Radice, Paolo, Ramus, Susan J., Rantala, Johanna, Rashid, Muhammad U., Rennert, Gad, Rennert, Hedy S., Risch, Harvey A., Romero, Atocha, Rookus, Matti A., Ruebner, Matthias, Ruediger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Scheuner, Maren T., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schoettker, Ben, Schuermann, Peter, Senter, Leigha, Sharma, Priyanka, Sherman, Mark E., Shu, Xiao-Ou, Singer, Christian F., Smichkoska, Snezhana, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Stone, Jennifer, Stoppa-Lyonnet, Dominique, Swerdlow, Anthony J., Szabo, Csilla, I, Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teixeira, Manuel R., Terry, MaryBeth, Thomassen, Mads, Thull, Darcy L., Tischkowitz, Marc, Toland, Amanda E., Tollenaar, Rob A. E. M., Tomlinson, Ian, Torres, Diana, Troester, Melissa A., Truong, Therese, Tung, Nadine, Untch, Michael, Vachon, Celine M., van den Ouweland, Ans M. W., van der Kolk, Lizet E., van Veen, Elke M., vanRensburg, Elizabeth J., Vega, Ana, Wappenschmidt, Barbara, Weinberg, Clarice R., Weitzel, Jeffrey N., Wildiers, Hans, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zheng, Wei, Zorn, Kristin K., Milne, Roger L., Kraft, Peter, Simard, Jacques, Pharoah, Paul D. P., Michailidou, Kyriaki, Antoniou, Antonis C., Schmidt, Marjanka K., Chenevix-Trench, Georgia, Easton, Douglas F., Chatterjee, Nilanjan, and Garcia-Closas, Montserrat
Abstract: Genome-wide analysis identifies 32 loci associated with breast cancer susceptibility, accounting for estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade. Breast cancer susceptibility variants frequently show heterogeneity in associations by tumor subtype(1-3). To identify novel loci, we performed a genome-wide association study including 133,384 breast cancer cases and 113,789 controls, plus 18,908 BRCA1 mutation carriers (9,414 with breast cancer) of European ancestry, using both standard and novel methodologies that account for underlying tumor heterogeneity by estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade. We identified 32 novel susceptibility loci (P < 5.0 x 10(-8)), 15 of which showed evidence for associations with at least one tumor feature (false discovery rate < 0.05). Five loci showed associations (P < 0.05) in opposite directions between luminal and non-luminal subtypes. In silico analyses showed that these five loci contained cell-specific enhancers that differed between normal luminal and basal mammary cells. The genetic correlations between five intrinsic-like subtypes ranged from 0.35 to 0.80. The proportion of genome-wide chip heritability explained by all known susceptibility loci was 54.2% for luminal A-like disease and 37.6% for triple-negative disease. The odds ratios of polygenic risk scores, which included 330 variants, for the highest 1% of quantiles compared with middle quantiles were 5.63 and 3.02 for luminal A-like and triple-negative disease, respectively. These findings provide an improved understanding of genetic predisposition to breast cancer subtypes and will inform the development of subtype-specific polygenic risk scores.
Published: 2020

29. Antibodies Against Chlamydia trachomatis and Ovarian Cancer Risk in Two Independent Populations

Author: Trabert, Britton, Waterboer, Tim, Idahl, Annika, Brenner, Nicole, Brinton, Louise A., Butt, Julia, Coburn, Sally B., Hartge, Patricia, Hufnagel, Katrin, Inturrisi, Federica, Lissowska, Jolanta, Mentzer, Alexander, Peplonska, Beata, Sherman, Mark E., Wills, Gillian S., Woodhall, Sarah C., Pawlita, Michael, Wentzensen, Nicolas, Trabert, Britton, Waterboer, Tim, Idahl, Annika, Brenner, Nicole, Brinton, Louise A., Butt, Julia, Coburn, Sally B., Hartge, Patricia, Hufnagel, Katrin, Inturrisi, Federica, Lissowska, Jolanta, Mentzer, Alexander, Peplonska, Beata, Sherman, Mark E., Wills, Gillian S., Woodhall, Sarah C., Pawlita, Michael, and Wentzensen, Nicolas
Abstract: Background: Pelvic inflammatory disease (PID) has been associated with ovarian cancer risk. To clarify the role of Chlamydia trachomatis and other infectious agents in the development of ovarian cancer, we evaluated the association of serologic markers with incident ovarian cancer using a staged approach in two independent populations. Methods: Studies included: 1) a case-control study in Poland (244 ovarian cancers/556 control subjects) and 2) a prospective nested case-control study in the PLCO Cancer Screening Trial (160 ovarian cancers/159 control subjects). Associations of serologic marker levels with ovarian cancer risk at diagnostic as well as higher thresholds, identified in Poland and independently evaluated in PLCO, were estimated using multivariable adjusted logistic regression. Results: In the Polish study, antibodies (based on laboratory cut-point) against the chlamydia plasmid-encoded Pgp3 protein (serological gold standard) were associated with increased ovarian cancer risk (adjusted odds ratio [OR] = 1.63, 95% confidence interval [CI] = 1.20 to 2.22); when a positive result was redefined at higher levels, ovarian cancer risk was increased (cut-point 2: OR = 2.00, 95% CI = 1.38 to 2.89; cut-point 3 [max OR]: OR = 2.19, 95% CI = 1.29 to 3.73). In the prospective PLCO study, Pgp3 antibodies were associated with elevated risk at the laboratory cut-point (OR = 1.43, 95% CI = 0.78 to 2.63) and more stringent cut-points (cut-point 2: OR = 2.25, 95% CI = 1.07 to 4.71); cut-point 3: OR = 2.53, 95% CI = 0.63 to 10.08). In both studies, antibodies against other infectious agents measured were not associated with risk. Conclusions: In two independent populations, antibodies against prior/current C. trachomatis (Pgp3) were associated with a doubling in ovarian cancer risk, whereas markers of other infectious agents were unrelated. These findings lend support for an association between PID and ovarian cancer.
Published: 2019
Full Text: View/download PDF

30. Application of convolutional neural networks to breast biopsies to delineate tissue correlates of mammographic breast density

Author: Mullooly, Maeve, Ehteshami Bejnordi, B., Pfeiffer, Ruth M., Fan, Shaoqi, Palakal, Maya, Hada, Manila, Karssemeijer, N., Laak, J.A.W.M. van der, Sherman, Mark E., Gierach, Gretchen L., Mullooly, Maeve, Ehteshami Bejnordi, B., Pfeiffer, Ruth M., Fan, Shaoqi, Palakal, Maya, Hada, Manila, Karssemeijer, N., Laak, J.A.W.M. van der, Sherman, Mark E., and Gierach, Gretchen L.
Abstract: Contains fulltext : 212635.pdf (publisher's version ) (Open Access)
Published: 2019

31. Polygenic Risk Scores for Prediction of Breast Cancer and Breast Cancer Subtypes

Author: Mavaddat, Nasim, Michailidou, Kyriaki, Dennis, Joe, Lush, Michael, Fachal, Laura, Lee, Andrew, Tyrer, Jonathan P., Chen, Ting-Huei, Wang, Qin, Bolla, Manjeet K., Yang, Xin, Adank, Muriel A., Ahearn, Thomas, Aittomaki, Kristiina, Allen, Jamie, Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Auvinen, Paivi, Barrdahl, Myrto, Freeman, Laura E. Beane, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Blomqvist, Carl, Bogdanova, Natalia, V, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Bremer, Michael, Brenner, Hermann, Brentnall, Adam, Brock, Ian W., Brooks-Wilson, Angela, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Campa, Daniele, Carter, Brian D., Castelao, Jose E., Chanock, Stephen J., Chlebowski, Rowan, Christiansen, Hans, Clarke, Christine L., Collee, J. Margriet, Cordina-Duverger, Emilie, Cornelissen, Sten, Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Doerk, Thilo, dos-Santos-Silva, Isabel, Dumont, Martine, Durcan, Lorraine, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Ellberg, Carolina, Engel, Christoph, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Fletcher, Olivia, Flyger, Henrik, Foersti, Asta, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Georgoulias, Vassilios, Giles, Graham G., Gilyazova, Irina R., Glendon, Gord, Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hakansson, Niclas, Hamann, Ute, Hankinson, Susan E., Harkness, Elaine F., Hart, Steven N., He, Wei, Hein, Alexander, Heyworth, Jane, Hillemanns, Peter, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Huang, Guanmengqian, Humphreys, Keith, Hunter, David J., Jakimovska, Milena, Jakubowska, Anna, Janni, Wolfgang, John, Esther M., Johnson, Nichola, Jones, Michael E., Jukkola-Vuorinen, Arja, Jung, Audrey, Kaaks, Rudolf, Kaczmarek, Katarzyna, Kataja, Vesa, Keeman, Renske, Kerin, Michael J., Khusnutdinova, Elza, Kiiski, Johanna, I, Knight, Julia A., Ko, Yon-Dschun, Kosma, Veli-Matti, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kuehl, Tabea, Lambrechts, Diether, Le Marchand, Loic, Lee, Eunjung, Lejbkowicz, Flavio, Lilyquist, Jenna, Lindblom, Annika, Lindstrom, Sara, Lissowska, Jolanta, Lo, Wing-Yee, Loibl, Sibylle, Long, Jirong, Lubinski, Jan, Lux, Michael P., MacInnis, Robert J., Maishman, Tom, Makalic, Enes, Kostovska, Ivana Maleva, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Martens, John W. M., Martinez, Maria Elena, Mavroudis, Dimitrios, McLean, Catriona, Meindl, Alfons, Menon, Usha, Middha, Pooja, Miller, Nicola, Moreno, Fernando, Mulligan, Anna Marie, Mulot, Claire, Munoz-Garzon, Victor M., Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Newman, William G., Nielsen, Sune F., Nordestgaard, Borge G., Norman, Aaron, Offit, Kenneth, Olson, Janet E., Olsson, Hakan, Orr, Nick, Pankratz, V. Shane, Park-Simon, Tjoung-Won, Perez, Jose I. A., Perez-Barrios, Clara, Peterlongo, Paolo, Peto, Julian, Pinchev, Mila, Plaseska-Karanfilska, Dijana, Polley, Eric C., Prentice, Ross, Presneau, Nadege, Prokofyeva, Darya, Purrington, Kristen, Pylkas, Katri, Rack, Brigitte, Radice, Paolo, Rau-Murthy, Rohini, Rennert, Gad, Rennert, Hedy S., Rhenius, Valerie, Robson, Mark, Romero, Atocha, Ruddy, Kathryn J., Ruebner, Matthias, Saloustros, Emmanouil, Sandler, Dale P., Sawyer, Elinor J., Schmidt, Daniel F., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schumacher, Fredrick, Schuermann, Peter, Schwentner, Lukas, Scott, Christopher, Scott, Rodney J., Seynaeve, Caroline, Shah, Mitul, Sherman, Mark E., Shrubsole, Martha J., Shu, Xiao-Ou, Slager, Susan, Smeets, Ann, Sohn, Christof, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Stegmaier, Christa, Stone, Jennifer, Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Terry, Mary Beth, Thoene, Kathrin, Tollenaar, Rob A. E. M., Tomlinson, Ian, Truong, Therese, Tzardi, Maria, Ulmer, Hans-Ulrich, Untch, Michael, Vachon, Celine M., van Veen, Elke M., Vijai, Joseph, Weinberg, Clarice R., Wendt, Camilla, Whittemore, Alice S., Wildiers, Hans, Willett, Walter, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zhang, Yan, Zheng, Wei, Ziogas, Argyrios, Clarke, Christine, Balleine, Rosemary, Baxter, Robert, Braye, Stephen, Carpenter, Jane, Dahlstrom, Jane, Forbes, John, Lee, C. Soon, Marsh, Deborah, Morey, Adrienne, Pathmanathan, Nirmala, Scott, Rodney, Simpson, Peter, Spigelman, Allan, Wilcken, Nicholas, Yip, Desmond, Zeps, Nikolajs, Sexton, Adrienne, Dobrovic, Alex, Christian, Alice, Trainer, Alison, Fellows, Andrew, Shelling, Andrew, De Fazio, Anna, Blackburn, Anneke, Crook, Ashley, Meiser, Bettina, Patterson, Briony, Clarke, Christobel, Saunders, Christobel, Hunt, Clare, Scott, Clare, Amor, David, Ortega, David Gallego, Marsh, Deb, Edkins, Edward, Salisbury, Elizabeth, Haan, Eric, Macrea, Finlay, Farshid, Gelareh, Lindeman, Geoff, Trench, Georgia, Mann, Graham, Giles, Graham, Gill, Grantley, Thorne, Heather, Campbell, Ian, Hickie, Ian, Caldon, Liz, Winship, Ingrid, Cui, James, Flanagan, James, Kollias, James, Visvader, Jane, Taylor, Jessica, Burke, Jo, Saunus, Jodi, Forbs, John, Hopper, John, Beesley, Jonathan, Kirk, Judy, French, Juliet, Tucker, Kathy, Wu, Kathy, Phillips, Kelly, Forrest, Laura, Lipton, Lara, Andrews, Leslie, Lobb, Lizz, Walker, Logan, Kentwell, Maira, Spurdle, Mandy, Cummings, Margaret, Gleeson, Margaret, Harris, Marion, Jenkins, Mark, Young, Mary Anne, Delatycki, Martin, Wallis, Mathew, Burgess, Matthew, Brown, Melissa, Southey, Melissa, Bogwitz, Michael, Field, Michael, Friedlander, Michael, Gattas, Michael, Saleh, Mona, Aghmesheh, Morteza, Hayward, Nick, Pachter, Nick, Cohen, Paul, Duijf, Pascal, James, Paul, Simpson, Pete, Fong, Peter, Butow, Phyllis, Williams, Rachael, Kefford, Rick, Simard, Jacques, Balleine, Rose-Mary, Dawson, Sarah-Jane, Lok, Sheau, O'connell, Shona, Greening, Sian, Nightingale, Sophie, Edwards, Stacey, Fox, Stephen, McLachlan, Sue-Anne, Lakhani, Sunil, Dudding, Tracy, Antill, Yoland, Sahlberg, Kristine K., Ottestad, Lars, Karesen, Rolf, Schlichting, Ellen, Holmen, Marit Muri, Sauer, Toril, Haakensen, Vilde, Engebraten, Olav, Naume, Bjorn, Fossa, Alexander, Kiserud, Cecile E., Reinertsen, Kristin, V, Helland, Aslaug, Riis, Margit, Geisler, Juergen, Dunning, Alison M., Thompson, Deborah J., Chenevix-Trench, Georgia, Chang-Claude, Jenny, Schmidt, Marjanka K., Hall, Per, Milne, Roger L., Pharoah, Paul D. P., Antoniou, Antonis C., Chatterjee, Nilanjan, Kraft, Peter, Garcia-Closas, Montserrat, Easton, Douglas F., Mavaddat, Nasim, Michailidou, Kyriaki, Dennis, Joe, Lush, Michael, Fachal, Laura, Lee, Andrew, Tyrer, Jonathan P., Chen, Ting-Huei, Wang, Qin, Bolla, Manjeet K., Yang, Xin, Adank, Muriel A., Ahearn, Thomas, Aittomaki, Kristiina, Allen, Jamie, Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Auvinen, Paivi, Barrdahl, Myrto, Freeman, Laura E. Beane, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Blomqvist, Carl, Bogdanova, Natalia, V, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Bremer, Michael, Brenner, Hermann, Brentnall, Adam, Brock, Ian W., Brooks-Wilson, Angela, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Campa, Daniele, Carter, Brian D., Castelao, Jose E., Chanock, Stephen J., Chlebowski, Rowan, Christiansen, Hans, Clarke, Christine L., Collee, J. Margriet, Cordina-Duverger, Emilie, Cornelissen, Sten, Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Doerk, Thilo, dos-Santos-Silva, Isabel, Dumont, Martine, Durcan, Lorraine, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Ellberg, Carolina, Engel, Christoph, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Fletcher, Olivia, Flyger, Henrik, Foersti, Asta, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Georgoulias, Vassilios, Giles, Graham G., Gilyazova, Irina R., Glendon, Gord, Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hakansson, Niclas, Hamann, Ute, Hankinson, Susan E., Harkness, Elaine F., Hart, Steven N., He, Wei, Hein, Alexander, Heyworth, Jane, Hillemanns, Peter, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Huang, Guanmengqian, Humphreys, Keith, Hunter, David J., Jakimovska, Milena, Jakubowska, Anna, Janni, Wolfgang, John, Esther M., Johnson, Nichola, Jones, Michael E., Jukkola-Vuorinen, Arja, Jung, Audrey, Kaaks, Rudolf, Kaczmarek, Katarzyna, Kataja, Vesa, Keeman, Renske, Kerin, Michael J., Khusnutdinova, Elza, Kiiski, Johanna, I, Knight, Julia A., Ko, Yon-Dschun, Kosma, Veli-Matti, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kuehl, Tabea, Lambrechts, Diether, Le Marchand, Loic, Lee, Eunjung, Lejbkowicz, Flavio, Lilyquist, Jenna, Lindblom, Annika, Lindstrom, Sara, Lissowska, Jolanta, Lo, Wing-Yee, Loibl, Sibylle, Long, Jirong, Lubinski, Jan, Lux, Michael P., MacInnis, Robert J., Maishman, Tom, Makalic, Enes, Kostovska, Ivana Maleva, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Martens, John W. M., Martinez, Maria Elena, Mavroudis, Dimitrios, McLean, Catriona, Meindl, Alfons, Menon, Usha, Middha, Pooja, Miller, Nicola, Moreno, Fernando, Mulligan, Anna Marie, Mulot, Claire, Munoz-Garzon, Victor M., Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Newman, William G., Nielsen, Sune F., Nordestgaard, Borge G., Norman, Aaron, Offit, Kenneth, Olson, Janet E., Olsson, Hakan, Orr, Nick, Pankratz, V. Shane, Park-Simon, Tjoung-Won, Perez, Jose I. A., Perez-Barrios, Clara, Peterlongo, Paolo, Peto, Julian, Pinchev, Mila, Plaseska-Karanfilska, Dijana, Polley, Eric C., Prentice, Ross, Presneau, Nadege, Prokofyeva, Darya, Purrington, Kristen, Pylkas, Katri, Rack, Brigitte, Radice, Paolo, Rau-Murthy, Rohini, Rennert, Gad, Rennert, Hedy S., Rhenius, Valerie, Robson, Mark, Romero, Atocha, Ruddy, Kathryn J., Ruebner, Matthias, Saloustros, Emmanouil, Sandler, Dale P., Sawyer, Elinor J., Schmidt, Daniel F., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schumacher, Fredrick, Schuermann, Peter, Schwentner, Lukas, Scott, Christopher, Scott, Rodney J., Seynaeve, Caroline, Shah, Mitul, Sherman, Mark E., Shrubsole, Martha J., Shu, Xiao-Ou, Slager, Susan, Smeets, Ann, Sohn, Christof, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Stegmaier, Christa, Stone, Jennifer, Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Terry, Mary Beth, Thoene, Kathrin, Tollenaar, Rob A. E. M., Tomlinson, Ian, Truong, Therese, Tzardi, Maria, Ulmer, Hans-Ulrich, Untch, Michael, Vachon, Celine M., van Veen, Elke M., Vijai, Joseph, Weinberg, Clarice R., Wendt, Camilla, Whittemore, Alice S., Wildiers, Hans, Willett, Walter, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zhang, Yan, Zheng, Wei, Ziogas, Argyrios, Clarke, Christine, Balleine, Rosemary, Baxter, Robert, Braye, Stephen, Carpenter, Jane, Dahlstrom, Jane, Forbes, John, Lee, C. Soon, Marsh, Deborah, Morey, Adrienne, Pathmanathan, Nirmala, Scott, Rodney, Simpson, Peter, Spigelman, Allan, Wilcken, Nicholas, Yip, Desmond, Zeps, Nikolajs, Sexton, Adrienne, Dobrovic, Alex, Christian, Alice, Trainer, Alison, Fellows, Andrew, Shelling, Andrew, De Fazio, Anna, Blackburn, Anneke, Crook, Ashley, Meiser, Bettina, Patterson, Briony, Clarke, Christobel, Saunders, Christobel, Hunt, Clare, Scott, Clare, Amor, David, Ortega, David Gallego, Marsh, Deb, Edkins, Edward, Salisbury, Elizabeth, Haan, Eric, Macrea, Finlay, Farshid, Gelareh, Lindeman, Geoff, Trench, Georgia, Mann, Graham, Giles, Graham, Gill, Grantley, Thorne, Heather, Campbell, Ian, Hickie, Ian, Caldon, Liz, Winship, Ingrid, Cui, James, Flanagan, James, Kollias, James, Visvader, Jane, Taylor, Jessica, Burke, Jo, Saunus, Jodi, Forbs, John, Hopper, John, Beesley, Jonathan, Kirk, Judy, French, Juliet, Tucker, Kathy, Wu, Kathy, Phillips, Kelly, Forrest, Laura, Lipton, Lara, Andrews, Leslie, Lobb, Lizz, Walker, Logan, Kentwell, Maira, Spurdle, Mandy, Cummings, Margaret, Gleeson, Margaret, Harris, Marion, Jenkins, Mark, Young, Mary Anne, Delatycki, Martin, Wallis, Mathew, Burgess, Matthew, Brown, Melissa, Southey, Melissa, Bogwitz, Michael, Field, Michael, Friedlander, Michael, Gattas, Michael, Saleh, Mona, Aghmesheh, Morteza, Hayward, Nick, Pachter, Nick, Cohen, Paul, Duijf, Pascal, James, Paul, Simpson, Pete, Fong, Peter, Butow, Phyllis, Williams, Rachael, Kefford, Rick, Simard, Jacques, Balleine, Rose-Mary, Dawson, Sarah-Jane, Lok, Sheau, O'connell, Shona, Greening, Sian, Nightingale, Sophie, Edwards, Stacey, Fox, Stephen, McLachlan, Sue-Anne, Lakhani, Sunil, Dudding, Tracy, Antill, Yoland, Sahlberg, Kristine K., Ottestad, Lars, Karesen, Rolf, Schlichting, Ellen, Holmen, Marit Muri, Sauer, Toril, Haakensen, Vilde, Engebraten, Olav, Naume, Bjorn, Fossa, Alexander, Kiserud, Cecile E., Reinertsen, Kristin, V, Helland, Aslaug, Riis, Margit, Geisler, Juergen, Dunning, Alison M., Thompson, Deborah J., Chenevix-Trench, Georgia, Chang-Claude, Jenny, Schmidt, Marjanka K., Hall, Per, Milne, Roger L., Pharoah, Paul D. P., Antoniou, Antonis C., Chatterjee, Nilanjan, Kraft, Peter, Garcia-Closas, Montserrat, and Easton, Douglas F.
Abstract: Stratification of women according to their risk of breast cancer based on polygenic risk scores (PRSs) could improve screening and prevention strategies. Our aim was to develop PRSs, optimized for prediction of estrogen receptor (ER)-specific disease, from the largest available genome-wide association dataset and to empirically validate the PRSs in prospective studies. The development dataset comprised 94,075 case subjects and 75,017 control subjects of European ancestry from 69 studies, divided into training and validation sets. Samples were genotyped using genome-wide arrays, and single-nucleotide polymorphisms (SNPs) were selected by stepwise regression or lasso penalized regression. The best performing PRSs were validated in an independent test set comprising 11,428 case subjects and 18,323 control subjects from 10 prospective studies and 190,040 women from UK Biobank (3,215 incident breast cancers). For the best PRSs (313 SNPs), the odds ratio for overall disease per 1 standard deviation in ten prospective studies was 1.61 (95%CI: 1.57-1.65) with area under receiver-operator curve (AUC) = 0.630 (95%CI: 0.628-0.651). The lifetime risk of overall breast cancer in the top centile of the PRSs was 32.6%. Compared with women in the middle quintile, those in the highest 1% of risk had 4.37- and 2.78-fold risks, and those in the lowest 1% of risk had 0.16- and 0.27-fold risks, of developing ER-positive and ER-negative disease, respectively. Goodness-of-fit tests indicated that this PRS was well calibrated and predicts disease risk accurately in the tails of the distribution. This PRS is a powerful and reliable predictor of breast cancer risk that may improve breast cancer prevention programs.
Published: 2019

32. Antibodies Against Chlamydia trachomatis and Ovarian Cancer Risk in Two Independent Populations

Author: Trabert, Britton, Waterboer, Tim, Idahl, Annika, Brenner, Nicole, Brinton, Louise A., Butt, Julia, Coburn, Sally B., Hartge, Patricia, Hufnagel, Katrin, Inturrisi, Federica, Lissowska, Jolanta, Mentzer, Alexander, Peplonska, Beata, Sherman, Mark E., Wills, Gillian S., Woodhall, Sarah C., Pawlita, Michael, Wentzensen, Nicolas, Trabert, Britton, Waterboer, Tim, Idahl, Annika, Brenner, Nicole, Brinton, Louise A., Butt, Julia, Coburn, Sally B., Hartge, Patricia, Hufnagel, Katrin, Inturrisi, Federica, Lissowska, Jolanta, Mentzer, Alexander, Peplonska, Beata, Sherman, Mark E., Wills, Gillian S., Woodhall, Sarah C., Pawlita, Michael, and Wentzensen, Nicolas
Abstract: Background: Pelvic inflammatory disease (PID) has been associated with ovarian cancer risk. To clarify the role of Chlamydia trachomatis and other infectious agents in the development of ovarian cancer, we evaluated the association of serologic markers with incident ovarian cancer using a staged approach in two independent populations. Methods: Studies included: 1) a case-control study in Poland (244 ovarian cancers/556 control subjects) and 2) a prospective nested case-control study in the PLCO Cancer Screening Trial (160 ovarian cancers/159 control subjects). Associations of serologic marker levels with ovarian cancer risk at diagnostic as well as higher thresholds, identified in Poland and independently evaluated in PLCO, were estimated using multivariable adjusted logistic regression. Results: In the Polish study, antibodies (based on laboratory cut-point) against the chlamydia plasmid-encoded Pgp3 protein (serological gold standard) were associated with increased ovarian cancer risk (adjusted odds ratio [OR] = 1.63, 95% confidence interval [CI] = 1.20 to 2.22); when a positive result was redefined at higher levels, ovarian cancer risk was increased (cut-point 2: OR = 2.00, 95% CI = 1.38 to 2.89; cut-point 3 [max OR]: OR = 2.19, 95% CI = 1.29 to 3.73). In the prospective PLCO study, Pgp3 antibodies were associated with elevated risk at the laboratory cut-point (OR = 1.43, 95% CI = 0.78 to 2.63) and more stringent cut-points (cut-point 2: OR = 2.25, 95% CI = 1.07 to 4.71); cut-point 3: OR = 2.53, 95% CI = 0.63 to 10.08). In both studies, antibodies against other infectious agents measured were not associated with risk. Conclusions: In two independent populations, antibodies against prior/current C. trachomatis (Pgp3) were associated with a doubling in ovarian cancer risk, whereas markers of other infectious agents were unrelated. These findings lend support for an association between PID and ovarian cancer.
Published: 2019
Full Text: View/download PDF

33. Application of convolutional neural networks to breast biopsies to delineate tissue correlates of mammographic breast density

Author: Mullooly, Maeve, Ehteshami Bejnordi, B., Pfeiffer, Ruth M., Fan, Shaoqi, Palakal, Maya, Hada, Manila, Karssemeijer, N., Laak, J.A.W.M. van der, Sherman, Mark E., Gierach, Gretchen L., Mullooly, Maeve, Ehteshami Bejnordi, B., Pfeiffer, Ruth M., Fan, Shaoqi, Palakal, Maya, Hada, Manila, Karssemeijer, N., Laak, J.A.W.M. van der, Sherman, Mark E., and Gierach, Gretchen L.
Abstract: Contains fulltext : 212635.pdf (publisher's version ) (Open Access)
Published: 2019

34. Application of convolutional neural networks to breast biopsies to delineate tissue correlates of mammographic breast density

Author: Mullooly, Maeve, Ehteshami Bejnordi, B., Pfeiffer, Ruth M., Fan, Shaoqi, Palakal, Maya, Hada, Manila, Karssemeijer, N., Laak, J.A.W.M. van der, Sherman, Mark E., Gierach, Gretchen L., Mullooly, Maeve, Ehteshami Bejnordi, B., Pfeiffer, Ruth M., Fan, Shaoqi, Palakal, Maya, Hada, Manila, Karssemeijer, N., Laak, J.A.W.M. van der, Sherman, Mark E., and Gierach, Gretchen L.
Abstract: Contains fulltext : 212635.pdf (publisher's version ) (Open Access)
Published: 2019

35. Polygenic Risk Scores for Prediction of Breast Cancer and Breast Cancer Subtypes

Author: Mavaddat, Nasim, Michailidou, Kyriaki, Dennis, Joe, Lush, Michael, Fachal, Laura, Lee, Andrew, Tyrer, Jonathan P., Chen, Ting-Huei, Wang, Qin, Bolla, Manjeet K., Yang, Xin, Adank, Muriel A., Ahearn, Thomas, Aittomaki, Kristiina, Allen, Jamie, Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Auvinen, Paivi, Barrdahl, Myrto, Freeman, Laura E. Beane, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Blomqvist, Carl, Bogdanova, Natalia, V, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Bremer, Michael, Brenner, Hermann, Brentnall, Adam, Brock, Ian W., Brooks-Wilson, Angela, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Campa, Daniele, Carter, Brian D., Castelao, Jose E., Chanock, Stephen J., Chlebowski, Rowan, Christiansen, Hans, Clarke, Christine L., Collee, J. Margriet, Cordina-Duverger, Emilie, Cornelissen, Sten, Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Doerk, Thilo, dos-Santos-Silva, Isabel, Dumont, Martine, Durcan, Lorraine, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Ellberg, Carolina, Engel, Christoph, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Fletcher, Olivia, Flyger, Henrik, Foersti, Asta, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Georgoulias, Vassilios, Giles, Graham G., Gilyazova, Irina R., Glendon, Gord, Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hakansson, Niclas, Hamann, Ute, Hankinson, Susan E., Harkness, Elaine F., Hart, Steven N., He, Wei, Hein, Alexander, Heyworth, Jane, Hillemanns, Peter, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Huang, Guanmengqian, Humphreys, Keith, Hunter, David J., Jakimovska, Milena, Jakubowska, Anna, Janni, Wolfgang, John, Esther M., Johnson, Nichola, Jones, Michael E., Jukkola-Vuorinen, Arja, Jung, Audrey, Kaaks, Rudolf, Kaczmarek, Katarzyna, Kataja, Vesa, Keeman, Renske, Kerin, Michael J., Khusnutdinova, Elza, Kiiski, Johanna, I, Knight, Julia A., Ko, Yon-Dschun, Kosma, Veli-Matti, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kuehl, Tabea, Lambrechts, Diether, Le Marchand, Loic, Lee, Eunjung, Lejbkowicz, Flavio, Lilyquist, Jenna, Lindblom, Annika, Lindstrom, Sara, Lissowska, Jolanta, Lo, Wing-Yee, Loibl, Sibylle, Long, Jirong, Lubinski, Jan, Lux, Michael P., MacInnis, Robert J., Maishman, Tom, Makalic, Enes, Kostovska, Ivana Maleva, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Martens, John W. M., Martinez, Maria Elena, Mavroudis, Dimitrios, McLean, Catriona, Meindl, Alfons, Menon, Usha, Middha, Pooja, Miller, Nicola, Moreno, Fernando, Mulligan, Anna Marie, Mulot, Claire, Munoz-Garzon, Victor M., Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Newman, William G., Nielsen, Sune F., Nordestgaard, Borge G., Norman, Aaron, Offit, Kenneth, Olson, Janet E., Olsson, Hakan, Orr, Nick, Pankratz, V. Shane, Park-Simon, Tjoung-Won, Perez, Jose I. A., Perez-Barrios, Clara, Peterlongo, Paolo, Peto, Julian, Pinchev, Mila, Plaseska-Karanfilska, Dijana, Polley, Eric C., Prentice, Ross, Presneau, Nadege, Prokofyeva, Darya, Purrington, Kristen, Pylkas, Katri, Rack, Brigitte, Radice, Paolo, Rau-Murthy, Rohini, Rennert, Gad, Rennert, Hedy S., Rhenius, Valerie, Robson, Mark, Romero, Atocha, Ruddy, Kathryn J., Ruebner, Matthias, Saloustros, Emmanouil, Sandler, Dale P., Sawyer, Elinor J., Schmidt, Daniel F., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schumacher, Fredrick, Schuermann, Peter, Schwentner, Lukas, Scott, Christopher, Scott, Rodney J., Seynaeve, Caroline, Shah, Mitul, Sherman, Mark E., Shrubsole, Martha J., Shu, Xiao-Ou, Slager, Susan, Smeets, Ann, Sohn, Christof, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Stegmaier, Christa, Stone, Jennifer, Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Terry, Mary Beth, Thoene, Kathrin, Tollenaar, Rob A. E. M., Tomlinson, Ian, Truong, Therese, Tzardi, Maria, Ulmer, Hans-Ulrich, Untch, Michael, Vachon, Celine M., van Veen, Elke M., Vijai, Joseph, Weinberg, Clarice R., Wendt, Camilla, Whittemore, Alice S., Wildiers, Hans, Willett, Walter, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zhang, Yan, Zheng, Wei, Ziogas, Argyrios, Clarke, Christine, Balleine, Rosemary, Baxter, Robert, Braye, Stephen, Carpenter, Jane, Dahlstrom, Jane, Forbes, John, Lee, C. Soon, Marsh, Deborah, Morey, Adrienne, Pathmanathan, Nirmala, Scott, Rodney, Simpson, Peter, Spigelman, Allan, Wilcken, Nicholas, Yip, Desmond, Zeps, Nikolajs, Sexton, Adrienne, Dobrovic, Alex, Christian, Alice, Trainer, Alison, Fellows, Andrew, Shelling, Andrew, De Fazio, Anna, Blackburn, Anneke, Crook, Ashley, Meiser, Bettina, Patterson, Briony, Clarke, Christobel, Saunders, Christobel, Hunt, Clare, Scott, Clare, Amor, David, Ortega, David Gallego, Marsh, Deb, Edkins, Edward, Salisbury, Elizabeth, Haan, Eric, Macrea, Finlay, Farshid, Gelareh, Lindeman, Geoff, Trench, Georgia, Mann, Graham, Giles, Graham, Gill, Grantley, Thorne, Heather, Campbell, Ian, Hickie, Ian, Caldon, Liz, Winship, Ingrid, Cui, James, Flanagan, James, Kollias, James, Visvader, Jane, Taylor, Jessica, Burke, Jo, Saunus, Jodi, Forbs, John, Hopper, John, Beesley, Jonathan, Kirk, Judy, French, Juliet, Tucker, Kathy, Wu, Kathy, Phillips, Kelly, Forrest, Laura, Lipton, Lara, Andrews, Leslie, Lobb, Lizz, Walker, Logan, Kentwell, Maira, Spurdle, Mandy, Cummings, Margaret, Gleeson, Margaret, Harris, Marion, Jenkins, Mark, Young, Mary Anne, Delatycki, Martin, Wallis, Mathew, Burgess, Matthew, Brown, Melissa, Southey, Melissa, Bogwitz, Michael, Field, Michael, Friedlander, Michael, Gattas, Michael, Saleh, Mona, Aghmesheh, Morteza, Hayward, Nick, Pachter, Nick, Cohen, Paul, Duijf, Pascal, James, Paul, Simpson, Pete, Fong, Peter, Butow, Phyllis, Williams, Rachael, Kefford, Rick, Simard, Jacques, Balleine, Rose-Mary, Dawson, Sarah-Jane, Lok, Sheau, O'connell, Shona, Greening, Sian, Nightingale, Sophie, Edwards, Stacey, Fox, Stephen, McLachlan, Sue-Anne, Lakhani, Sunil, Dudding, Tracy, Antill, Yoland, Sahlberg, Kristine K., Ottestad, Lars, Karesen, Rolf, Schlichting, Ellen, Holmen, Marit Muri, Sauer, Toril, Haakensen, Vilde, Engebraten, Olav, Naume, Bjorn, Fossa, Alexander, Kiserud, Cecile E., Reinertsen, Kristin, V, Helland, Aslaug, Riis, Margit, Geisler, Juergen, Dunning, Alison M., Thompson, Deborah J., Chenevix-Trench, Georgia, Chang-Claude, Jenny, Schmidt, Marjanka K., Hall, Per, Milne, Roger L., Pharoah, Paul D. P., Antoniou, Antonis C., Chatterjee, Nilanjan, Kraft, Peter, Garcia-Closas, Montserrat, Easton, Douglas F., Mavaddat, Nasim, Michailidou, Kyriaki, Dennis, Joe, Lush, Michael, Fachal, Laura, Lee, Andrew, Tyrer, Jonathan P., Chen, Ting-Huei, Wang, Qin, Bolla, Manjeet K., Yang, Xin, Adank, Muriel A., Ahearn, Thomas, Aittomaki, Kristiina, Allen, Jamie, Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Aronson, Kristan J., Auer, Paul L., Auvinen, Paivi, Barrdahl, Myrto, Freeman, Laura E. Beane, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Blomqvist, Carl, Bogdanova, Natalia, V, Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brauch, Hiltrud, Bremer, Michael, Brenner, Hermann, Brentnall, Adam, Brock, Ian W., Brooks-Wilson, Angela, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Campa, Daniele, Carter, Brian D., Castelao, Jose E., Chanock, Stephen J., Chlebowski, Rowan, Christiansen, Hans, Clarke, Christine L., Collee, J. Margriet, Cordina-Duverger, Emilie, Cornelissen, Sten, Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Doerk, Thilo, dos-Santos-Silva, Isabel, Dumont, Martine, Durcan, Lorraine, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Ellberg, Carolina, Engel, Christoph, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Fletcher, Olivia, Flyger, Henrik, Foersti, Asta, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Georgoulias, Vassilios, Giles, Graham G., Gilyazova, Irina R., Glendon, Gord, Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hakansson, Niclas, Hamann, Ute, Hankinson, Susan E., Harkness, Elaine F., Hart, Steven N., He, Wei, Hein, Alexander, Heyworth, Jane, Hillemanns, Peter, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Huang, Guanmengqian, Humphreys, Keith, Hunter, David J., Jakimovska, Milena, Jakubowska, Anna, Janni, Wolfgang, John, Esther M., Johnson, Nichola, Jones, Michael E., Jukkola-Vuorinen, Arja, Jung, Audrey, Kaaks, Rudolf, Kaczmarek, Katarzyna, Kataja, Vesa, Keeman, Renske, Kerin, Michael J., Khusnutdinova, Elza, Kiiski, Johanna, I, Knight, Julia A., Ko, Yon-Dschun, Kosma, Veli-Matti, Koutros, Stella, Kristensen, Vessela N., Kruger, Ute, Kuehl, Tabea, Lambrechts, Diether, Le Marchand, Loic, Lee, Eunjung, Lejbkowicz, Flavio, Lilyquist, Jenna, Lindblom, Annika, Lindstrom, Sara, Lissowska, Jolanta, Lo, Wing-Yee, Loibl, Sibylle, Long, Jirong, Lubinski, Jan, Lux, Michael P., MacInnis, Robert J., Maishman, Tom, Makalic, Enes, Kostovska, Ivana Maleva, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Martens, John W. M., Martinez, Maria Elena, Mavroudis, Dimitrios, McLean, Catriona, Meindl, Alfons, Menon, Usha, Middha, Pooja, Miller, Nicola, Moreno, Fernando, Mulligan, Anna Marie, Mulot, Claire, Munoz-Garzon, Victor M., Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Newman, William G., Nielsen, Sune F., Nordestgaard, Borge G., Norman, Aaron, Offit, Kenneth, Olson, Janet E., Olsson, Hakan, Orr, Nick, Pankratz, V. Shane, Park-Simon, Tjoung-Won, Perez, Jose I. A., Perez-Barrios, Clara, Peterlongo, Paolo, Peto, Julian, Pinchev, Mila, Plaseska-Karanfilska, Dijana, Polley, Eric C., Prentice, Ross, Presneau, Nadege, Prokofyeva, Darya, Purrington, Kristen, Pylkas, Katri, Rack, Brigitte, Radice, Paolo, Rau-Murthy, Rohini, Rennert, Gad, Rennert, Hedy S., Rhenius, Valerie, Robson, Mark, Romero, Atocha, Ruddy, Kathryn J., Ruebner, Matthias, Saloustros, Emmanouil, Sandler, Dale P., Sawyer, Elinor J., Schmidt, Daniel F., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schumacher, Fredrick, Schuermann, Peter, Schwentner, Lukas, Scott, Christopher, Scott, Rodney J., Seynaeve, Caroline, Shah, Mitul, Sherman, Mark E., Shrubsole, Martha J., Shu, Xiao-Ou, Slager, Susan, Smeets, Ann, Sohn, Christof, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Stegmaier, Christa, Stone, Jennifer, Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Terry, Mary Beth, Thoene, Kathrin, Tollenaar, Rob A. E. M., Tomlinson, Ian, Truong, Therese, Tzardi, Maria, Ulmer, Hans-Ulrich, Untch, Michael, Vachon, Celine M., van Veen, Elke M., Vijai, Joseph, Weinberg, Clarice R., Wendt, Camilla, Whittemore, Alice S., Wildiers, Hans, Willett, Walter, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zhang, Yan, Zheng, Wei, Ziogas, Argyrios, Clarke, Christine, Balleine, Rosemary, Baxter, Robert, Braye, Stephen, Carpenter, Jane, Dahlstrom, Jane, Forbes, John, Lee, C. Soon, Marsh, Deborah, Morey, Adrienne, Pathmanathan, Nirmala, Scott, Rodney, Simpson, Peter, Spigelman, Allan, Wilcken, Nicholas, Yip, Desmond, Zeps, Nikolajs, Sexton, Adrienne, Dobrovic, Alex, Christian, Alice, Trainer, Alison, Fellows, Andrew, Shelling, Andrew, De Fazio, Anna, Blackburn, Anneke, Crook, Ashley, Meiser, Bettina, Patterson, Briony, Clarke, Christobel, Saunders, Christobel, Hunt, Clare, Scott, Clare, Amor, David, Ortega, David Gallego, Marsh, Deb, Edkins, Edward, Salisbury, Elizabeth, Haan, Eric, Macrea, Finlay, Farshid, Gelareh, Lindeman, Geoff, Trench, Georgia, Mann, Graham, Giles, Graham, Gill, Grantley, Thorne, Heather, Campbell, Ian, Hickie, Ian, Caldon, Liz, Winship, Ingrid, Cui, James, Flanagan, James, Kollias, James, Visvader, Jane, Taylor, Jessica, Burke, Jo, Saunus, Jodi, Forbs, John, Hopper, John, Beesley, Jonathan, Kirk, Judy, French, Juliet, Tucker, Kathy, Wu, Kathy, Phillips, Kelly, Forrest, Laura, Lipton, Lara, Andrews, Leslie, Lobb, Lizz, Walker, Logan, Kentwell, Maira, Spurdle, Mandy, Cummings, Margaret, Gleeson, Margaret, Harris, Marion, Jenkins, Mark, Young, Mary Anne, Delatycki, Martin, Wallis, Mathew, Burgess, Matthew, Brown, Melissa, Southey, Melissa, Bogwitz, Michael, Field, Michael, Friedlander, Michael, Gattas, Michael, Saleh, Mona, Aghmesheh, Morteza, Hayward, Nick, Pachter, Nick, Cohen, Paul, Duijf, Pascal, James, Paul, Simpson, Pete, Fong, Peter, Butow, Phyllis, Williams, Rachael, Kefford, Rick, Simard, Jacques, Balleine, Rose-Mary, Dawson, Sarah-Jane, Lok, Sheau, O'connell, Shona, Greening, Sian, Nightingale, Sophie, Edwards, Stacey, Fox, Stephen, McLachlan, Sue-Anne, Lakhani, Sunil, Dudding, Tracy, Antill, Yoland, Sahlberg, Kristine K., Ottestad, Lars, Karesen, Rolf, Schlichting, Ellen, Holmen, Marit Muri, Sauer, Toril, Haakensen, Vilde, Engebraten, Olav, Naume, Bjorn, Fossa, Alexander, Kiserud, Cecile E., Reinertsen, Kristin, V, Helland, Aslaug, Riis, Margit, Geisler, Juergen, Dunning, Alison M., Thompson, Deborah J., Chenevix-Trench, Georgia, Chang-Claude, Jenny, Schmidt, Marjanka K., Hall, Per, Milne, Roger L., Pharoah, Paul D. P., Antoniou, Antonis C., Chatterjee, Nilanjan, Kraft, Peter, Garcia-Closas, Montserrat, and Easton, Douglas F.
Abstract: Stratification of women according to their risk of breast cancer based on polygenic risk scores (PRSs) could improve screening and prevention strategies. Our aim was to develop PRSs, optimized for prediction of estrogen receptor (ER)-specific disease, from the largest available genome-wide association dataset and to empirically validate the PRSs in prospective studies. The development dataset comprised 94,075 case subjects and 75,017 control subjects of European ancestry from 69 studies, divided into training and validation sets. Samples were genotyped using genome-wide arrays, and single-nucleotide polymorphisms (SNPs) were selected by stepwise regression or lasso penalized regression. The best performing PRSs were validated in an independent test set comprising 11,428 case subjects and 18,323 control subjects from 10 prospective studies and 190,040 women from UK Biobank (3,215 incident breast cancers). For the best PRSs (313 SNPs), the odds ratio for overall disease per 1 standard deviation in ten prospective studies was 1.61 (95%CI: 1.57-1.65) with area under receiver-operator curve (AUC) = 0.630 (95%CI: 0.628-0.651). The lifetime risk of overall breast cancer in the top centile of the PRSs was 32.6%. Compared with women in the middle quintile, those in the highest 1% of risk had 4.37- and 2.78-fold risks, and those in the lowest 1% of risk had 0.16- and 0.27-fold risks, of developing ER-positive and ER-negative disease, respectively. Goodness-of-fit tests indicated that this PRS was well calibrated and predicts disease risk accurately in the tails of the distribution. This PRS is a powerful and reliable predictor of breast cancer risk that may improve breast cancer prevention programs.
Published: 2019

36. Using deep convolutional neural networks to identify and classify tumor-associated stroma in diagnostic breast biopsies

Author: Ehteshami Bejnordi, B., Mullooly, Maeve, Pfeiffer, Ruth M., Fan, Shaoqi, Vacek, Pamela M., Weaver, Donald L., Ginneken, B. van, Karssemeijer, N., Laak, J.A.W.M. van der, Sherman, Mark E., Ehteshami Bejnordi, B., Mullooly, Maeve, Pfeiffer, Ruth M., Fan, Shaoqi, Vacek, Pamela M., Weaver, Donald L., Ginneken, B. van, Karssemeijer, N., Laak, J.A.W.M. van der, and Sherman, Mark E.
Abstract: Contains fulltext : 196562.pdf (Publisher’s version ) (Open Access)
Published: 2018

37. Using deep convolutional neural networks to identify and classify tumor-associated stroma in diagnostic breast biopsies

Author: Ehteshami Bejnordi, B., Mullooly, Maeve, Pfeiffer, Ruth M., Fan, Shaoqi, Vacek, Pamela M., Weaver, Donald L., Ginneken, B. van, Karssemeijer, N., Laak, J.A.W.M. van der, Sherman, Mark E., Ehteshami Bejnordi, B., Mullooly, Maeve, Pfeiffer, Ruth M., Fan, Shaoqi, Vacek, Pamela M., Weaver, Donald L., Ginneken, B. van, Karssemeijer, N., Laak, J.A.W.M. van der, and Sherman, Mark E.
Abstract: Contains fulltext : 196562.pdf (Publisher’s version ) (Open Access)
Published: 2018

38. Using deep convolutional neural networks to identify and classify tumor-associated stroma in diagnostic breast biopsies

Author: Ehteshami Bejnordi, B., Mullooly, Maeve, Pfeiffer, Ruth M., Fan, Shaoqi, Vacek, Pamela M., Weaver, Donald L., Ginneken, B. van, Karssemeijer, N., Laak, J.A.W.M. van der, Sherman, Mark E., Ehteshami Bejnordi, B., Mullooly, Maeve, Pfeiffer, Ruth M., Fan, Shaoqi, Vacek, Pamela M., Weaver, Donald L., Ginneken, B. van, Karssemeijer, N., Laak, J.A.W.M. van der, and Sherman, Mark E.
Abstract: Contains fulltext : 196562.pdf (Publisher’s version ) (Open Access)
Published: 2018

39. Pathologic findings at risk-reducing salpingo-oophorectomy: primary results from Gynecologic Oncology Group Trial GOG-0199.

Author: Sherman, Mark E, Sherman, Mark E, Piedmonte, Marion, Mai, Phuong L, Ioffe, Olga B, Ronnett, Brigitte M, Van Le, Linda, Ivanov, Iouri, Bell, Maria C, Blank, Stephanie V, DiSilvestro, Paul, Hamilton, Chad A, Tewari, Krishnansu S, Wakeley, Katie, Kauff, Noah D, Yamada, S Diane, Rodriguez, Gustavo, Skates, Steven J, Alberts, David S, Walker, Joan L, Minasian, Lori, Lu, Karen, Greene, Mark H, Sherman, Mark E, Sherman, Mark E, Piedmonte, Marion, Mai, Phuong L, Ioffe, Olga B, Ronnett, Brigitte M, Van Le, Linda, Ivanov, Iouri, Bell, Maria C, Blank, Stephanie V, DiSilvestro, Paul, Hamilton, Chad A, Tewari, Krishnansu S, Wakeley, Katie, Kauff, Noah D, Yamada, S Diane, Rodriguez, Gustavo, Skates, Steven J, Alberts, David S, Walker, Joan L, Minasian, Lori, Lu, Karen, and Greene, Mark H
Abstract: PurposeRisk-reducing salpingo-oophorectomy (RRSO) lowers mortality from ovarian/tubal and breast cancers among BRCA1/2 mutation carriers. Uncertainties persist regarding potential benefits of RRSO among high-risk noncarriers, optimal surgical age, and anatomic origin of clinically occult cancers detected at surgery. To address these topics, we analyzed surgical treatment arm results from Gynecologic Oncology Group Protocol-0199 (GOG-0199), the National Ovarian Cancer Prevention and Early Detection Study.Participants and methodsThis analysis included asymptomatic high-risk women age ≥ 30 years who elected RRSO at enrollment. Women provided risk factor data and underwent preoperative cancer antigen 125 (CA-125) serum testing and transvaginal ultrasound (TVU). RRSO specimens were processed according to a standardized tissue processing protocol and underwent central pathology panel review. Research-based BRCA1/2 mutation testing was performed when a participant's mutation status was unknown at enrollment. Relationships between participant characteristics and diagnostic findings were assessed using univariable statistics and multivariable logistic regression.ResultsInvasive or intraepithelial ovarian/tubal/peritoneal neoplasms were detected in 25 (2.6%) of 966 RRSOs (BRCA1 mutation carriers, 4.6%; BRCA2 carriers, 3.5%; and noncarriers, 0.5%; P < .001). In multivariable models, positive BRCA1/2 mutation status (P = .0056), postmenopausal status (P = .0023), and abnormal CA-125 levels and/or TVU examinations (P < .001) were associated with detection of clinically occult neoplasms at RRSO. For 387 women with negative BRCA1/2 mutation testing and normal CA-125 levels, findings at RRSO were benign.ConclusionClinically occult cancer was detected among 2.6% of high-risk women undergoing RRSO. BRCA1/2 mutation, postmenopausal status, and abnormal preoperative CA-125 and/or TVU were associated with cancer detection at RRSO. These data can inform management decisions among w
Published: 2014

40. Association analysis identifies 65 new breast cancer risk loci.

Author: Michailidou, Kyriaki, Lindström, Sara, Dennis, Joe, Beesley, Jonathan, Hui, Shirley, Kar, Siddhartha, Lemaçon, Audrey, Soucy, Penny, Glubb, Dylan, Rostamianfar, Asha, Bolla, Manjeet K, Wang, Qin, Tyrer, Jonathan, Dicks, Ed, Lee, Andrew, Wang, Zhaoming, Allen, Jamie, Keeman, Renske, Eilber, Ursula, French, Juliet D, Qing Chen, Xiao, Fachal, Laura, McCue, Karen, McCart Reed, Amy E, Ghoussaini, Maya, Carroll, Jason S, Jiang, Xia, Finucane, Hilary, Adams, Marcia, Adank, Muriel A, Ahsan, Habibul, Aittomäki, Kristiina, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Aronson, Kristan J, Arun, Banu, Auer, Paul L, Bacot, François, Barrdahl, Myrto, Baynes, Caroline, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Blomqvist, Carl, Bogdanova, Natalia V, Bojesen, Stig E, Bonanni, Bernardo, Børresen-Dale, Anne-Lise, Brand, Judith S, Brauch, Hiltrud, Brennan, Paul, Brenner, Hermann, Brinton, Louise, Broberg, Per, Brock, Ian W, Broeks, Annegien, Brooks-Wilson, Angela, Brucker, Sara Y, Brüning, Thomas, Burwinkel, Barbara, Butterbach, Katja, Cai, Qiuyin, Cai, Hui, Caldés, Trinidad, Canzian, Federico, Carracedo, Angel, Carter, Brian D, Castelao, Jose E, Chan, Tsun L, David Cheng, Ting-Yuan, Seng Chia, Kee, Choi, Ji-Yeob, Christiansen, Hans, Clarke, Christine L, Collée, Margriet, Conroy, Don M, Cordina-Duverger, Emilie, Cornelissen, Sten, Cox, David G, Cox, Angela, Cross, Simon S, Cunningham, Julie M, Czene, Kamila, Daly, Mary B, Devilee, Peter, Doheny, Kimberly F, Dörk, Thilo, Dos-Santos-Silva, Isabel, Dumont, Martine, Durcan, Lorraine, Dwek, Miriam, Eccles, Diana M, Ekici, Arif B, Eliassen, A Heather, Ellberg, Carolina, Elvira, Mingajeva, Engel, Christoph, Eriksson, Mikael, Fasching, Peter A, Figueroa, Jonine, Flesch-Janys, Dieter, Fletcher, Olivia, Flyger, Henrik, Fritschi, Lin, Gaborieau, Valerie, Gabrielson, Marike, Gago-Dominguez, Manuela, Gao, Yu-Tang, Gapstur, Susan M, García-Sáenz, José A, Gaudet, Mia M, Georgoulias, Vassilios, Giles, Graham G, Glendon, Gord, Goldberg, Mark S, Goldgar, David E, González-Neira, Anna, Grenaker Alnæs, Grethe I, Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Guénel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hamann, Ute, Hamel, Nathalie, Hankinson, Susan, Harrington, Patricia, Hart, Steven N, Hartikainen, Jaana M, Hartman, Mikael, Hein, Alexander, Heyworth, Jane, Hicks, Belynda, Hillemanns, Peter, Ho, Dona N, Hollestelle, Antoinette, Hooning, Maartje J, Hoover, Robert N, Hopper, John L, Hou, Ming-Feng, Hsiung, Chia-Ni, Huang, Guanmengqian, Humphreys, Keith, Ishiguro, Junko, Ito, Hidemi, Iwasaki, Motoki, Iwata, Hiroji, Jakubowska, Anna, Janni, Wolfgang, John, Esther M, Johnson, Nichola, Jones, Kristine, Jones, Michael, Jukkola-Vuorinen, Arja, Kaaks, Rudolf, Kabisch, Maria, Kaczmarek, Katarzyna, Kang, Daehee, Kasuga, Yoshio, Kerin, Michael J, Khan, Sofia, Khusnutdinova, Elza, Kiiski, Johanna I, Kim, Sung-Won, Knight, Julia A, Kosma, Veli-Matti, Kristensen, Vessela N, Krüger, Ute, Kwong, Ava, Lambrechts, Diether, Le Marchand, Loic, Lee, Eunjung, Lee, Min Hyuk, Lee, Jong Won, Neng Lee, Chuen, Lejbkowicz, Flavio, Li, Jingmei, Lilyquist, Jenna, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loibl, Sibylle, Long, Jirong, Lophatananon, Artitaya, Lubinski, Jan, Luccarini, Craig, Lux, Michael P, Ma, Edmond S K, MacInnis, Robert J, Maishman, Tom, Makalic, Enes, Malone, Kathleen E, Kostovska, Ivana Maleva, Mannermaa, Arto, Manoukian, Siranoush, Manson, JoAnn E, Margolin, Sara, Mariapun, Shivaani, Martinez, Maria Elena, Matsuo, Keitaro, Mavroudis, Dimitrios, McKay, James, McLean, Catriona, Meijers-Heijboer, Hanne, Meindl, Alfons, Menéndez, Primitiva, Menon, Usha, Meyer, Jeffery, Miao, Hui, Miller, Nicola, Taib, Nur Aishah Mohd, Muir, Kenneth, Mulligan, Anna Marie, Mulot, Claire, Neuhausen, Susan L, Nevanlinna, Heli, Neven, Patrick, Nielsen, Sune F, Noh, Dong-Young, Nordestgaard, Børge G, Norman, Aaron, Olopade, Olufunmilayo I, Olson, Janet E, Olsson, Håkan, Olswold, Curtis, Orr, Nick, Pankratz, V Shane, Park, Sue K, Park-Simon, Tjoung-Won, Lloyd, Rachel, Perez, Jose I A, Peterlongo, Paolo, Peto, Julian, Phillips, Kelly-Anne, Pinchev, Mila, Plaseska-Karanfilska, Dijana, Prentice, Ross, Presneau, Nadege, Prokofyeva, Darya, Pugh, Elizabeth, Pylkäs, Katri, Rack, Brigitte, Radice, Paolo, Rahman, Nazneen, Rennert, Gadi, Rennert, Hedy S, Rhenius, Valerie, Romero, Atocha, Romm, Jane, Ruddy, Kathryn J, Rüdiger, Thomas, Rudolph, Anja, Ruebner, Matthias, Rutgers, Emiel J T, Saloustros, Emmanouil, Sandler, Dale P, Sangrajrang, Suleeporn, Sawyer, Elinor J, Schmidt, Daniel F, Schmutzler, Rita K, Schneeweiss, Andreas, Schoemaker, Minouk J, Schumacher, Fredrick, Schürmann, Peter, Scott, Rodney J, Scott, Christopher, Seal, Sheila, Seynaeve, Caroline, Shah, Mitul, Sharma, Priyanka, Shen, Chen-Yang, Sheng, Grace, Sherman, Mark E, Shrubsole, Martha J, Shu, Xiao-Ou, Smeets, Ann, Sohn, Christof, Southey, Melissa C, Spinelli, John J, Stegmaier, Christa, Stewart-Brown, Sarah, Stone, Jennifer, Stram, Daniel O, Surowy, Harald, Swerdlow, Anthony, Tamimi, Rulla, Taylor, Jack A, Tengström, Maria, Teo, Soo H, Beth Terry, Mary, Tessier, Daniel C, Thanasitthichai, Somchai, Thöne, Kathrin, Tollenaar, Rob A E M, Tomlinson, Ian, Tong, Ling, Torres, Diana, Truong, Thérèse, Tseng, Chiu-Chen, Tsugane, Shoichiro, Ulmer, Hans-Ulrich, Ursin, Giske, Untch, Michael, Vachon, Celine, van Asperen, Christi J, Van Den Berg, David, van den Ouweland, Ans M W, van der Kolk, Lizet, van der Luijt, Rob B, Vincent, Daniel, Vollenweider, Jason, Waisfisz, Quinten, Wang-Gohrke, Shan, Weinberg, Clarice R, Wendt, Camilla, Whittemore, Alice S, Wildiers, Hans, Willett, Walter, Winqvist, Robert, Wolk, Alicja, Wu, Anna H, Xia, Lucy, Yamaji, Taiki, Yang, Xiaohong R, Har Yip, Cheng, Yoo, Keun-Young, Yu, Jyh-Cherng, Zheng, Wei, Zheng, Ying, Zhu, Bin, Ziogas, Argyrios, Ziv, Elad, Lakhani, Sunil R, Antoniou, Antonis C, Droit, Arnaud, Andrulis, Irene L, Amos, Christopher I, Couch, Fergus J, Pharoah, Paul D P, Chang-Claude, Jenny, Hall, Per, Hunter, David J, Milne, Roger L, García-Closas, Montserrat, Schmidt, Marjanka K, Chanock, Stephen J, Dunning, Alison M, Edwards, Stacey L, Bader, Gary D, Chenevix-Trench, Georgia, Simard, Jacques, Kraft, Peter, Easton, Douglas F, Michailidou, Kyriaki, Lindström, Sara, Dennis, Joe, Beesley, Jonathan, Hui, Shirley, Kar, Siddhartha, Lemaçon, Audrey, Soucy, Penny, Glubb, Dylan, Rostamianfar, Asha, Bolla, Manjeet K, Wang, Qin, Tyrer, Jonathan, Dicks, Ed, Lee, Andrew, Wang, Zhaoming, Allen, Jamie, Keeman, Renske, Eilber, Ursula, French, Juliet D, Qing Chen, Xiao, Fachal, Laura, McCue, Karen, McCart Reed, Amy E, Ghoussaini, Maya, Carroll, Jason S, Jiang, Xia, Finucane, Hilary, Adams, Marcia, Adank, Muriel A, Ahsan, Habibul, Aittomäki, Kristiina, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Aronson, Kristan J, Arun, Banu, Auer, Paul L, Bacot, François, Barrdahl, Myrto, Baynes, Caroline, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Blomqvist, Carl, Bogdanova, Natalia V, Bojesen, Stig E, Bonanni, Bernardo, Børresen-Dale, Anne-Lise, Brand, Judith S, Brauch, Hiltrud, Brennan, Paul, Brenner, Hermann, Brinton, Louise, Broberg, Per, Brock, Ian W, Broeks, Annegien, Brooks-Wilson, Angela, Brucker, Sara Y, Brüning, Thomas, Burwinkel, Barbara, Butterbach, Katja, Cai, Qiuyin, Cai, Hui, Caldés, Trinidad, Canzian, Federico, Carracedo, Angel, Carter, Brian D, Castelao, Jose E, Chan, Tsun L, David Cheng, Ting-Yuan, Seng Chia, Kee, Choi, Ji-Yeob, Christiansen, Hans, Clarke, Christine L, Collée, Margriet, Conroy, Don M, Cordina-Duverger, Emilie, Cornelissen, Sten, Cox, David G, Cox, Angela, Cross, Simon S, Cunningham, Julie M, Czene, Kamila, Daly, Mary B, Devilee, Peter, Doheny, Kimberly F, Dörk, Thilo, Dos-Santos-Silva, Isabel, Dumont, Martine, Durcan, Lorraine, Dwek, Miriam, Eccles, Diana M, Ekici, Arif B, Eliassen, A Heather, Ellberg, Carolina, Elvira, Mingajeva, Engel, Christoph, Eriksson, Mikael, Fasching, Peter A, Figueroa, Jonine, Flesch-Janys, Dieter, Fletcher, Olivia, Flyger, Henrik, Fritschi, Lin, Gaborieau, Valerie, Gabrielson, Marike, Gago-Dominguez, Manuela, Gao, Yu-Tang, Gapstur, Susan M, García-Sáenz, José A, Gaudet, Mia M, Georgoulias, Vassilios, Giles, Graham G, Glendon, Gord, Goldberg, Mark S, Goldgar, David E, González-Neira, Anna, Grenaker Alnæs, Grethe I, Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Guénel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hamann, Ute, Hamel, Nathalie, Hankinson, Susan, Harrington, Patricia, Hart, Steven N, Hartikainen, Jaana M, Hartman, Mikael, Hein, Alexander, Heyworth, Jane, Hicks, Belynda, Hillemanns, Peter, Ho, Dona N, Hollestelle, Antoinette, Hooning, Maartje J, Hoover, Robert N, Hopper, John L, Hou, Ming-Feng, Hsiung, Chia-Ni, Huang, Guanmengqian, Humphreys, Keith, Ishiguro, Junko, Ito, Hidemi, Iwasaki, Motoki, Iwata, Hiroji, Jakubowska, Anna, Janni, Wolfgang, John, Esther M, Johnson, Nichola, Jones, Kristine, Jones, Michael, Jukkola-Vuorinen, Arja, Kaaks, Rudolf, Kabisch, Maria, Kaczmarek, Katarzyna, Kang, Daehee, Kasuga, Yoshio, Kerin, Michael J, Khan, Sofia, Khusnutdinova, Elza, Kiiski, Johanna I, Kim, Sung-Won, Knight, Julia A, Kosma, Veli-Matti, Kristensen, Vessela N, Krüger, Ute, Kwong, Ava, Lambrechts, Diether, Le Marchand, Loic, Lee, Eunjung, Lee, Min Hyuk, Lee, Jong Won, Neng Lee, Chuen, Lejbkowicz, Flavio, Li, Jingmei, Lilyquist, Jenna, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loibl, Sibylle, Long, Jirong, Lophatananon, Artitaya, Lubinski, Jan, Luccarini, Craig, Lux, Michael P, Ma, Edmond S K, MacInnis, Robert J, Maishman, Tom, Makalic, Enes, Malone, Kathleen E, Kostovska, Ivana Maleva, Mannermaa, Arto, Manoukian, Siranoush, Manson, JoAnn E, Margolin, Sara, Mariapun, Shivaani, Martinez, Maria Elena, Matsuo, Keitaro, Mavroudis, Dimitrios, McKay, James, McLean, Catriona, Meijers-Heijboer, Hanne, Meindl, Alfons, Menéndez, Primitiva, Menon, Usha, Meyer, Jeffery, Miao, Hui, Miller, Nicola, Taib, Nur Aishah Mohd, Muir, Kenneth, Mulligan, Anna Marie, Mulot, Claire, Neuhausen, Susan L, Nevanlinna, Heli, Neven, Patrick, Nielsen, Sune F, Noh, Dong-Young, Nordestgaard, Børge G, Norman, Aaron, Olopade, Olufunmilayo I, Olson, Janet E, Olsson, Håkan, Olswold, Curtis, Orr, Nick, Pankratz, V Shane, Park, Sue K, Park-Simon, Tjoung-Won, Lloyd, Rachel, Perez, Jose I A, Peterlongo, Paolo, Peto, Julian, Phillips, Kelly-Anne, Pinchev, Mila, Plaseska-Karanfilska, Dijana, Prentice, Ross, Presneau, Nadege, Prokofyeva, Darya, Pugh, Elizabeth, Pylkäs, Katri, Rack, Brigitte, Radice, Paolo, Rahman, Nazneen, Rennert, Gadi, Rennert, Hedy S, Rhenius, Valerie, Romero, Atocha, Romm, Jane, Ruddy, Kathryn J, Rüdiger, Thomas, Rudolph, Anja, Ruebner, Matthias, Rutgers, Emiel J T, Saloustros, Emmanouil, Sandler, Dale P, Sangrajrang, Suleeporn, Sawyer, Elinor J, Schmidt, Daniel F, Schmutzler, Rita K, Schneeweiss, Andreas, Schoemaker, Minouk J, Schumacher, Fredrick, Schürmann, Peter, Scott, Rodney J, Scott, Christopher, Seal, Sheila, Seynaeve, Caroline, Shah, Mitul, Sharma, Priyanka, Shen, Chen-Yang, Sheng, Grace, Sherman, Mark E, Shrubsole, Martha J, Shu, Xiao-Ou, Smeets, Ann, Sohn, Christof, Southey, Melissa C, Spinelli, John J, Stegmaier, Christa, Stewart-Brown, Sarah, Stone, Jennifer, Stram, Daniel O, Surowy, Harald, Swerdlow, Anthony, Tamimi, Rulla, Taylor, Jack A, Tengström, Maria, Teo, Soo H, Beth Terry, Mary, Tessier, Daniel C, Thanasitthichai, Somchai, Thöne, Kathrin, Tollenaar, Rob A E M, Tomlinson, Ian, Tong, Ling, Torres, Diana, Truong, Thérèse, Tseng, Chiu-Chen, Tsugane, Shoichiro, Ulmer, Hans-Ulrich, Ursin, Giske, Untch, Michael, Vachon, Celine, van Asperen, Christi J, Van Den Berg, David, van den Ouweland, Ans M W, van der Kolk, Lizet, van der Luijt, Rob B, Vincent, Daniel, Vollenweider, Jason, Waisfisz, Quinten, Wang-Gohrke, Shan, Weinberg, Clarice R, Wendt, Camilla, Whittemore, Alice S, Wildiers, Hans, Willett, Walter, Winqvist, Robert, Wolk, Alicja, Wu, Anna H, Xia, Lucy, Yamaji, Taiki, Yang, Xiaohong R, Har Yip, Cheng, Yoo, Keun-Young, Yu, Jyh-Cherng, Zheng, Wei, Zheng, Ying, Zhu, Bin, Ziogas, Argyrios, Ziv, Elad, Lakhani, Sunil R, Antoniou, Antonis C, Droit, Arnaud, Andrulis, Irene L, Amos, Christopher I, Couch, Fergus J, Pharoah, Paul D P, Chang-Claude, Jenny, Hall, Per, Hunter, David J, Milne, Roger L, García-Closas, Montserrat, Schmidt, Marjanka K, Chanock, Stephen J, Dunning, Alison M, Edwards, Stacey L, Bader, Gary D, Chenevix-Trench, Georgia, Simard, Jacques, Kraft, Peter, and Easton, Douglas F
Abstract: Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as BRCA1, and many common, mostly non-coding variants. However, much of the genetic contribution to breast cancer risk remains unknown. Here we report the results of a genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry. We identified 65 new loci that are associated with overall breast cancer risk at P < 5 × 10-8. The majority of credible risk single-nucleotide polymorphisms in these loci fall in distal regulatory elements, and by integrating in silico data to predict target genes in breast cells at each locus, we demonstrate a strong overlap between candidate target genes and somatic driver genes in breast tumours. We also find that heritability of breast cancer due to all single-nucleotide polymorphisms in regulatory features was 2-5-fold enriched relative to the genome-wide average, with strong enrichment for particular transcription factor binding sites. These results provide further insight into genetic susceptibility to breast cancer and will improve the use of genetic risk scores for individualized screening and prevention.
Published: 2017
Full Text: View/download PDF

41. Association analysis identifies 65 new breast cancer risk loci

Author: Michailidou, Kyriaki, Lindstrom, Sara, Dennis, Joe, Beesley, Jonathan, Hui, Shirley, Kar, Siddhartha, Lemacon, Audrey, Soucy, Penny, Glubb, Dylan, Rostamianfar, Asha, Bolla, Manjeet K., Wang, Qin, Tyrer, Jonathan, Dicks, Ed, Lee, Andrew, Wang, Zhaoming, Allen, Jamie, Keeman, Renske, Eilber, Ursula, French, Juliet D., Chen, Xiao Qing, Fachal, Laura, McCue, Karen, McCart, Amy E., Reed, Amy E. McCart, Ghoussaini, Maya, Carroll, Jason S., Jiang, Xia, Finucane, Hilary, Adams, Marcia, Adank, Muriel A., Ahsan, Habibul, Aittomaki, Kristiina, Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Aronson, Kristan J., Arun, Banu, Auer, Paul L., Bacot, Francois, Barrdahl, Myrto, Baynes, Caroline, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Blomqvist, Carl, Bogdanova, Natalia V., Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brand, Judith S., Brauch, Hiltrud, Brennan, Paul, Brenner, Hermann, Brinton, Louise, Broberg, Per, Brock, Ian W., Broeks, Annegien, Brooks-Wilson, Angela, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Butterbach, Katja, Cai, Qiuyin, Cai, Hui, Caldes, Trinidad, Canzian, Federico, Carracedo, Angel, Carter, Brian D., Castelao, Jose E., Chan, Tsun L., Cheng, Ting-Yuan David, Chia, Kee Seng, Choi, Ji-Yeob, Christiansen, Hans, Clarke, Christine L., Collee, Margriet, Conroy, Don M., Cordina-Duverger, Emilie, Cornelissen, Sten, Cox, David G., Cox, Angela, Cross, Simon S., Cunningham, Julie M., Czene, Kamila, Daly, Mary B., Devilee, Peter, Doheny, Kimberly F., Doerk, Thilo, dos-Santos-Silva, Isabel, Dumont, Martine, Durcan, Lorraine, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Ellberg, Carolina, Elvira, Mingajeva, Engel, Christoph, Eriksson, Mikael, Fasching, Peter A., Figueroa, Jonine, Flesch-Janys, Dieter, Fletcher, Olivia, Flyger, Henrik, Fritschi, Lin, Gaborieau, Valerie, Gabrielson, Marike, Gago-Dominguez, Manuela, Gao, Yu-Tang, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Georgoulias, Vassilios, Giles, Graham G., Glendon, Gord, Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hakansson, Niclas, Hamann, Ute, Hamel, Nathalie, Hankinson, Susan, Harrington, Patricia, Hart, Steven N., Hartikainen, Jaana M., Hartman, Mikael, Hein, Alexander, Heyworth, Jane, Hicks, Belynda, Hillemanns, Peter, Ho, Dona N., Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Hou, Ming-Feng, Hsiung, Chia-Ni, Huang, Guanmengqian, Humphreys, Keith, Ishiguro, Junko, Ito, Hidemi, Iwasaki, Motoki, Iwata, Hiroji, Jakubowska, Anna, Janni, Wolfgang, John, Esther M., Johnson, Nichola, Jones, Kristine, Jones, Michael, Jukkola-Vuorinen, Arja, Kaaks, Rudolf, Kabisch, Maria, Kaczmarek, Katarzyna, Kang, Daehee, Kasuga, Yoshio, Kerin, Michael J., Khan, Sofia, Khusnutdinova, Elza, Kiiski, Johanna I., Kim, Sung-Won, Knight, Julia A., Kosma, Veli-Matti, Kristensen, Vessela N., Kruger, Ute, Kwong, Ava, Lambrechts, Diether, Le Marchand, Loic, Lee, Eunjung, Lee, Min Hyuk, Lee, Jong Won, Lee, Chuen Neng, Lejbkowicz, Flavio, Li, Jingmei, Lilyquist, Jenna, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loibl, Sibylle, Long, Jirong, Lophatananon, Artitaya, Lubinski, Jan, Luccarini, Craig, Lux, Michael P., Ma, Edmond S. K., MacInnis, Robert J., Maishman, Tom, Makalic, Enes, Malone, Kathleen E., Kostovska, Ivana Maleva, Mannermaa, Arto, Manoukian, Siranoush, Manson, Joann E., Margolin, Sara, Mariapun, Shivaani, Martinez, Maria Elena, Matsuo, Keitaro, Mavroudis, Dimitrios, McKay, James, McLean, Catriona, Meijers-Heijboer, Hanne, Meindl, Alfons, Menendez, Primitiva, Menon, Usha, Meyer, Jeffery, Miao, Hui, Miller, Nicola, Taib, Nur Aishah Mohd, Muir, Kenneth, Mulligan, Anna Marie, Mulot, Claire, Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Nielsen, Sune F., Noh, Dong-Young, Nordestgaard, Borge G., Norman, Aaron, Olopade, Olufunmilayo I., Olson, Janet E., Olsson, Hakan, Olswold, Curtis, Orr, Nick, Pankratz, V. Shane, Park, Sue K., Park-Simon, Tjoung-Won, Lloyd, Rachel, Perez, Jose I. A., Peterlongo, Paolo, Peto, Julian, Phillips, Kelly-Anne, Pinchev, Mila, Plaseska-Karanfilska, Dijana, Prentice, Ross, Presneau, Nadege, Prokofyeva, Darya, Pugh, Elizabeth, Pylkas, Katri, Rack, Brigitte, Radice, Paolo, Rahman, Nazneen, Rennert, Gadi, Rennert, Hedy S., Rhenius, Valerie, Romero, Atocha, Romm, Jane, Ruddy, Kathryn J., Ruediger, Thomas, Rudolph, Anja, Ruebner, Matthias, Rutgers, Emiel J. T., Saloustros, Emmanouil, Sandler, Dale P., Sangrajrang, Suleeporn, Sawyer, Elinor J., Schmidt, Daniel F., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schumacher, Fredrick, Schuermann, Peter, Scott, Rodney J., Scott, Christopher, Seal, Sheila, Seynaeve, Caroline, Shah, Mitul, Sharma, Priyanka, Shen, Chen-Yang, Sheng, Grace, Sherman, Mark E., Shrubsole, Martha J., Shu, Xiao-Ou, Smeets, Ann, Sohn, Christof, Southey, Melissa C., Spinelli, John J., Stegmaier, Christa, Stewart-Brown, Sarah, Stone, Jennifer, Stram, Daniel O., Surowy, Harald, Swerdlow, Anthony, Tamimi, Rulla, Taylor, Jack A., Tengstrom, Maria, Teo, Soo H., Terry, Mary Beth, Tessier, Daniel C., Thanasitthichai, Somchai, Thoene, Kathrin, Tollenaar, Rob A. E. M., Tomlinson, Ian, Tong, Ling, Torres, Diana, Truong, Therese, Tseng, Chiu-Chen, Tsugane, Shoichiro, Ulmer, Hans-Ulrich, Ursin, Giske, Untch, Michael, Vachon, Celine, van Asperen, Christi J., Van Den Berg, David, van den Ouweland, Ans M. W., van der Kolk, Lizet, van der Luijt, Rob B., Vincent, Daniel, Vollenweider, Jason, Waisfisz, Quinten, Wang-Gohrke, Shan, Weinberg, Clarice R., Wendt, Camilla, Whittemore, Alice S., Wildiers, Hans, Willett, Walter, Winqvist, Robert, Wolk, Alicja, Wu, Anna H., Xia, Lucy, Yamaji, Taiki, Yang, Xiaohong R., Yip, Cheng Har, Yoo, Keun-Young, Yu, Jyh-Cherng, Zheng, Wei, Zheng, Ying, Zhu, Bin, Ziogas, Argyrios, Ziv, Elad, Lakhani, Sunil R., Antoniou, Antonis C., Droit, Arnaud, Andrulis, Irene L., Amos, Christopher I., Couch, Fergus J., Pharoah, Paul D. P., Chang-Claude, Jenny, Hall, Per, Hunter, David J., Milne, Roger L., Garcia-Closas, Montserrat, Schmidt, Marjanka K., Chanock, Stephen J., Dunning, Alison M., Edwards, Stacey L., Bader, Gary D., Chenevix-Trench, Georgia, Simard, Jacques, Kraft, Peter, Easton, Douglas F., Michailidou, Kyriaki, Lindstrom, Sara, Dennis, Joe, Beesley, Jonathan, Hui, Shirley, Kar, Siddhartha, Lemacon, Audrey, Soucy, Penny, Glubb, Dylan, Rostamianfar, Asha, Bolla, Manjeet K., Wang, Qin, Tyrer, Jonathan, Dicks, Ed, Lee, Andrew, Wang, Zhaoming, Allen, Jamie, Keeman, Renske, Eilber, Ursula, French, Juliet D., Chen, Xiao Qing, Fachal, Laura, McCue, Karen, McCart, Amy E., Reed, Amy E. McCart, Ghoussaini, Maya, Carroll, Jason S., Jiang, Xia, Finucane, Hilary, Adams, Marcia, Adank, Muriel A., Ahsan, Habibul, Aittomaki, Kristiina, Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Aronson, Kristan J., Arun, Banu, Auer, Paul L., Bacot, Francois, Barrdahl, Myrto, Baynes, Caroline, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Blomqvist, Carl, Bogdanova, Natalia V., Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brand, Judith S., Brauch, Hiltrud, Brennan, Paul, Brenner, Hermann, Brinton, Louise, Broberg, Per, Brock, Ian W., Broeks, Annegien, Brooks-Wilson, Angela, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Butterbach, Katja, Cai, Qiuyin, Cai, Hui, Caldes, Trinidad, Canzian, Federico, Carracedo, Angel, Carter, Brian D., Castelao, Jose E., Chan, Tsun L., Cheng, Ting-Yuan David, Chia, Kee Seng, Choi, Ji-Yeob, Christiansen, Hans, Clarke, Christine L., Collee, Margriet, Conroy, Don M., Cordina-Duverger, Emilie, Cornelissen, Sten, Cox, David G., Cox, Angela, Cross, Simon S., Cunningham, Julie M., Czene, Kamila, Daly, Mary B., Devilee, Peter, Doheny, Kimberly F., Doerk, Thilo, dos-Santos-Silva, Isabel, Dumont, Martine, Durcan, Lorraine, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Ellberg, Carolina, Elvira, Mingajeva, Engel, Christoph, Eriksson, Mikael, Fasching, Peter A., Figueroa, Jonine, Flesch-Janys, Dieter, Fletcher, Olivia, Flyger, Henrik, Fritschi, Lin, Gaborieau, Valerie, Gabrielson, Marike, Gago-Dominguez, Manuela, Gao, Yu-Tang, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Georgoulias, Vassilios, Giles, Graham G., Glendon, Gord, Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hakansson, Niclas, Hamann, Ute, Hamel, Nathalie, Hankinson, Susan, Harrington, Patricia, Hart, Steven N., Hartikainen, Jaana M., Hartman, Mikael, Hein, Alexander, Heyworth, Jane, Hicks, Belynda, Hillemanns, Peter, Ho, Dona N., Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Hou, Ming-Feng, Hsiung, Chia-Ni, Huang, Guanmengqian, Humphreys, Keith, Ishiguro, Junko, Ito, Hidemi, Iwasaki, Motoki, Iwata, Hiroji, Jakubowska, Anna, Janni, Wolfgang, John, Esther M., Johnson, Nichola, Jones, Kristine, Jones, Michael, Jukkola-Vuorinen, Arja, Kaaks, Rudolf, Kabisch, Maria, Kaczmarek, Katarzyna, Kang, Daehee, Kasuga, Yoshio, Kerin, Michael J., Khan, Sofia, Khusnutdinova, Elza, Kiiski, Johanna I., Kim, Sung-Won, Knight, Julia A., Kosma, Veli-Matti, Kristensen, Vessela N., Kruger, Ute, Kwong, Ava, Lambrechts, Diether, Le Marchand, Loic, Lee, Eunjung, Lee, Min Hyuk, Lee, Jong Won, Lee, Chuen Neng, Lejbkowicz, Flavio, Li, Jingmei, Lilyquist, Jenna, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loibl, Sibylle, Long, Jirong, Lophatananon, Artitaya, Lubinski, Jan, Luccarini, Craig, Lux, Michael P., Ma, Edmond S. K., MacInnis, Robert J., Maishman, Tom, Makalic, Enes, Malone, Kathleen E., Kostovska, Ivana Maleva, Mannermaa, Arto, Manoukian, Siranoush, Manson, Joann E., Margolin, Sara, Mariapun, Shivaani, Martinez, Maria Elena, Matsuo, Keitaro, Mavroudis, Dimitrios, McKay, James, McLean, Catriona, Meijers-Heijboer, Hanne, Meindl, Alfons, Menendez, Primitiva, Menon, Usha, Meyer, Jeffery, Miao, Hui, Miller, Nicola, Taib, Nur Aishah Mohd, Muir, Kenneth, Mulligan, Anna Marie, Mulot, Claire, Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Nielsen, Sune F., Noh, Dong-Young, Nordestgaard, Borge G., Norman, Aaron, Olopade, Olufunmilayo I., Olson, Janet E., Olsson, Hakan, Olswold, Curtis, Orr, Nick, Pankratz, V. Shane, Park, Sue K., Park-Simon, Tjoung-Won, Lloyd, Rachel, Perez, Jose I. A., Peterlongo, Paolo, Peto, Julian, Phillips, Kelly-Anne, Pinchev, Mila, Plaseska-Karanfilska, Dijana, Prentice, Ross, Presneau, Nadege, Prokofyeva, Darya, Pugh, Elizabeth, Pylkas, Katri, Rack, Brigitte, Radice, Paolo, Rahman, Nazneen, Rennert, Gadi, Rennert, Hedy S., Rhenius, Valerie, Romero, Atocha, Romm, Jane, Ruddy, Kathryn J., Ruediger, Thomas, Rudolph, Anja, Ruebner, Matthias, Rutgers, Emiel J. T., Saloustros, Emmanouil, Sandler, Dale P., Sangrajrang, Suleeporn, Sawyer, Elinor J., Schmidt, Daniel F., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schumacher, Fredrick, Schuermann, Peter, Scott, Rodney J., Scott, Christopher, Seal, Sheila, Seynaeve, Caroline, Shah, Mitul, Sharma, Priyanka, Shen, Chen-Yang, Sheng, Grace, Sherman, Mark E., Shrubsole, Martha J., Shu, Xiao-Ou, Smeets, Ann, Sohn, Christof, Southey, Melissa C., Spinelli, John J., Stegmaier, Christa, Stewart-Brown, Sarah, Stone, Jennifer, Stram, Daniel O., Surowy, Harald, Swerdlow, Anthony, Tamimi, Rulla, Taylor, Jack A., Tengstrom, Maria, Teo, Soo H., Terry, Mary Beth, Tessier, Daniel C., Thanasitthichai, Somchai, Thoene, Kathrin, Tollenaar, Rob A. E. M., Tomlinson, Ian, Tong, Ling, Torres, Diana, Truong, Therese, Tseng, Chiu-Chen, Tsugane, Shoichiro, Ulmer, Hans-Ulrich, Ursin, Giske, Untch, Michael, Vachon, Celine, van Asperen, Christi J., Van Den Berg, David, van den Ouweland, Ans M. W., van der Kolk, Lizet, van der Luijt, Rob B., Vincent, Daniel, Vollenweider, Jason, Waisfisz, Quinten, Wang-Gohrke, Shan, Weinberg, Clarice R., Wendt, Camilla, Whittemore, Alice S., Wildiers, Hans, Willett, Walter, Winqvist, Robert, Wolk, Alicja, Wu, Anna H., Xia, Lucy, Yamaji, Taiki, Yang, Xiaohong R., Yip, Cheng Har, Yoo, Keun-Young, Yu, Jyh-Cherng, Zheng, Wei, Zheng, Ying, Zhu, Bin, Ziogas, Argyrios, Ziv, Elad, Lakhani, Sunil R., Antoniou, Antonis C., Droit, Arnaud, Andrulis, Irene L., Amos, Christopher I., Couch, Fergus J., Pharoah, Paul D. P., Chang-Claude, Jenny, Hall, Per, Hunter, David J., Milne, Roger L., Garcia-Closas, Montserrat, Schmidt, Marjanka K., Chanock, Stephen J., Dunning, Alison M., Edwards, Stacey L., Bader, Gary D., Chenevix-Trench, Georgia, Simard, Jacques, Kraft, Peter, and Easton, Douglas F.
Abstract: Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as BRCA1, and many common, mostly non-coding variants. However, much of the genetic contribution to breast cancer risk remains unknown. Here we report the results of a genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry(1). We identified 65 new loci that are associated with overall breast cancer risk at P < 5 x 10(-8). The majority of credible risk single-nucleotide polymorphisms in these loci fall in distal regulatory elements, and by integrating in silico data to predict target genes in breast cells at each locus, we demonstrate a strong overlap between candidate target genes and somatic driver genes in breast tumours. We also find that heritability of breast cancer due to all single-nucleotide polymorphisms in regulatory features was 2-5-fold enriched relative to the genome-wide average, with strong enrichment for particular transcription factor binding sites. These results provide further insight into genetic susceptibility to breast cancer and will improve the use of genetic risk scores for individualized screening and prevention.
Published: 2017

42. Association analysis identifies 65 new breast cancer risk loci

Author: Michailidou, Kyriaki, Lindstrom, Sara, Dennis, Joe, Beesley, Jonathan, Hui, Shirley, Kar, Siddhartha, Lemacon, Audrey, Soucy, Penny, Glubb, Dylan, Rostamianfar, Asha, Bolla, Manjeet K., Wang, Qin, Tyrer, Jonathan, Dicks, Ed, Lee, Andrew, Wang, Zhaoming, Allen, Jamie, Keeman, Renske, Eilber, Ursula, French, Juliet D., Chen, Xiao Qing, Fachal, Laura, McCue, Karen, McCart, Amy E., Reed, Amy E. McCart, Ghoussaini, Maya, Carroll, Jason S., Jiang, Xia, Finucane, Hilary, Adams, Marcia, Adank, Muriel A., Ahsan, Habibul, Aittomaki, Kristiina, Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Aronson, Kristan J., Arun, Banu, Auer, Paul L., Bacot, Francois, Barrdahl, Myrto, Baynes, Caroline, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Blomqvist, Carl, Bogdanova, Natalia V., Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brand, Judith S., Brauch, Hiltrud, Brennan, Paul, Brenner, Hermann, Brinton, Louise, Broberg, Per, Brock, Ian W., Broeks, Annegien, Brooks-Wilson, Angela, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Butterbach, Katja, Cai, Qiuyin, Cai, Hui, Caldes, Trinidad, Canzian, Federico, Carracedo, Angel, Carter, Brian D., Castelao, Jose E., Chan, Tsun L., Cheng, Ting-Yuan David, Chia, Kee Seng, Choi, Ji-Yeob, Christiansen, Hans, Clarke, Christine L., Collee, Margriet, Conroy, Don M., Cordina-Duverger, Emilie, Cornelissen, Sten, Cox, David G., Cox, Angela, Cross, Simon S., Cunningham, Julie M., Czene, Kamila, Daly, Mary B., Devilee, Peter, Doheny, Kimberly F., Doerk, Thilo, dos-Santos-Silva, Isabel, Dumont, Martine, Durcan, Lorraine, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Ellberg, Carolina, Elvira, Mingajeva, Engel, Christoph, Eriksson, Mikael, Fasching, Peter A., Figueroa, Jonine, Flesch-Janys, Dieter, Fletcher, Olivia, Flyger, Henrik, Fritschi, Lin, Gaborieau, Valerie, Gabrielson, Marike, Gago-Dominguez, Manuela, Gao, Yu-Tang, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Georgoulias, Vassilios, Giles, Graham G., Glendon, Gord, Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hakansson, Niclas, Hamann, Ute, Hamel, Nathalie, Hankinson, Susan, Harrington, Patricia, Hart, Steven N., Hartikainen, Jaana M., Hartman, Mikael, Hein, Alexander, Heyworth, Jane, Hicks, Belynda, Hillemanns, Peter, Ho, Dona N., Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Hou, Ming-Feng, Hsiung, Chia-Ni, Huang, Guanmengqian, Humphreys, Keith, Ishiguro, Junko, Ito, Hidemi, Iwasaki, Motoki, Iwata, Hiroji, Jakubowska, Anna, Janni, Wolfgang, John, Esther M., Johnson, Nichola, Jones, Kristine, Jones, Michael, Jukkola-Vuorinen, Arja, Kaaks, Rudolf, Kabisch, Maria, Kaczmarek, Katarzyna, Kang, Daehee, Kasuga, Yoshio, Kerin, Michael J., Khan, Sofia, Khusnutdinova, Elza, Kiiski, Johanna I., Kim, Sung-Won, Knight, Julia A., Kosma, Veli-Matti, Kristensen, Vessela N., Kruger, Ute, Kwong, Ava, Lambrechts, Diether, Le Marchand, Loic, Lee, Eunjung, Lee, Min Hyuk, Lee, Jong Won, Lee, Chuen Neng, Lejbkowicz, Flavio, Li, Jingmei, Lilyquist, Jenna, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loibl, Sibylle, Long, Jirong, Lophatananon, Artitaya, Lubinski, Jan, Luccarini, Craig, Lux, Michael P., Ma, Edmond S. K., MacInnis, Robert J., Maishman, Tom, Makalic, Enes, Malone, Kathleen E., Kostovska, Ivana Maleva, Mannermaa, Arto, Manoukian, Siranoush, Manson, Joann E., Margolin, Sara, Mariapun, Shivaani, Martinez, Maria Elena, Matsuo, Keitaro, Mavroudis, Dimitrios, McKay, James, McLean, Catriona, Meijers-Heijboer, Hanne, Meindl, Alfons, Menendez, Primitiva, Menon, Usha, Meyer, Jeffery, Miao, Hui, Miller, Nicola, Taib, Nur Aishah Mohd, Muir, Kenneth, Mulligan, Anna Marie, Mulot, Claire, Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Nielsen, Sune F., Noh, Dong-Young, Nordestgaard, Borge G., Norman, Aaron, Olopade, Olufunmilayo I., Olson, Janet E., Olsson, Hakan, Olswold, Curtis, Orr, Nick, Pankratz, V. Shane, Park, Sue K., Park-Simon, Tjoung-Won, Lloyd, Rachel, Perez, Jose I. A., Peterlongo, Paolo, Peto, Julian, Phillips, Kelly-Anne, Pinchev, Mila, Plaseska-Karanfilska, Dijana, Prentice, Ross, Presneau, Nadege, Prokofyeva, Darya, Pugh, Elizabeth, Pylkas, Katri, Rack, Brigitte, Radice, Paolo, Rahman, Nazneen, Rennert, Gadi, Rennert, Hedy S., Rhenius, Valerie, Romero, Atocha, Romm, Jane, Ruddy, Kathryn J., Ruediger, Thomas, Rudolph, Anja, Ruebner, Matthias, Rutgers, Emiel J. T., Saloustros, Emmanouil, Sandler, Dale P., Sangrajrang, Suleeporn, Sawyer, Elinor J., Schmidt, Daniel F., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schumacher, Fredrick, Schuermann, Peter, Scott, Rodney J., Scott, Christopher, Seal, Sheila, Seynaeve, Caroline, Shah, Mitul, Sharma, Priyanka, Shen, Chen-Yang, Sheng, Grace, Sherman, Mark E., Shrubsole, Martha J., Shu, Xiao-Ou, Smeets, Ann, Sohn, Christof, Southey, Melissa C., Spinelli, John J., Stegmaier, Christa, Stewart-Brown, Sarah, Stone, Jennifer, Stram, Daniel O., Surowy, Harald, Swerdlow, Anthony, Tamimi, Rulla, Taylor, Jack A., Tengstrom, Maria, Teo, Soo H., Terry, Mary Beth, Tessier, Daniel C., Thanasitthichai, Somchai, Thoene, Kathrin, Tollenaar, Rob A. E. M., Tomlinson, Ian, Tong, Ling, Torres, Diana, Truong, Therese, Tseng, Chiu-Chen, Tsugane, Shoichiro, Ulmer, Hans-Ulrich, Ursin, Giske, Untch, Michael, Vachon, Celine, van Asperen, Christi J., Van Den Berg, David, van den Ouweland, Ans M. W., van der Kolk, Lizet, van der Luijt, Rob B., Vincent, Daniel, Vollenweider, Jason, Waisfisz, Quinten, Wang-Gohrke, Shan, Weinberg, Clarice R., Wendt, Camilla, Whittemore, Alice S., Wildiers, Hans, Willett, Walter, Winqvist, Robert, Wolk, Alicja, Wu, Anna H., Xia, Lucy, Yamaji, Taiki, Yang, Xiaohong R., Yip, Cheng Har, Yoo, Keun-Young, Yu, Jyh-Cherng, Zheng, Wei, Zheng, Ying, Zhu, Bin, Ziogas, Argyrios, Ziv, Elad, Lakhani, Sunil R., Antoniou, Antonis C., Droit, Arnaud, Andrulis, Irene L., Amos, Christopher I., Couch, Fergus J., Pharoah, Paul D. P., Chang-Claude, Jenny, Hall, Per, Hunter, David J., Milne, Roger L., Garcia-Closas, Montserrat, Schmidt, Marjanka K., Chanock, Stephen J., Dunning, Alison M., Edwards, Stacey L., Bader, Gary D., Chenevix-Trench, Georgia, Simard, Jacques, Kraft, Peter, Easton, Douglas F., Michailidou, Kyriaki, Lindstrom, Sara, Dennis, Joe, Beesley, Jonathan, Hui, Shirley, Kar, Siddhartha, Lemacon, Audrey, Soucy, Penny, Glubb, Dylan, Rostamianfar, Asha, Bolla, Manjeet K., Wang, Qin, Tyrer, Jonathan, Dicks, Ed, Lee, Andrew, Wang, Zhaoming, Allen, Jamie, Keeman, Renske, Eilber, Ursula, French, Juliet D., Chen, Xiao Qing, Fachal, Laura, McCue, Karen, McCart, Amy E., Reed, Amy E. McCart, Ghoussaini, Maya, Carroll, Jason S., Jiang, Xia, Finucane, Hilary, Adams, Marcia, Adank, Muriel A., Ahsan, Habibul, Aittomaki, Kristiina, Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Aronson, Kristan J., Arun, Banu, Auer, Paul L., Bacot, Francois, Barrdahl, Myrto, Baynes, Caroline, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Blomqvist, Carl, Bogdanova, Natalia V., Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brand, Judith S., Brauch, Hiltrud, Brennan, Paul, Brenner, Hermann, Brinton, Louise, Broberg, Per, Brock, Ian W., Broeks, Annegien, Brooks-Wilson, Angela, Brucker, Sara Y., Bruening, Thomas, Burwinkel, Barbara, Butterbach, Katja, Cai, Qiuyin, Cai, Hui, Caldes, Trinidad, Canzian, Federico, Carracedo, Angel, Carter, Brian D., Castelao, Jose E., Chan, Tsun L., Cheng, Ting-Yuan David, Chia, Kee Seng, Choi, Ji-Yeob, Christiansen, Hans, Clarke, Christine L., Collee, Margriet, Conroy, Don M., Cordina-Duverger, Emilie, Cornelissen, Sten, Cox, David G., Cox, Angela, Cross, Simon S., Cunningham, Julie M., Czene, Kamila, Daly, Mary B., Devilee, Peter, Doheny, Kimberly F., Doerk, Thilo, dos-Santos-Silva, Isabel, Dumont, Martine, Durcan, Lorraine, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Ellberg, Carolina, Elvira, Mingajeva, Engel, Christoph, Eriksson, Mikael, Fasching, Peter A., Figueroa, Jonine, Flesch-Janys, Dieter, Fletcher, Olivia, Flyger, Henrik, Fritschi, Lin, Gaborieau, Valerie, Gabrielson, Marike, Gago-Dominguez, Manuela, Gao, Yu-Tang, Gapstur, Susan M., Garcia-Saenz, Jose A., Gaudet, Mia M., Georgoulias, Vassilios, Giles, Graham G., Glendon, Gord, Goldberg, Mark S., Goldgar, David E., Gonzalez-Neira, Anna, Alnaes, Grethe I. Grenaker, Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Guenel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hakansson, Niclas, Hamann, Ute, Hamel, Nathalie, Hankinson, Susan, Harrington, Patricia, Hart, Steven N., Hartikainen, Jaana M., Hartman, Mikael, Hein, Alexander, Heyworth, Jane, Hicks, Belynda, Hillemanns, Peter, Ho, Dona N., Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Hou, Ming-Feng, Hsiung, Chia-Ni, Huang, Guanmengqian, Humphreys, Keith, Ishiguro, Junko, Ito, Hidemi, Iwasaki, Motoki, Iwata, Hiroji, Jakubowska, Anna, Janni, Wolfgang, John, Esther M., Johnson, Nichola, Jones, Kristine, Jones, Michael, Jukkola-Vuorinen, Arja, Kaaks, Rudolf, Kabisch, Maria, Kaczmarek, Katarzyna, Kang, Daehee, Kasuga, Yoshio, Kerin, Michael J., Khan, Sofia, Khusnutdinova, Elza, Kiiski, Johanna I., Kim, Sung-Won, Knight, Julia A., Kosma, Veli-Matti, Kristensen, Vessela N., Kruger, Ute, Kwong, Ava, Lambrechts, Diether, Le Marchand, Loic, Lee, Eunjung, Lee, Min Hyuk, Lee, Jong Won, Lee, Chuen Neng, Lejbkowicz, Flavio, Li, Jingmei, Lilyquist, Jenna, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loibl, Sibylle, Long, Jirong, Lophatananon, Artitaya, Lubinski, Jan, Luccarini, Craig, Lux, Michael P., Ma, Edmond S. K., MacInnis, Robert J., Maishman, Tom, Makalic, Enes, Malone, Kathleen E., Kostovska, Ivana Maleva, Mannermaa, Arto, Manoukian, Siranoush, Manson, Joann E., Margolin, Sara, Mariapun, Shivaani, Martinez, Maria Elena, Matsuo, Keitaro, Mavroudis, Dimitrios, McKay, James, McLean, Catriona, Meijers-Heijboer, Hanne, Meindl, Alfons, Menendez, Primitiva, Menon, Usha, Meyer, Jeffery, Miao, Hui, Miller, Nicola, Taib, Nur Aishah Mohd, Muir, Kenneth, Mulligan, Anna Marie, Mulot, Claire, Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Nielsen, Sune F., Noh, Dong-Young, Nordestgaard, Borge G., Norman, Aaron, Olopade, Olufunmilayo I., Olson, Janet E., Olsson, Hakan, Olswold, Curtis, Orr, Nick, Pankratz, V. Shane, Park, Sue K., Park-Simon, Tjoung-Won, Lloyd, Rachel, Perez, Jose I. A., Peterlongo, Paolo, Peto, Julian, Phillips, Kelly-Anne, Pinchev, Mila, Plaseska-Karanfilska, Dijana, Prentice, Ross, Presneau, Nadege, Prokofyeva, Darya, Pugh, Elizabeth, Pylkas, Katri, Rack, Brigitte, Radice, Paolo, Rahman, Nazneen, Rennert, Gadi, Rennert, Hedy S., Rhenius, Valerie, Romero, Atocha, Romm, Jane, Ruddy, Kathryn J., Ruediger, Thomas, Rudolph, Anja, Ruebner, Matthias, Rutgers, Emiel J. T., Saloustros, Emmanouil, Sandler, Dale P., Sangrajrang, Suleeporn, Sawyer, Elinor J., Schmidt, Daniel F., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schumacher, Fredrick, Schuermann, Peter, Scott, Rodney J., Scott, Christopher, Seal, Sheila, Seynaeve, Caroline, Shah, Mitul, Sharma, Priyanka, Shen, Chen-Yang, Sheng, Grace, Sherman, Mark E., Shrubsole, Martha J., Shu, Xiao-Ou, Smeets, Ann, Sohn, Christof, Southey, Melissa C., Spinelli, John J., Stegmaier, Christa, Stewart-Brown, Sarah, Stone, Jennifer, Stram, Daniel O., Surowy, Harald, Swerdlow, Anthony, Tamimi, Rulla, Taylor, Jack A., Tengstrom, Maria, Teo, Soo H., Terry, Mary Beth, Tessier, Daniel C., Thanasitthichai, Somchai, Thoene, Kathrin, Tollenaar, Rob A. E. M., Tomlinson, Ian, Tong, Ling, Torres, Diana, Truong, Therese, Tseng, Chiu-Chen, Tsugane, Shoichiro, Ulmer, Hans-Ulrich, Ursin, Giske, Untch, Michael, Vachon, Celine, van Asperen, Christi J., Van Den Berg, David, van den Ouweland, Ans M. W., van der Kolk, Lizet, van der Luijt, Rob B., Vincent, Daniel, Vollenweider, Jason, Waisfisz, Quinten, Wang-Gohrke, Shan, Weinberg, Clarice R., Wendt, Camilla, Whittemore, Alice S., Wildiers, Hans, Willett, Walter, Winqvist, Robert, Wolk, Alicja, Wu, Anna H., Xia, Lucy, Yamaji, Taiki, Yang, Xiaohong R., Yip, Cheng Har, Yoo, Keun-Young, Yu, Jyh-Cherng, Zheng, Wei, Zheng, Ying, Zhu, Bin, Ziogas, Argyrios, Ziv, Elad, Lakhani, Sunil R., Antoniou, Antonis C., Droit, Arnaud, Andrulis, Irene L., Amos, Christopher I., Couch, Fergus J., Pharoah, Paul D. P., Chang-Claude, Jenny, Hall, Per, Hunter, David J., Milne, Roger L., Garcia-Closas, Montserrat, Schmidt, Marjanka K., Chanock, Stephen J., Dunning, Alison M., Edwards, Stacey L., Bader, Gary D., Chenevix-Trench, Georgia, Simard, Jacques, Kraft, Peter, and Easton, Douglas F.
Abstract: Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as BRCA1, and many common, mostly non-coding variants. However, much of the genetic contribution to breast cancer risk remains unknown. Here we report the results of a genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry(1). We identified 65 new loci that are associated with overall breast cancer risk at P < 5 x 10(-8). The majority of credible risk single-nucleotide polymorphisms in these loci fall in distal regulatory elements, and by integrating in silico data to predict target genes in breast cells at each locus, we demonstrate a strong overlap between candidate target genes and somatic driver genes in breast tumours. We also find that heritability of breast cancer due to all single-nucleotide polymorphisms in regulatory features was 2-5-fold enriched relative to the genome-wide average, with strong enrichment for particular transcription factor binding sites. These results provide further insight into genetic susceptibility to breast cancer and will improve the use of genetic risk scores for individualized screening and prevention.
Published: 2017

43. Deep learning-based assessment of tumor-associated stroma for diagnosing breast cancer in histopathology images

Author: Bejnordi, Babak Ehteshami, Linz, Jimmy, Glass, Ben, Mullooly, Maeve, Gierach, Gretchen L, Sherman, Mark E, Karssemeijer, Nico, van der Laak, Jeroen, Beck, Andrew H, Bejnordi, Babak Ehteshami, Linz, Jimmy, Glass, Ben, Mullooly, Maeve, Gierach, Gretchen L, Sherman, Mark E, Karssemeijer, Nico, van der Laak, Jeroen, and Beck, Andrew H
Abstract: Diagnosis of breast carcinomas has so far been limited to the morphological interpretation of epithelial cells and the assessment of epithelial tissue architecture. Consequently, most of the automated systems have focused on characterizing the epithelial regions of the breast to detect cancer. In this paper, we propose a system for classification of hematoxylin and eosin (H&E) stained breast specimens based on convolutional neural networks that primarily targets the assessment of tumor-associated stroma to diagnose breast cancer patients. We evaluate the performance of our proposed system using a large cohort containing 646 breast tissue biopsies. Our evaluations show that the proposed system achieves an area under ROC of 0.92, demonstrating the discriminative power of previously neglected tumor-associated stroma as a diagnostic biomarker., Comment: 5 pages, 2 figures, ISBI 2017 Submission
Published: 2017

44. Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170

Author: Dunning, Alison M., Michailidou, Kyriaki, Kuchenbaecker, Karoline B., Thompson, Deborah, French, Juliet D., Beesley, Jonathan, Healey, Catherine S., Kar, Siddhartha, Pooley, Karen A., Lopez-Knowles, Elena, Dicks, Ed, Barrowdale, Daniel, Sinnott-Armstrong, Nicholas A., Sallari, Richard C., Hillman, Kristine M., Kaufmann, Susanne, Sivakumaran, Haran, Marjaneh, Mahdi Moradi, Lee, Jason S., Hills, Margaret, Jarosz, Monika, Drury, Suzie, Canisius, Sander, Bolla, Manjeet K., Dennis, Joe, Wang, Qin, Hopper, John L., Southey, Melissa C., Broeks, Annegien, Schmidt, Marjanka K., Lophatananon, Artitaya, Muir, Kenneth, Beckmann, Matthias W., Fasching, Peter A., dos-Santos-Silva, Isabel, Peto, Julian, Sawyer, Elinor J., Tomlinson, Ian, Burwinkel, Barbara, Marme, Frederik, Guenel, Pascal, Truong, Therese, Bojesen, Stig E., Flyger, Henrik, Gonzalez-Neira, Anna, Perez, Jose I. A., Anton-Culver, Hoda, Eunjung, Lee, Arndt, Volker, Brenner, Hermann, Meindl, Alfons, Schmutzler, Rita K., Brauch, Hiltrud, Hamann, Ute, Aittomaki, Kristiina, Blomqvist, Carl, Ito, Hidemi, Matsuo, Keitaro, Bogdanova, Natasha, Dork, Thilo, Lindblom, Annika, Margolin, Sara, Kosma, Veli-Matti, Mannermaa, Arto, Tseng, Chiu-chen, Wu, Anna H., Lambrechts, Diether, Wildiers, Hans, Chang-Claude, Jenny, Rudolph, Anja, Peterlongo, Paolo, Radice, Paolo, Olson, Janet E., Giles, Graham G., Milne, Roger L., Haiman, Christopher A., Henderson, Brian E., Goldberg, Mark S., Teo, Soo H., Yip, Cheng Har, Nord, Silje, Borresen-Dale, Anne-Lise, Kristensen, Vessela, Long, Jirong, Zheng, Wei, Pylkas, Katri, Winqvist, Robert, Andrulis, Irene L., Knight, Julia A., Devilee, Peter, Seynaeve, Caroline, Figueroa, Jonine, Sherman, Mark E., Czene, Kamila, Darabi, Hatef, Hollestelle, Antoinette, van den Ouweland, Ans M. W., Humphreys, Keith, Gao, Yu-Tang, Shu, Xiao-Ou, Cox, Angela, Cross, Simon S., Blot, William, Cai, Qiuyin, Ghoussaini, Maya, Perkins, Barbara J., Shah, Mitul, Choi, Ji-Yeob, Kang, Daehee, Lee, Soo Chin, Hartman, Mikael, Kabisch, Maria, Torres, Diana, Jakubowska, Anna, Lubinski, Jan, Brennan, Paul, Sangrajrang, Suleeporn, Ambrosone, Christine B., Toland, Amanda E., Shen, Chen-Yang, Wu, Pei-Ei, Orr, Nick, Swerdlow, Anthony, McGuffog, Lesley, Healey, Sue, Lee, Andrew, Kapuscinski, Miroslav, John, Esther M., Terry, Mary Beth, Daly, Mary B., Goldgar, David E., Buys, Saundra S., Janavicius, Ramunas, Tihomirova, Laima, Tung, Nadine, Dorfling, Cecilia M., van Rensburg, Elizabeth J., Neuhausen, Susan L., Ejlertsen, Bent, Hansen, Thomas V. O., Osorio, Ana, Benitez, Javier, Rando, Rachel, Weitzel, Jeffrey N., Bonanni, Bernardo, Peissel, Bernard, Manoukian, Siranoush, Papi, Laura, Ottini, Laura, Konstantopoulou, Irene, Apostolou, Paraskevi, Garber, Judy, Rashid, Muhammad Usman, Frost, Debra, Izatt, Louise, Ellis, Steve, Godwin, Andrew K., Arnold, Norbert, Niederacher, Dieter, Rhiem, Kerstin, Bogdanova-Markov, Nadja, Sagne, Charlotte, Stoppa-Lyonnet, Dominique, Damiola, Francesca, Sinilnikova, Olga M., Mazoyer, Sylvie, Isaacs, Claudine, Claes, Kathleen B. M., De Leeneer, Kim, De la Hoya, Miguel, Caldes, Trinidad, Nevanlinna, Heli, Khan, Sofia, Mensenkamp, Arjen R., Hooning, Maartje J., Rookus, Matti A., Kwong, Ava, Olah, Edith, Diez, Orland, Brunet, Joan, Pujana, Miquel Angel, Gronwald, Jacek, Huzarski, Tomasz, Barkardottir, Rosa B., Laframboise, Rachel, Soucy, Penny, Montagna, Marco, Agata, Simona, Teixeira, Manuel R., Park, Sue Kyung, Lindor, Noralane, Couch, Fergus J., Tischkowitz, Marc, Foretova, Lenka, Vijai, Joseph, Offit, Kenneth, Singer, Christian F., Rappaport, Christine, Phelan, Catherine M., Greene, Mark H., Mai, Phuong L., Rennert, Gad, Imyanitov, Evgeny N., Hulick, Peter J., Phillips, Kelly-Anne, Piedmonte, Marion, Mulligan, Anna Marie, Glendon, Gord, Bojesen, Anders, Thomassen, Mads, Caligo, Maria A., Yoon, Sook-Yee, Friedman, Eitan, Laitman, Yael, Borg, Ake, Von Wachenfeldt, Anna, Ehrencrona, Hans, Rantala, Johanna, Olopade, Olufunmilayo I., Ganz, Patricia A., Nussbaum, Robert L., Gayther, Simon A., Nathanson, Katherine L., Domchek, Susan M., Arun, Banu K., Mitchell, Gillian, Karlan, Beth Y., Lester, Jenny, Maskarinec, Gertraud, Woolcott, Christy, Scott, Christopher, Stone, Jennifer, Apicella, Carmel, Tamimi, Rulla, Luben, Robert, Khaw, Kay-Tee, Helland, Aslaug, Haakensen, Vilde, Dowsett, Mitch, Pharoah, Paul D. P., Simard, Jacques, Hall, Per, Garcia-Closas, Montserrat, Vachon, Celine, Chenevix-Trench, Georgia, Antoniou, Antonis C., Easton, Douglas F., Edwards, Stacey L., Dunning, Alison M., Michailidou, Kyriaki, Kuchenbaecker, Karoline B., Thompson, Deborah, French, Juliet D., Beesley, Jonathan, Healey, Catherine S., Kar, Siddhartha, Pooley, Karen A., Lopez-Knowles, Elena, Dicks, Ed, Barrowdale, Daniel, Sinnott-Armstrong, Nicholas A., Sallari, Richard C., Hillman, Kristine M., Kaufmann, Susanne, Sivakumaran, Haran, Marjaneh, Mahdi Moradi, Lee, Jason S., Hills, Margaret, Jarosz, Monika, Drury, Suzie, Canisius, Sander, Bolla, Manjeet K., Dennis, Joe, Wang, Qin, Hopper, John L., Southey, Melissa C., Broeks, Annegien, Schmidt, Marjanka K., Lophatananon, Artitaya, Muir, Kenneth, Beckmann, Matthias W., Fasching, Peter A., dos-Santos-Silva, Isabel, Peto, Julian, Sawyer, Elinor J., Tomlinson, Ian, Burwinkel, Barbara, Marme, Frederik, Guenel, Pascal, Truong, Therese, Bojesen, Stig E., Flyger, Henrik, Gonzalez-Neira, Anna, Perez, Jose I. A., Anton-Culver, Hoda, Eunjung, Lee, Arndt, Volker, Brenner, Hermann, Meindl, Alfons, Schmutzler, Rita K., Brauch, Hiltrud, Hamann, Ute, Aittomaki, Kristiina, Blomqvist, Carl, Ito, Hidemi, Matsuo, Keitaro, Bogdanova, Natasha, Dork, Thilo, Lindblom, Annika, Margolin, Sara, Kosma, Veli-Matti, Mannermaa, Arto, Tseng, Chiu-chen, Wu, Anna H., Lambrechts, Diether, Wildiers, Hans, Chang-Claude, Jenny, Rudolph, Anja, Peterlongo, Paolo, Radice, Paolo, Olson, Janet E., Giles, Graham G., Milne, Roger L., Haiman, Christopher A., Henderson, Brian E., Goldberg, Mark S., Teo, Soo H., Yip, Cheng Har, Nord, Silje, Borresen-Dale, Anne-Lise, Kristensen, Vessela, Long, Jirong, Zheng, Wei, Pylkas, Katri, Winqvist, Robert, Andrulis, Irene L., Knight, Julia A., Devilee, Peter, Seynaeve, Caroline, Figueroa, Jonine, Sherman, Mark E., Czene, Kamila, Darabi, Hatef, Hollestelle, Antoinette, van den Ouweland, Ans M. W., Humphreys, Keith, Gao, Yu-Tang, Shu, Xiao-Ou, Cox, Angela, Cross, Simon S., Blot, William, Cai, Qiuyin, Ghoussaini, Maya, Perkins, Barbara J., Shah, Mitul, Choi, Ji-Yeob, Kang, Daehee, Lee, Soo Chin, Hartman, Mikael, Kabisch, Maria, Torres, Diana, Jakubowska, Anna, Lubinski, Jan, Brennan, Paul, Sangrajrang, Suleeporn, Ambrosone, Christine B., Toland, Amanda E., Shen, Chen-Yang, Wu, Pei-Ei, Orr, Nick, Swerdlow, Anthony, McGuffog, Lesley, Healey, Sue, Lee, Andrew, Kapuscinski, Miroslav, John, Esther M., Terry, Mary Beth, Daly, Mary B., Goldgar, David E., Buys, Saundra S., Janavicius, Ramunas, Tihomirova, Laima, Tung, Nadine, Dorfling, Cecilia M., van Rensburg, Elizabeth J., Neuhausen, Susan L., Ejlertsen, Bent, Hansen, Thomas V. O., Osorio, Ana, Benitez, Javier, Rando, Rachel, Weitzel, Jeffrey N., Bonanni, Bernardo, Peissel, Bernard, Manoukian, Siranoush, Papi, Laura, Ottini, Laura, Konstantopoulou, Irene, Apostolou, Paraskevi, Garber, Judy, Rashid, Muhammad Usman, Frost, Debra, Izatt, Louise, Ellis, Steve, Godwin, Andrew K., Arnold, Norbert, Niederacher, Dieter, Rhiem, Kerstin, Bogdanova-Markov, Nadja, Sagne, Charlotte, Stoppa-Lyonnet, Dominique, Damiola, Francesca, Sinilnikova, Olga M., Mazoyer, Sylvie, Isaacs, Claudine, Claes, Kathleen B. M., De Leeneer, Kim, De la Hoya, Miguel, Caldes, Trinidad, Nevanlinna, Heli, Khan, Sofia, Mensenkamp, Arjen R., Hooning, Maartje J., Rookus, Matti A., Kwong, Ava, Olah, Edith, Diez, Orland, Brunet, Joan, Pujana, Miquel Angel, Gronwald, Jacek, Huzarski, Tomasz, Barkardottir, Rosa B., Laframboise, Rachel, Soucy, Penny, Montagna, Marco, Agata, Simona, Teixeira, Manuel R., Park, Sue Kyung, Lindor, Noralane, Couch, Fergus J., Tischkowitz, Marc, Foretova, Lenka, Vijai, Joseph, Offit, Kenneth, Singer, Christian F., Rappaport, Christine, Phelan, Catherine M., Greene, Mark H., Mai, Phuong L., Rennert, Gad, Imyanitov, Evgeny N., Hulick, Peter J., Phillips, Kelly-Anne, Piedmonte, Marion, Mulligan, Anna Marie, Glendon, Gord, Bojesen, Anders, Thomassen, Mads, Caligo, Maria A., Yoon, Sook-Yee, Friedman, Eitan, Laitman, Yael, Borg, Ake, Von Wachenfeldt, Anna, Ehrencrona, Hans, Rantala, Johanna, Olopade, Olufunmilayo I., Ganz, Patricia A., Nussbaum, Robert L., Gayther, Simon A., Nathanson, Katherine L., Domchek, Susan M., Arun, Banu K., Mitchell, Gillian, Karlan, Beth Y., Lester, Jenny, Maskarinec, Gertraud, Woolcott, Christy, Scott, Christopher, Stone, Jennifer, Apicella, Carmel, Tamimi, Rulla, Luben, Robert, Khaw, Kay-Tee, Helland, Aslaug, Haakensen, Vilde, Dowsett, Mitch, Pharoah, Paul D. P., Simard, Jacques, Hall, Per, Garcia-Closas, Montserrat, Vachon, Celine, Chenevix-Trench, Georgia, Antoniou, Antonis C., Easton, Douglas F., and Edwards, Stacey L.
Abstract: We analyzed 3,872 common genetic variants across the ESR1 locus (encoding estrogen receptor a) in 118,816 subjects from three international consortia. We found evidence for at least five independent causal variants, each associated with different phenotype sets, including estrogen receptor (ER+ or ER-) and human ERBB2 (HER2(+) or HER2(-)) tumor subtypes, mammographic density and tumor grade. The best candidate causal variants for ER-tumors lie in four separate enhancer elements, and their risk alleles reduce expression of ESR1, RMND1 and CCDC170, whereas the risk alleles of the strongest candidates for the remaining independent causal variant disrupt a silencer element and putatively increase ESR1 and RMND1 expression., Funding: We thank all the individuals who took part in these studies and all the researchers, clinicians, technicians and administrative staff who have enabled this work to be carried out. This study would not have been possible without the contributions of the following: A. Berchuck (OCAC), R.A. Eeles, A. A. Al Olama, Z. Kote-Jarai and S. Benlloch (PRACTICAL), C. Luccarini and the staff of the Centre for Genetic Epidemiology Laboratory, the staff of the CNIO genotyping unit, D.C. Tessier, F. Bacot, D. Vincent, S. LaBoissiere, F. Robidoux and the staff of the McGill University and Genome Quebec Innovation Centre, S. F. Nielsen, B.G. Nordestgaard and the staff of the Copenhagen DNA laboratory, and J.M. Cunningham, S. A. Windebank, C. A. Hilker, J. Meyer and the staff of the Mayo Clinic Genotyping Core Facility. Normal human tissues from the Susan G. Komen for the Cure Tissue Bank at the Indiana University Simon Cancer Center (Indianapolis) were used in this study. We thank the contributors, including Indiana University who collected samples used in this study, as well as the donors and their families, whose help and participation made this work possible. We also acknowledge National Institute for Health Research (NIHR) support to the Royal Marsden Biomedical Research Centre. Funding for the iCOGS infrastructure came from the European Community's Seventh Framework Programme under grant agreement 223175 (HEALTH-F2-2009-223175) (COGS), Cancer Research UK (C1287/A10118, C1287/A10710, C12292/A11174, C1281/A12014, C5047/A8384, C5047/A15007, C5047/A10692 and C8197/A16565), the US National Institutes of Health (NIH; CA128978, CA192393, CA116167, CA176785 and an NIH Specialized Program of Research Excellence (SPORE) in Breast Cancer (CA116201)) and Post-Cancer GWAS initiative (1U19 CA148537, 1U19 CA148065 and 1U19 CA148112, the GAME-ON initiative), the US Department of Defense (W81XWH-10-1-0341), the Canadian Institutes of Health Research (CIHR) for the CIHR Team in Famili
Published: 2016
Full Text: View/download PDF

45. Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170

Author: Dunning, Alison M., Michailidou, Kyriaki, Kuchenbaecker, Karoline B., Thompson, Deborah, French, Juliet D., Beesley, Jonathan, Healey, Catherine S., Kar, Siddhartha, Pooley, Karen A., Lopez-Knowles, Elena, Dicks, Ed, Barrowdale, Daniel, Sinnott-Armstrong, Nicholas A., Sallari, Richard C., Hillman, Kristine M., Kaufmann, Susanne, Sivakumaran, Haran, Marjaneh, Mahdi Moradi, Lee, Jason S., Hills, Margaret, Jarosz, Monika, Drury, Suzie, Canisius, Sander, Bolla, Manjeet K., Dennis, Joe, Wang, Qin, Hopper, John L., Southey, Melissa C., Broeks, Annegien, Schmidt, Marjanka K., Lophatananon, Artitaya, Muir, Kenneth, Beckmann, Matthias W., Fasching, Peter A., dos-Santos-Silva, Isabel, Peto, Julian, Sawyer, Elinor J., Tomlinson, Ian, Burwinkel, Barbara, Marme, Frederik, Guenel, Pascal, Truong, Therese, Bojesen, Stig E., Flyger, Henrik, Gonzalez-Neira, Anna, Perez, Jose I. A., Anton-Culver, Hoda, Eunjung, Lee, Arndt, Volker, Brenner, Hermann, Meindl, Alfons, Schmutzler, Rita K., Brauch, Hiltrud, Hamann, Ute, Aittomaki, Kristiina, Blomqvist, Carl, Ito, Hidemi, Matsuo, Keitaro, Bogdanova, Natasha, Dork, Thilo, Lindblom, Annika, Margolin, Sara, Kosma, Veli-Matti, Mannermaa, Arto, Tseng, Chiu-chen, Wu, Anna H., Lambrechts, Diether, Wildiers, Hans, Chang-Claude, Jenny, Rudolph, Anja, Peterlongo, Paolo, Radice, Paolo, Olson, Janet E., Giles, Graham G., Milne, Roger L., Haiman, Christopher A., Henderson, Brian E., Goldberg, Mark S., Teo, Soo H., Yip, Cheng Har, Nord, Silje, Borresen-Dale, Anne-Lise, Kristensen, Vessela, Long, Jirong, Zheng, Wei, Pylkas, Katri, Winqvist, Robert, Andrulis, Irene L., Knight, Julia A., Devilee, Peter, Seynaeve, Caroline, Figueroa, Jonine, Sherman, Mark E., Czene, Kamila, Darabi, Hatef, Hollestelle, Antoinette, van den Ouweland, Ans M. W., Humphreys, Keith, Gao, Yu-Tang, Shu, Xiao-Ou, Cox, Angela, Cross, Simon S., Blot, William, Cai, Qiuyin, Ghoussaini, Maya, Perkins, Barbara J., Shah, Mitul, Choi, Ji-Yeob, Kang, Daehee, Lee, Soo Chin, Hartman, Mikael, Kabisch, Maria, Torres, Diana, Jakubowska, Anna, Lubinski, Jan, Brennan, Paul, Sangrajrang, Suleeporn, Ambrosone, Christine B., Toland, Amanda E., Shen, Chen-Yang, Wu, Pei-Ei, Orr, Nick, Swerdlow, Anthony, McGuffog, Lesley, Healey, Sue, Lee, Andrew, Kapuscinski, Miroslav, John, Esther M., Terry, Mary Beth, Daly, Mary B., Goldgar, David E., Buys, Saundra S., Janavicius, Ramunas, Tihomirova, Laima, Tung, Nadine, Dorfling, Cecilia M., van Rensburg, Elizabeth J., Neuhausen, Susan L., Ejlertsen, Bent, Hansen, Thomas V. O., Osorio, Ana, Benitez, Javier, Rando, Rachel, Weitzel, Jeffrey N., Bonanni, Bernardo, Peissel, Bernard, Manoukian, Siranoush, Papi, Laura, Ottini, Laura, Konstantopoulou, Irene, Apostolou, Paraskevi, Garber, Judy, Rashid, Muhammad Usman, Frost, Debra, Izatt, Louise, Ellis, Steve, Godwin, Andrew K., Arnold, Norbert, Niederacher, Dieter, Rhiem, Kerstin, Bogdanova-Markov, Nadja, Sagne, Charlotte, Stoppa-Lyonnet, Dominique, Damiola, Francesca, Sinilnikova, Olga M., Mazoyer, Sylvie, Isaacs, Claudine, Claes, Kathleen B. M., De Leeneer, Kim, De la Hoya, Miguel, Caldes, Trinidad, Nevanlinna, Heli, Khan, Sofia, Mensenkamp, Arjen R., Hooning, Maartje J., Rookus, Matti A., Kwong, Ava, Olah, Edith, Diez, Orland, Brunet, Joan, Pujana, Miquel Angel, Gronwald, Jacek, Huzarski, Tomasz, Barkardottir, Rosa B., Laframboise, Rachel, Soucy, Penny, Montagna, Marco, Agata, Simona, Teixeira, Manuel R., Park, Sue Kyung, Lindor, Noralane, Couch, Fergus J., Tischkowitz, Marc, Foretova, Lenka, Vijai, Joseph, Offit, Kenneth, Singer, Christian F., Rappaport, Christine, Phelan, Catherine M., Greene, Mark H., Mai, Phuong L., Rennert, Gad, Imyanitov, Evgeny N., Hulick, Peter J., Phillips, Kelly-Anne, Piedmonte, Marion, Mulligan, Anna Marie, Glendon, Gord, Bojesen, Anders, Thomassen, Mads, Caligo, Maria A., Yoon, Sook-Yee, Friedman, Eitan, Laitman, Yael, Borg, Ake, Von Wachenfeldt, Anna, Ehrencrona, Hans, Rantala, Johanna, Olopade, Olufunmilayo I., Ganz, Patricia A., Nussbaum, Robert L., Gayther, Simon A., Nathanson, Katherine L., Domchek, Susan M., Arun, Banu K., Mitchell, Gillian, Karlan, Beth Y., Lester, Jenny, Maskarinec, Gertraud, Woolcott, Christy, Scott, Christopher, Stone, Jennifer, Apicella, Carmel, Tamimi, Rulla, Luben, Robert, Khaw, Kay-Tee, Helland, Aslaug, Haakensen, Vilde, Dowsett, Mitch, Pharoah, Paul D. P., Simard, Jacques, Hall, Per, Garcia-Closas, Montserrat, Vachon, Celine, Chenevix-Trench, Georgia, Antoniou, Antonis C., Easton, Douglas F., Edwards, Stacey L., Dunning, Alison M., Michailidou, Kyriaki, Kuchenbaecker, Karoline B., Thompson, Deborah, French, Juliet D., Beesley, Jonathan, Healey, Catherine S., Kar, Siddhartha, Pooley, Karen A., Lopez-Knowles, Elena, Dicks, Ed, Barrowdale, Daniel, Sinnott-Armstrong, Nicholas A., Sallari, Richard C., Hillman, Kristine M., Kaufmann, Susanne, Sivakumaran, Haran, Marjaneh, Mahdi Moradi, Lee, Jason S., Hills, Margaret, Jarosz, Monika, Drury, Suzie, Canisius, Sander, Bolla, Manjeet K., Dennis, Joe, Wang, Qin, Hopper, John L., Southey, Melissa C., Broeks, Annegien, Schmidt, Marjanka K., Lophatananon, Artitaya, Muir, Kenneth, Beckmann, Matthias W., Fasching, Peter A., dos-Santos-Silva, Isabel, Peto, Julian, Sawyer, Elinor J., Tomlinson, Ian, Burwinkel, Barbara, Marme, Frederik, Guenel, Pascal, Truong, Therese, Bojesen, Stig E., Flyger, Henrik, Gonzalez-Neira, Anna, Perez, Jose I. A., Anton-Culver, Hoda, Eunjung, Lee, Arndt, Volker, Brenner, Hermann, Meindl, Alfons, Schmutzler, Rita K., Brauch, Hiltrud, Hamann, Ute, Aittomaki, Kristiina, Blomqvist, Carl, Ito, Hidemi, Matsuo, Keitaro, Bogdanova, Natasha, Dork, Thilo, Lindblom, Annika, Margolin, Sara, Kosma, Veli-Matti, Mannermaa, Arto, Tseng, Chiu-chen, Wu, Anna H., Lambrechts, Diether, Wildiers, Hans, Chang-Claude, Jenny, Rudolph, Anja, Peterlongo, Paolo, Radice, Paolo, Olson, Janet E., Giles, Graham G., Milne, Roger L., Haiman, Christopher A., Henderson, Brian E., Goldberg, Mark S., Teo, Soo H., Yip, Cheng Har, Nord, Silje, Borresen-Dale, Anne-Lise, Kristensen, Vessela, Long, Jirong, Zheng, Wei, Pylkas, Katri, Winqvist, Robert, Andrulis, Irene L., Knight, Julia A., Devilee, Peter, Seynaeve, Caroline, Figueroa, Jonine, Sherman, Mark E., Czene, Kamila, Darabi, Hatef, Hollestelle, Antoinette, van den Ouweland, Ans M. W., Humphreys, Keith, Gao, Yu-Tang, Shu, Xiao-Ou, Cox, Angela, Cross, Simon S., Blot, William, Cai, Qiuyin, Ghoussaini, Maya, Perkins, Barbara J., Shah, Mitul, Choi, Ji-Yeob, Kang, Daehee, Lee, Soo Chin, Hartman, Mikael, Kabisch, Maria, Torres, Diana, Jakubowska, Anna, Lubinski, Jan, Brennan, Paul, Sangrajrang, Suleeporn, Ambrosone, Christine B., Toland, Amanda E., Shen, Chen-Yang, Wu, Pei-Ei, Orr, Nick, Swerdlow, Anthony, McGuffog, Lesley, Healey, Sue, Lee, Andrew, Kapuscinski, Miroslav, John, Esther M., Terry, Mary Beth, Daly, Mary B., Goldgar, David E., Buys, Saundra S., Janavicius, Ramunas, Tihomirova, Laima, Tung, Nadine, Dorfling, Cecilia M., van Rensburg, Elizabeth J., Neuhausen, Susan L., Ejlertsen, Bent, Hansen, Thomas V. O., Osorio, Ana, Benitez, Javier, Rando, Rachel, Weitzel, Jeffrey N., Bonanni, Bernardo, Peissel, Bernard, Manoukian, Siranoush, Papi, Laura, Ottini, Laura, Konstantopoulou, Irene, Apostolou, Paraskevi, Garber, Judy, Rashid, Muhammad Usman, Frost, Debra, Izatt, Louise, Ellis, Steve, Godwin, Andrew K., Arnold, Norbert, Niederacher, Dieter, Rhiem, Kerstin, Bogdanova-Markov, Nadja, Sagne, Charlotte, Stoppa-Lyonnet, Dominique, Damiola, Francesca, Sinilnikova, Olga M., Mazoyer, Sylvie, Isaacs, Claudine, Claes, Kathleen B. M., De Leeneer, Kim, De la Hoya, Miguel, Caldes, Trinidad, Nevanlinna, Heli, Khan, Sofia, Mensenkamp, Arjen R., Hooning, Maartje J., Rookus, Matti A., Kwong, Ava, Olah, Edith, Diez, Orland, Brunet, Joan, Pujana, Miquel Angel, Gronwald, Jacek, Huzarski, Tomasz, Barkardottir, Rosa B., Laframboise, Rachel, Soucy, Penny, Montagna, Marco, Agata, Simona, Teixeira, Manuel R., Park, Sue Kyung, Lindor, Noralane, Couch, Fergus J., Tischkowitz, Marc, Foretova, Lenka, Vijai, Joseph, Offit, Kenneth, Singer, Christian F., Rappaport, Christine, Phelan, Catherine M., Greene, Mark H., Mai, Phuong L., Rennert, Gad, Imyanitov, Evgeny N., Hulick, Peter J., Phillips, Kelly-Anne, Piedmonte, Marion, Mulligan, Anna Marie, Glendon, Gord, Bojesen, Anders, Thomassen, Mads, Caligo, Maria A., Yoon, Sook-Yee, Friedman, Eitan, Laitman, Yael, Borg, Ake, Von Wachenfeldt, Anna, Ehrencrona, Hans, Rantala, Johanna, Olopade, Olufunmilayo I., Ganz, Patricia A., Nussbaum, Robert L., Gayther, Simon A., Nathanson, Katherine L., Domchek, Susan M., Arun, Banu K., Mitchell, Gillian, Karlan, Beth Y., Lester, Jenny, Maskarinec, Gertraud, Woolcott, Christy, Scott, Christopher, Stone, Jennifer, Apicella, Carmel, Tamimi, Rulla, Luben, Robert, Khaw, Kay-Tee, Helland, Aslaug, Haakensen, Vilde, Dowsett, Mitch, Pharoah, Paul D. P., Simard, Jacques, Hall, Per, Garcia-Closas, Montserrat, Vachon, Celine, Chenevix-Trench, Georgia, Antoniou, Antonis C., Easton, Douglas F., and Edwards, Stacey L.
Abstract: We analyzed 3,872 common genetic variants across the ESR1 locus (encoding estrogen receptor a) in 118,816 subjects from three international consortia. We found evidence for at least five independent causal variants, each associated with different phenotype sets, including estrogen receptor (ER+ or ER-) and human ERBB2 (HER2(+) or HER2(-)) tumor subtypes, mammographic density and tumor grade. The best candidate causal variants for ER-tumors lie in four separate enhancer elements, and their risk alleles reduce expression of ESR1, RMND1 and CCDC170, whereas the risk alleles of the strongest candidates for the remaining independent causal variant disrupt a silencer element and putatively increase ESR1 and RMND1 expression.
Published: 2016

46. Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170

Author: Dunning, Alison M., Michailidou, Kyriaki, Kuchenbaecker, Karoline B., Thompson, Deborah, French, Juliet D., Beesley, Jonathan, Healey, Catherine S., Kar, Siddhartha, Pooley, Karen A., Lopez-Knowles, Elena, Dicks, Ed, Barrowdale, Daniel, Sinnott-Armstrong, Nicholas A., Sallari, Richard C., Hillman, Kristine M., Kaufmann, Susanne, Sivakumaran, Haran, Marjaneh, Mahdi Moradi, Lee, Jason S., Hills, Margaret, Jarosz, Monika, Drury, Suzie, Canisius, Sander, Bolla, Manjeet K., Dennis, Joe, Wang, Qin, Hopper, John L., Southey, Melissa C., Broeks, Annegien, Schmidt, Marjanka K., Lophatananon, Artitaya, Muir, Kenneth, Beckmann, Matthias W., Fasching, Peter A., dos-Santos-Silva, Isabel, Peto, Julian, Sawyer, Elinor J., Tomlinson, Ian, Burwinkel, Barbara, Marme, Frederik, Guenel, Pascal, Truong, Therese, Bojesen, Stig E., Flyger, Henrik, Gonzalez-Neira, Anna, Perez, Jose I. A., Anton-Culver, Hoda, Eunjung, Lee, Arndt, Volker, Brenner, Hermann, Meindl, Alfons, Schmutzler, Rita K., Brauch, Hiltrud, Hamann, Ute, Aittomaki, Kristiina, Blomqvist, Carl, Ito, Hidemi, Matsuo, Keitaro, Bogdanova, Natasha, Dork, Thilo, Lindblom, Annika, Margolin, Sara, Kosma, Veli-Matti, Mannermaa, Arto, Tseng, Chiu-chen, Wu, Anna H., Lambrechts, Diether, Wildiers, Hans, Chang-Claude, Jenny, Rudolph, Anja, Peterlongo, Paolo, Radice, Paolo, Olson, Janet E., Giles, Graham G., Milne, Roger L., Haiman, Christopher A., Henderson, Brian E., Goldberg, Mark S., Teo, Soo H., Yip, Cheng Har, Nord, Silje, Borresen-Dale, Anne-Lise, Kristensen, Vessela, Long, Jirong, Zheng, Wei, Pylkas, Katri, Winqvist, Robert, Andrulis, Irene L., Knight, Julia A., Devilee, Peter, Seynaeve, Caroline, Figueroa, Jonine, Sherman, Mark E., Czene, Kamila, Darabi, Hatef, Hollestelle, Antoinette, van den Ouweland, Ans M. W., Humphreys, Keith, Gao, Yu-Tang, Shu, Xiao-Ou, Cox, Angela, Cross, Simon S., Blot, William, Cai, Qiuyin, Ghoussaini, Maya, Perkins, Barbara J., Shah, Mitul, Choi, Ji-Yeob, Kang, Daehee, Lee, Soo Chin, Hartman, Mikael, Kabisch, Maria, Torres, Diana, Jakubowska, Anna, Lubinski, Jan, Brennan, Paul, Sangrajrang, Suleeporn, Ambrosone, Christine B., Toland, Amanda E., Shen, Chen-Yang, Wu, Pei-Ei, Orr, Nick, Swerdlow, Anthony, McGuffog, Lesley, Healey, Sue, Lee, Andrew, Kapuscinski, Miroslav, John, Esther M., Terry, Mary Beth, Daly, Mary B., Goldgar, David E., Buys, Saundra S., Janavicius, Ramunas, Tihomirova, Laima, Tung, Nadine, Dorfling, Cecilia M., van Rensburg, Elizabeth J., Neuhausen, Susan L., Ejlertsen, Bent, Hansen, Thomas V. O., Osorio, Ana, Benitez, Javier, Rando, Rachel, Weitzel, Jeffrey N., Bonanni, Bernardo, Peissel, Bernard, Manoukian, Siranoush, Papi, Laura, Ottini, Laura, Konstantopoulou, Irene, Apostolou, Paraskevi, Garber, Judy, Rashid, Muhammad Usman, Frost, Debra, Izatt, Louise, Ellis, Steve, Godwin, Andrew K., Arnold, Norbert, Niederacher, Dieter, Rhiem, Kerstin, Bogdanova-Markov, Nadja, Sagne, Charlotte, Stoppa-Lyonnet, Dominique, Damiola, Francesca, Sinilnikova, Olga M., Mazoyer, Sylvie, Isaacs, Claudine, Claes, Kathleen B. M., De Leeneer, Kim, De la Hoya, Miguel, Caldes, Trinidad, Nevanlinna, Heli, Khan, Sofia, Mensenkamp, Arjen R., Hooning, Maartje J., Rookus, Matti A., Kwong, Ava, Olah, Edith, Diez, Orland, Brunet, Joan, Pujana, Miquel Angel, Gronwald, Jacek, Huzarski, Tomasz, Barkardottir, Rosa B., Laframboise, Rachel, Soucy, Penny, Montagna, Marco, Agata, Simona, Teixeira, Manuel R., Park, Sue Kyung, Lindor, Noralane, Couch, Fergus J., Tischkowitz, Marc, Foretova, Lenka, Vijai, Joseph, Offit, Kenneth, Singer, Christian F., Rappaport, Christine, Phelan, Catherine M., Greene, Mark H., Mai, Phuong L., Rennert, Gad, Imyanitov, Evgeny N., Hulick, Peter J., Phillips, Kelly-Anne, Piedmonte, Marion, Mulligan, Anna Marie, Glendon, Gord, Bojesen, Anders, Thomassen, Mads, Caligo, Maria A., Yoon, Sook-Yee, Friedman, Eitan, Laitman, Yael, Borg, Ake, Von Wachenfeldt, Anna, Ehrencrona, Hans, Rantala, Johanna, Olopade, Olufunmilayo I., Ganz, Patricia A., Nussbaum, Robert L., Gayther, Simon A., Nathanson, Katherine L., Domchek, Susan M., Arun, Banu K., Mitchell, Gillian, Karlan, Beth Y., Lester, Jenny, Maskarinec, Gertraud, Woolcott, Christy, Scott, Christopher, Stone, Jennifer, Apicella, Carmel, Tamimi, Rulla, Luben, Robert, Khaw, Kay-Tee, Helland, Aslaug, Haakensen, Vilde, Dowsett, Mitch, Pharoah, Paul D. P., Simard, Jacques, Hall, Per, Garcia-Closas, Montserrat, Vachon, Celine, Chenevix-Trench, Georgia, Antoniou, Antonis C., Easton, Douglas F., Edwards, Stacey L., Dunning, Alison M., Michailidou, Kyriaki, Kuchenbaecker, Karoline B., Thompson, Deborah, French, Juliet D., Beesley, Jonathan, Healey, Catherine S., Kar, Siddhartha, Pooley, Karen A., Lopez-Knowles, Elena, Dicks, Ed, Barrowdale, Daniel, Sinnott-Armstrong, Nicholas A., Sallari, Richard C., Hillman, Kristine M., Kaufmann, Susanne, Sivakumaran, Haran, Marjaneh, Mahdi Moradi, Lee, Jason S., Hills, Margaret, Jarosz, Monika, Drury, Suzie, Canisius, Sander, Bolla, Manjeet K., Dennis, Joe, Wang, Qin, Hopper, John L., Southey, Melissa C., Broeks, Annegien, Schmidt, Marjanka K., Lophatananon, Artitaya, Muir, Kenneth, Beckmann, Matthias W., Fasching, Peter A., dos-Santos-Silva, Isabel, Peto, Julian, Sawyer, Elinor J., Tomlinson, Ian, Burwinkel, Barbara, Marme, Frederik, Guenel, Pascal, Truong, Therese, Bojesen, Stig E., Flyger, Henrik, Gonzalez-Neira, Anna, Perez, Jose I. A., Anton-Culver, Hoda, Eunjung, Lee, Arndt, Volker, Brenner, Hermann, Meindl, Alfons, Schmutzler, Rita K., Brauch, Hiltrud, Hamann, Ute, Aittomaki, Kristiina, Blomqvist, Carl, Ito, Hidemi, Matsuo, Keitaro, Bogdanova, Natasha, Dork, Thilo, Lindblom, Annika, Margolin, Sara, Kosma, Veli-Matti, Mannermaa, Arto, Tseng, Chiu-chen, Wu, Anna H., Lambrechts, Diether, Wildiers, Hans, Chang-Claude, Jenny, Rudolph, Anja, Peterlongo, Paolo, Radice, Paolo, Olson, Janet E., Giles, Graham G., Milne, Roger L., Haiman, Christopher A., Henderson, Brian E., Goldberg, Mark S., Teo, Soo H., Yip, Cheng Har, Nord, Silje, Borresen-Dale, Anne-Lise, Kristensen, Vessela, Long, Jirong, Zheng, Wei, Pylkas, Katri, Winqvist, Robert, Andrulis, Irene L., Knight, Julia A., Devilee, Peter, Seynaeve, Caroline, Figueroa, Jonine, Sherman, Mark E., Czene, Kamila, Darabi, Hatef, Hollestelle, Antoinette, van den Ouweland, Ans M. W., Humphreys, Keith, Gao, Yu-Tang, Shu, Xiao-Ou, Cox, Angela, Cross, Simon S., Blot, William, Cai, Qiuyin, Ghoussaini, Maya, Perkins, Barbara J., Shah, Mitul, Choi, Ji-Yeob, Kang, Daehee, Lee, Soo Chin, Hartman, Mikael, Kabisch, Maria, Torres, Diana, Jakubowska, Anna, Lubinski, Jan, Brennan, Paul, Sangrajrang, Suleeporn, Ambrosone, Christine B., Toland, Amanda E., Shen, Chen-Yang, Wu, Pei-Ei, Orr, Nick, Swerdlow, Anthony, McGuffog, Lesley, Healey, Sue, Lee, Andrew, Kapuscinski, Miroslav, John, Esther M., Terry, Mary Beth, Daly, Mary B., Goldgar, David E., Buys, Saundra S., Janavicius, Ramunas, Tihomirova, Laima, Tung, Nadine, Dorfling, Cecilia M., van Rensburg, Elizabeth J., Neuhausen, Susan L., Ejlertsen, Bent, Hansen, Thomas V. O., Osorio, Ana, Benitez, Javier, Rando, Rachel, Weitzel, Jeffrey N., Bonanni, Bernardo, Peissel, Bernard, Manoukian, Siranoush, Papi, Laura, Ottini, Laura, Konstantopoulou, Irene, Apostolou, Paraskevi, Garber, Judy, Rashid, Muhammad Usman, Frost, Debra, Izatt, Louise, Ellis, Steve, Godwin, Andrew K., Arnold, Norbert, Niederacher, Dieter, Rhiem, Kerstin, Bogdanova-Markov, Nadja, Sagne, Charlotte, Stoppa-Lyonnet, Dominique, Damiola, Francesca, Sinilnikova, Olga M., Mazoyer, Sylvie, Isaacs, Claudine, Claes, Kathleen B. M., De Leeneer, Kim, De la Hoya, Miguel, Caldes, Trinidad, Nevanlinna, Heli, Khan, Sofia, Mensenkamp, Arjen R., Hooning, Maartje J., Rookus, Matti A., Kwong, Ava, Olah, Edith, Diez, Orland, Brunet, Joan, Pujana, Miquel Angel, Gronwald, Jacek, Huzarski, Tomasz, Barkardottir, Rosa B., Laframboise, Rachel, Soucy, Penny, Montagna, Marco, Agata, Simona, Teixeira, Manuel R., Park, Sue Kyung, Lindor, Noralane, Couch, Fergus J., Tischkowitz, Marc, Foretova, Lenka, Vijai, Joseph, Offit, Kenneth, Singer, Christian F., Rappaport, Christine, Phelan, Catherine M., Greene, Mark H., Mai, Phuong L., Rennert, Gad, Imyanitov, Evgeny N., Hulick, Peter J., Phillips, Kelly-Anne, Piedmonte, Marion, Mulligan, Anna Marie, Glendon, Gord, Bojesen, Anders, Thomassen, Mads, Caligo, Maria A., Yoon, Sook-Yee, Friedman, Eitan, Laitman, Yael, Borg, Ake, Von Wachenfeldt, Anna, Ehrencrona, Hans, Rantala, Johanna, Olopade, Olufunmilayo I., Ganz, Patricia A., Nussbaum, Robert L., Gayther, Simon A., Nathanson, Katherine L., Domchek, Susan M., Arun, Banu K., Mitchell, Gillian, Karlan, Beth Y., Lester, Jenny, Maskarinec, Gertraud, Woolcott, Christy, Scott, Christopher, Stone, Jennifer, Apicella, Carmel, Tamimi, Rulla, Luben, Robert, Khaw, Kay-Tee, Helland, Aslaug, Haakensen, Vilde, Dowsett, Mitch, Pharoah, Paul D. P., Simard, Jacques, Hall, Per, Garcia-Closas, Montserrat, Vachon, Celine, Chenevix-Trench, Georgia, Antoniou, Antonis C., Easton, Douglas F., and Edwards, Stacey L.
Abstract: We analyzed 3,872 common genetic variants across the ESR1 locus (encoding estrogen receptor a) in 118,816 subjects from three international consortia. We found evidence for at least five independent causal variants, each associated with different phenotype sets, including estrogen receptor (ER+ or ER-) and human ERBB2 (HER2(+) or HER2(-)) tumor subtypes, mammographic density and tumor grade. The best candidate causal variants for ER-tumors lie in four separate enhancer elements, and their risk alleles reduce expression of ESR1, RMND1 and CCDC170, whereas the risk alleles of the strongest candidates for the remaining independent causal variant disrupt a silencer element and putatively increase ESR1 and RMND1 expression.
Published: 2016

47. Investigation of gene-environment interactions between 47 newly identified breast cancer susceptibility loci and environmental risk factors.

Author: Rudolph, Anja, Rudolph, Anja, Milne, Roger L, Truong, Thérèse, Knight, Julia A, Seibold, Petra, Flesch-Janys, Dieter, Behrens, Sabine, Eilber, Ursula, Bolla, Manjeet K, Wang, Qin, Dennis, Joe, Dunning, Alison M, Shah, Mitul, Munday, Hannah R, Darabi, Hatef, Eriksson, Mikael, Brand, Judith S, Olson, Janet, Vachon, Celine M, Hallberg, Emily, Castelao, J Esteban, Carracedo, Angel, Torres, Maria, Li, Jingmei, Humphreys, Keith, Cordina-Duverger, Emilie, Menegaux, Florence, Flyger, Henrik, Nordestgaard, Børge G, Nielsen, Sune F, Yesilyurt, Betul T, Floris, Giuseppe, Leunen, Karin, Engelhardt, Ellen G, Broeks, Annegien, Rutgers, Emiel J, Glendon, Gord, Mulligan, Anna Marie, Cross, Simon, Reed, Malcolm, Gonzalez-Neira, Anna, Arias Perez, José Ignacio, Provenzano, Elena, Apicella, Carmel, Southey, Melissa C, Spurdle, Amanda, kConFab Investigators, AOCS Group, Häberle, Lothar, Beckmann, Matthias W, Ekici, Arif B, Dieffenbach, Aida Karina, Arndt, Volker, Stegmaier, Christa, McLean, Catriona, Baglietto, Laura, Chanock, Stephen J, Lissowska, Jolanta, Sherman, Mark E, Brüning, Thomas, Hamann, Ute, Ko, Yon-Dschun, Orr, Nick, Schoemaker, Minouk, Ashworth, Alan, Kosma, Veli-Matti, Kataja, Vesa, Hartikainen, Jaana M, Mannermaa, Arto, Swerdlow, Anthony, GENICA-Network, Giles, Graham G, Brenner, Hermann, Fasching, Peter A, Chenevix-Trench, Georgia, Hopper, John, Benítez, Javier, Cox, Angela, Andrulis, Irene L, Lambrechts, Diether, Gago-Dominguez, Manuela, Couch, Fergus, Czene, Kamila, Bojesen, Stig E, Easton, Doug F, Schmidt, Marjanka K, Guénel, Pascal, Hall, Per, Pharoah, Paul DP, Garcia-Closas, Montserrat, Chang-Claude, Jenny, Rudolph, Anja, Rudolph, Anja, Milne, Roger L, Truong, Thérèse, Knight, Julia A, Seibold, Petra, Flesch-Janys, Dieter, Behrens, Sabine, Eilber, Ursula, Bolla, Manjeet K, Wang, Qin, Dennis, Joe, Dunning, Alison M, Shah, Mitul, Munday, Hannah R, Darabi, Hatef, Eriksson, Mikael, Brand, Judith S, Olson, Janet, Vachon, Celine M, Hallberg, Emily, Castelao, J Esteban, Carracedo, Angel, Torres, Maria, Li, Jingmei, Humphreys, Keith, Cordina-Duverger, Emilie, Menegaux, Florence, Flyger, Henrik, Nordestgaard, Børge G, Nielsen, Sune F, Yesilyurt, Betul T, Floris, Giuseppe, Leunen, Karin, Engelhardt, Ellen G, Broeks, Annegien, Rutgers, Emiel J, Glendon, Gord, Mulligan, Anna Marie, Cross, Simon, Reed, Malcolm, Gonzalez-Neira, Anna, Arias Perez, José Ignacio, Provenzano, Elena, Apicella, Carmel, Southey, Melissa C, Spurdle, Amanda, kConFab Investigators, AOCS Group, Häberle, Lothar, Beckmann, Matthias W, Ekici, Arif B, Dieffenbach, Aida Karina, Arndt, Volker, Stegmaier, Christa, McLean, Catriona, Baglietto, Laura, Chanock, Stephen J, Lissowska, Jolanta, Sherman, Mark E, Brüning, Thomas, Hamann, Ute, Ko, Yon-Dschun, Orr, Nick, Schoemaker, Minouk, Ashworth, Alan, Kosma, Veli-Matti, Kataja, Vesa, Hartikainen, Jaana M, Mannermaa, Arto, Swerdlow, Anthony, GENICA-Network, Giles, Graham G, Brenner, Hermann, Fasching, Peter A, Chenevix-Trench, Georgia, Hopper, John, Benítez, Javier, Cox, Angela, Andrulis, Irene L, Lambrechts, Diether, Gago-Dominguez, Manuela, Couch, Fergus, Czene, Kamila, Bojesen, Stig E, Easton, Doug F, Schmidt, Marjanka K, Guénel, Pascal, Hall, Per, Pharoah, Paul DP, Garcia-Closas, Montserrat, and Chang-Claude, Jenny
Abstract: A large genotyping project within the Breast Cancer Association Consortium (BCAC) recently identified 41 associations between single nucleotide polymorphisms (SNPs) and overall breast cancer (BC) risk. We investigated whether the effects of these 41 SNPs, as well as six SNPs associated with estrogen receptor (ER) negative BC risk are modified by 13 environmental risk factors for BC. Data from 22 studies participating in BCAC were pooled, comprising up to 26,633 cases and 30,119 controls. Interactions between SNPs and environmental factors were evaluated using an empirical Bayes-type shrinkage estimator. Six SNPs showed interactions with associated p-values (pint ) <1.1 × 10(-3) . None of the observed interactions was significant after accounting for multiple testing. The Bayesian False Discovery Probability was used to rank the findings, which indicated three interactions as being noteworthy at 1% prior probability of interaction. SNP rs6828523 was associated with increased ER-negative BC risk in women ≥170 cm (OR = 1.22, p = 0.017), but inversely associated with ER-negative BC risk in women <160 cm (OR = 0.83, p = 0.039, pint = 1.9 × 10(-4) ). The inverse association between rs4808801 and overall BC risk was stronger for women who had had four or more pregnancies (OR = 0.85, p = 2.0 × 10(-4) ), and absent in women who had had just one (OR = 0.96, p = 0.19, pint = 6.1 × 10(-4) ). SNP rs11242675 was inversely associated with overall BC risk in never/former smokers (OR = 0.93, p = 2.8 × 10(-5) ), but no association was observed in current smokers (OR = 1.07, p = 0.14, pint = 3.4 × 10(-4) ). In conclusion, recently identified BC susceptibility loci are not strongly modified by established risk factors and the observed potential interactions require confirmation in independent studies.
Published: 2015

48. Performance of automated scoring of ER, PR, HER2, CK5/6 and EGFR in breast cancer tissue microarrays in the Breast Cancer Association Consortium

Author: Howat, William J, Blows, Fiona M, Provenzano, Elena, Brook, Mark N, Morris, Lorna, Gazinska, Patrycja, Johnson, Nicola, McDuffus, Leigh-Anne, Miller, Jodi, Sawyer, Elinor J, Pinder, Sarah, van Deurzen, Carolien H M, Jones, Louise, Sironen, Reijo, Visscher, Daniel, Caldas, Carlos, Daley, Frances, Coulson, Penny, Broeks, Annegien, Sanders, Joyce, Wesseling, Jelle, Nevanlinna, Heli, Fagerholm, Rainer, Blomqvist, Carl, Heikkilä, Päivi, Ali, H Raza, Dawson, Sarah-Jane, Figueroa, Jonine, Lissowska, Jolanta, Brinton, Louise, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Cox, Angela, Brock, Ian W, Cross, Simon S, Reed, Malcolm W, Couch, Fergus J, Olson, Janet E, Devillee, Peter, Mesker, Wilma E, Seyaneve, Caroline M, Hollestelle, Antoinette, Benitez, Javier, Perez, Jose Ignacio Arias, Menéndez, Primitiva, Bolla, Manjeet K, Easton, Douglas F, Schmidt, Marjanka K, Pharoah, Paul D, Sherman, Mark E, García-Closas, Montserrat, Howat, William J, Blows, Fiona M, Provenzano, Elena, Brook, Mark N, Morris, Lorna, Gazinska, Patrycja, Johnson, Nicola, McDuffus, Leigh-Anne, Miller, Jodi, Sawyer, Elinor J, Pinder, Sarah, van Deurzen, Carolien H M, Jones, Louise, Sironen, Reijo, Visscher, Daniel, Caldas, Carlos, Daley, Frances, Coulson, Penny, Broeks, Annegien, Sanders, Joyce, Wesseling, Jelle, Nevanlinna, Heli, Fagerholm, Rainer, Blomqvist, Carl, Heikkilä, Päivi, Ali, H Raza, Dawson, Sarah-Jane, Figueroa, Jonine, Lissowska, Jolanta, Brinton, Louise, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Cox, Angela, Brock, Ian W, Cross, Simon S, Reed, Malcolm W, Couch, Fergus J, Olson, Janet E, Devillee, Peter, Mesker, Wilma E, Seyaneve, Caroline M, Hollestelle, Antoinette, Benitez, Javier, Perez, Jose Ignacio Arias, Menéndez, Primitiva, Bolla, Manjeet K, Easton, Douglas F, Schmidt, Marjanka K, Pharoah, Paul D, Sherman, Mark E, and García-Closas, Montserrat
Abstract: Breast cancer risk factors and clinical outcomes vary by tumour marker expression. However, individual studies often lack the power required to assess these relationships, and large-scale analyses are limited by the need for high throughput, standardized scoring methods. To address these limitations, we assessed whether automated image analysis of immunohistochemically stained tissue microarrays can permit rapid, standardized scoring of tumour markers from multiple studies. Tissue microarray sections prepared in nine studies containing 20 263 cores from 8267 breast cancers stained for two nuclear (oestrogen receptor, progesterone receptor), two membranous (human epidermal growth factor receptor 2 and epidermal growth factor receptor) and one cytoplasmic (cytokeratin 5/6) marker were scanned as digital images. Automated algorithms were used to score markers in tumour cells using the Ariol system. We compared automated scores against visual reads, and their associations with breast cancer survival. Approximately 65-70% of tissue microarray cores were satisfactory for scoring. Among satisfactory cores, agreement between dichotomous automated and visual scores was highest for oestrogen receptor (Kappa = 0.76), followed by human epidermal growth factor receptor 2 (Kappa = 0.69) and progesterone receptor (Kappa = 0.67). Automated quantitative scores for these markers were associated with hazard ratios for breast cancer mortality in a dose-response manner. Considering visual scores of epidermal growth factor receptor or cytokeratin 5/6 as the reference, automated scoring achieved excellent negative predictive value (96-98%), but yielded many false positives (positive predictive value = 30-32%). For all markers, we observed substantial heterogeneity in automated scoring performance across tissue microarrays. Automated analysis is a potentially useful tool for large-scale, quantitative scoring of immunohistochemically stained tissue microarrays available in consortia. How
Published: 2015

49. Genetic Predisposition to In Situ and Invasive Lobular Carcinoma of the Breast

Author: University of Helsinki, Department of Obstetrics and Gynecology, University of Helsinki, Haartman Institute, University of Helsinki, Clinicum, Sawyer, Elinor, Roylance, Rebecca, Petridis, Christos, Brook, Mark N., Nowinski, Salpie, Papouli, Efterpi, Fletcher, Olivia, Pinder, Sarah, Hanby, Andrew, Kohut, Kelly, Gorman, Patricia, Caneppele, Michele, Peto, Julian, Silva, Isabel dos Santos, Johnson, Nichola, Swann, Ruth, Dwek, Miriam, Perkins, Katherine-Anne, Gillett, Cheryl, Houlston, Richard, Ross, Gillian, De Ieso, Paolo, Southey, Melissa C., Hopper, John L., Provenzano, Elena, Apicella, Carmel, Wesseling, Jelle, Cornelissen, Sten, Keeman, Renske, Fasching, Peter A., Jud, Sebastian M., Ekici, Arif B., Beckmann, Matthias W., Kerin, Michael J., Marme, Federick, Schneeweiss, Andreas, Sohn, Christof, Burwinkel, Barbara, Guenel, Pascal, Truong, Therese, Laurent-Puig, Pierre, Kerbrat, Pierre, Bojesen, Stig E., Nordestgaard, Borge G., Nielsen, Sune F., Flyger, Henrik, Milne, Roger L., Perez, Jose Ignacio Arias, Menendez, Primitiva, Benitez, Javier, Brenner, Hermann, Dieffenbach, Aida Karina, Arndt, Volker, Stegmaier, Christa, Meindl, Alfons, Lichtner, Peter, Schmutzler, Rita K., Lochmann, Magdalena, Brauch, Hiltrud, Fischer, Hans-Peter, Ko, Yon-Dschun, Nevanlinna, Heli, Muranen, Taru A., Aittomaki, Kristiina, Blomqvist, Carl, Bogdanova, Natalia V., Dork, Thilo, Lindblom, Annika, Margolin, Sara, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M., Chenevix-Trench, Georgia, Lambrechts, Diether, Weltens, Caroline, Van Limbergen, Erik, Hatse, Sigrid, Chang-Claude, Jenny, Rudolph, Anja, Seibold, Petra, Flesch-Janys, Dieter, Radice, Paolo, Peterlongo, Paolo, Bonanni, Bernardo, Volorio, Sara, Giles, Graham G., Severi, Gianluca, Baglietto, Laura, Mclean, Catriona A., Haiman, Christopher A., Henderson, Brian E., Schumacher, Fredrick, Le Marchand, Loic, Simard, Jacques, Goldberg, Mark S., Labreche, France, Dumont, Martine, Kristensen, Vessela, Winqvist, Robert, Pylkas, Katri, Jukkola-Vuorinen, Arja, Kauppila, Saila, Andrulis, Irene L., Knight, Julia A., Glendon, Gord, Mulligan, Anna Marie, Devillee, Peter, Tollenaar, Rob A. E. M., Seynaeve, Caroline M., Kriege, Mieke, Figueroa, Jonine, Chanock, Stephen J., Sherman, Mark E., Hooning, Maartje J., Hollestelle, Antoinette, van den Ouweland, Ans M. W., van Deurzen, Carolien H. M., Li, Jingmei, Czene, Kamila, Humphreys, Keith, Cox, Angela, Cross, Simon S., Reed, Malcolm W. R., Shah, Mitul, Jakubowska, Anna, Lubinski, Jan, Jaworska-Bieniek, Katarzyna, Durda, Katarzyna, Swerdlow, Anthony, Ashworth, Alan, Orr, Nicholas, Schoemaker, Minouk, Couch, Fergus J., Hallberg, Emily, Gonzalez-Neira, Anna, Pita, Guillermo, Alonso, M. Rosario, Tessier, Daniel C., Vincent, Daniel, Bacot, Francois, Bolla, Manjeet K., Wang, Qin, Dennis, Joe, Michailidou, Kyriaki, Dunning, Alison M., Hall, Per, Easton, Doug, Pharoah, Paul, Schmidt, Marjanka K., Tomlinson, Ian, Garcia-Closas, Montserrat, GENICA Network, KConFab Investigators, University of Helsinki, Department of Obstetrics and Gynecology, University of Helsinki, Haartman Institute, University of Helsinki, Clinicum, Sawyer, Elinor, Roylance, Rebecca, Petridis, Christos, Brook, Mark N., Nowinski, Salpie, Papouli, Efterpi, Fletcher, Olivia, Pinder, Sarah, Hanby, Andrew, Kohut, Kelly, Gorman, Patricia, Caneppele, Michele, Peto, Julian, Silva, Isabel dos Santos, Johnson, Nichola, Swann, Ruth, Dwek, Miriam, Perkins, Katherine-Anne, Gillett, Cheryl, Houlston, Richard, Ross, Gillian, De Ieso, Paolo, Southey, Melissa C., Hopper, John L., Provenzano, Elena, Apicella, Carmel, Wesseling, Jelle, Cornelissen, Sten, Keeman, Renske, Fasching, Peter A., Jud, Sebastian M., Ekici, Arif B., Beckmann, Matthias W., Kerin, Michael J., Marme, Federick, Schneeweiss, Andreas, Sohn, Christof, Burwinkel, Barbara, Guenel, Pascal, Truong, Therese, Laurent-Puig, Pierre, Kerbrat, Pierre, Bojesen, Stig E., Nordestgaard, Borge G., Nielsen, Sune F., Flyger, Henrik, Milne, Roger L., Perez, Jose Ignacio Arias, Menendez, Primitiva, Benitez, Javier, Brenner, Hermann, Dieffenbach, Aida Karina, Arndt, Volker, Stegmaier, Christa, Meindl, Alfons, Lichtner, Peter, Schmutzler, Rita K., Lochmann, Magdalena, Brauch, Hiltrud, Fischer, Hans-Peter, Ko, Yon-Dschun, Nevanlinna, Heli, Muranen, Taru A., Aittomaki, Kristiina, Blomqvist, Carl, Bogdanova, Natalia V., Dork, Thilo, Lindblom, Annika, Margolin, Sara, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M., Chenevix-Trench, Georgia, Lambrechts, Diether, Weltens, Caroline, Van Limbergen, Erik, Hatse, Sigrid, Chang-Claude, Jenny, Rudolph, Anja, Seibold, Petra, Flesch-Janys, Dieter, Radice, Paolo, Peterlongo, Paolo, Bonanni, Bernardo, Volorio, Sara, Giles, Graham G., Severi, Gianluca, Baglietto, Laura, Mclean, Catriona A., Haiman, Christopher A., Henderson, Brian E., Schumacher, Fredrick, Le Marchand, Loic, Simard, Jacques, Goldberg, Mark S., Labreche, France, Dumont, Martine, Kristensen, Vessela, Winqvist, Robert, Pylkas, Katri, Jukkola-Vuorinen, Arja, Kauppila, Saila, Andrulis, Irene L., Knight, Julia A., Glendon, Gord, Mulligan, Anna Marie, Devillee, Peter, Tollenaar, Rob A. E. M., Seynaeve, Caroline M., Kriege, Mieke, Figueroa, Jonine, Chanock, Stephen J., Sherman, Mark E., Hooning, Maartje J., Hollestelle, Antoinette, van den Ouweland, Ans M. W., van Deurzen, Carolien H. M., Li, Jingmei, Czene, Kamila, Humphreys, Keith, Cox, Angela, Cross, Simon S., Reed, Malcolm W. R., Shah, Mitul, Jakubowska, Anna, Lubinski, Jan, Jaworska-Bieniek, Katarzyna, Durda, Katarzyna, Swerdlow, Anthony, Ashworth, Alan, Orr, Nicholas, Schoemaker, Minouk, Couch, Fergus J., Hallberg, Emily, Gonzalez-Neira, Anna, Pita, Guillermo, Alonso, M. Rosario, Tessier, Daniel C., Vincent, Daniel, Bacot, Francois, Bolla, Manjeet K., Wang, Qin, Dennis, Joe, Michailidou, Kyriaki, Dunning, Alison M., Hall, Per, Easton, Doug, Pharoah, Paul, Schmidt, Marjanka K., Tomlinson, Ian, Garcia-Closas, Montserrat, GENICA Network, and KConFab Investigators
Published: 2014

50. Genetic variation at CYP3A is associated with age at menarche and breast cancer risk: a case-control study

Author: Johnson, Nichola, Dudbridge, Frank, Orr, Nick, Gibson, Lorna, Jones, Michael E., Schoemaker, Minouk J., Folkerd, Elizabeth J., Haynes, Ben P., Hopper, John L., Southey, Melissa C., Dite, Gillian S., Apicella, Carmel, Schmidt, Marjanka K., Broeks, Annegien, Van't Veer, Laura J., Atsma, Femke, Muir, Kenneth, Lophatananon, Artitaya, Fasching, Peter A., Beckmann, Matthias W., Ekici, Arif B., Renner, Stefan P., Sawyer, Elinor, Tomlinson, Ian, Kerin, Michael, Miller, Nicola, Burwinkel, Barbara, Marme, Frederik, Schneeweiss, Andreas, Sohn, Christof, Guenel, Pascal, Truong, Therese, Cordina, Emilie, Menegaux, Florence, Bojesen, Stig E., Nordestgaard, Borge G., Flyger, Henrik, Milne, Roger, Zamora, M. Pilar, Arias Perez, Jose Ignacio, Benitez, Javier, Bernstein, Leslie, Anton-Culver, Hoda, Ziogas, Argyrios, Dur, Christina Clarke, Brenner, Hermann, Mueller, Heiko, Arndt, Volker, Dieffenbach, Aida Karina, Meindl, Alfons, Heil, Joerg, Bartram, Claus R., Schmutzler, Rita K., Brauch, Hiltrud, Justenhoven, Christina, Ko, Yon-Dschun, Nevanlinna, Heli, Muranen, Taru A., Aittomaeki, Kristiina, Blomqvist, Carl, Matsuo, Keitaro, Doerk, Thilo, Bogdanova, Natalia V., Antonenkova, Natalia N., Lindblom, Annika, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M., Chenevix-Trench, Georgia, Beesley, Jonathan, Wu, Anna H., Van den Berg, David, Tseng, Chiu-Chen, Lambrechts, Diether, Smeets, Dominiek, Neven, Patrick, Wildiers, Hans, Chang-Claude, Jenny, Rudolph, Anja, Nickels, Stefan, Flesch-Janys, Dieter, Radice, Paolo, Peterlongo, Paolo, Bonanni, Bernardo, Pensotti, Valeria, Couch, Fergus J., Olson, Janet E., Wang, Xianshu, Fredericksen, Zachary, Pankratz, Vernon S., Giles, Graham G., Severi, Gianluca, Baglietto, Laura, Haiman, Chris, Simard, Jacques, Goldberg, Mark S., Labreche, France, Dumont, Martine, Soucy, Penny, Teo, Soo, Yip, Cheng Har, Phuah, Sze Yee, Cornes, Belinda K., Kristensen, Vessela N., Alnaes, Grethe Grenaker, Borresen-Dale, Anne-Lise, Zheng, Wei, Winqvist, Robert, Pylkaes, Katri, Jukkola-Vuorinen, Arja, Grip, Mervi, Andrulis, Irene L., Knight, Julia A., Glendon, Gord, Mulligan, Anna Marie, Devillee, Peter, Figueroa, Jonine, Chanock, Stephen J., Lissowska, Jolanta, Sherman, Mark E., Hall, Per, Schoof, Nils, Hooning, Maartje, Hollestelle, Antoinette, Oldenburg, Rogier A., Tilanus-Linthorst, Madeleine, Liu, Jianjun, Cox, Angie, Brock, Ian W., Reed, Malcolm W. R., Cross, Simon S., Blot, William, Signorello, Lisa B., Pharoah, Paul D. P., Dunning, Alison M., Shah, Mitul, Kang, Daehee, Noh, Dong-Young, Park, Sue K., Choi, Ji-Yeob, Hartman, Mikael, Miao, Hui, Lim, Wei Yen, Tang, Anthony, Hamann, Ute, Foersti, Asta, Ruediger, Thomas, Ulmer, Hans Ulrich, Jakubowska, Anna, Lubinski, Jan, Jaworska-Bieniek, Katarzyna, Durda, Katarzyna, Sangrajrang, Suleeporn, Gaborieau, Valerie, Brennan, Paul, Mckay, James, Slager, Susan, Toland, Amanda E., Vachon, Celine, Yannoukakos, Drakoulis, Shen, Chen-Yang, Yu, Jyh-Cherng, Huang, Chiun-Sheng, Hou, Ming-Feng, Gonzalez-Neira, Anna, Tessier, Daniel C., Vincent, Daniel, Bacot, Francois, Luccarini, Craig, Dennis, Joe, Michailidou, Kyriaki, Bolla, Manjeet K., Wang, Jean, Easton, Douglas F., Garcia-Closas, Montserrat, Dowsett, Mitch, Ashworth, Alan, Swerdlow, Anthony J., Peto, Julian, Silva, Isabel dos Santos, Fletcher, Olivia, Johnson, Nichola, Dudbridge, Frank, Orr, Nick, Gibson, Lorna, Jones, Michael E., Schoemaker, Minouk J., Folkerd, Elizabeth J., Haynes, Ben P., Hopper, John L., Southey, Melissa C., Dite, Gillian S., Apicella, Carmel, Schmidt, Marjanka K., Broeks, Annegien, Van't Veer, Laura J., Atsma, Femke, Muir, Kenneth, Lophatananon, Artitaya, Fasching, Peter A., Beckmann, Matthias W., Ekici, Arif B., Renner, Stefan P., Sawyer, Elinor, Tomlinson, Ian, Kerin, Michael, Miller, Nicola, Burwinkel, Barbara, Marme, Frederik, Schneeweiss, Andreas, Sohn, Christof, Guenel, Pascal, Truong, Therese, Cordina, Emilie, Menegaux, Florence, Bojesen, Stig E., Nordestgaard, Borge G., Flyger, Henrik, Milne, Roger, Zamora, M. Pilar, Arias Perez, Jose Ignacio, Benitez, Javier, Bernstein, Leslie, Anton-Culver, Hoda, Ziogas, Argyrios, Dur, Christina Clarke, Brenner, Hermann, Mueller, Heiko, Arndt, Volker, Dieffenbach, Aida Karina, Meindl, Alfons, Heil, Joerg, Bartram, Claus R., Schmutzler, Rita K., Brauch, Hiltrud, Justenhoven, Christina, Ko, Yon-Dschun, Nevanlinna, Heli, Muranen, Taru A., Aittomaeki, Kristiina, Blomqvist, Carl, Matsuo, Keitaro, Doerk, Thilo, Bogdanova, Natalia V., Antonenkova, Natalia N., Lindblom, Annika, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M., Chenevix-Trench, Georgia, Beesley, Jonathan, Wu, Anna H., Van den Berg, David, Tseng, Chiu-Chen, Lambrechts, Diether, Smeets, Dominiek, Neven, Patrick, Wildiers, Hans, Chang-Claude, Jenny, Rudolph, Anja, Nickels, Stefan, Flesch-Janys, Dieter, Radice, Paolo, Peterlongo, Paolo, Bonanni, Bernardo, Pensotti, Valeria, Couch, Fergus J., Olson, Janet E., Wang, Xianshu, Fredericksen, Zachary, Pankratz, Vernon S., Giles, Graham G., Severi, Gianluca, Baglietto, Laura, Haiman, Chris, Simard, Jacques, Goldberg, Mark S., Labreche, France, Dumont, Martine, Soucy, Penny, Teo, Soo, Yip, Cheng Har, Phuah, Sze Yee, Cornes, Belinda K., Kristensen, Vessela N., Alnaes, Grethe Grenaker, Borresen-Dale, Anne-Lise, Zheng, Wei, Winqvist, Robert, Pylkaes, Katri, Jukkola-Vuorinen, Arja, Grip, Mervi, Andrulis, Irene L., Knight, Julia A., Glendon, Gord, Mulligan, Anna Marie, Devillee, Peter, Figueroa, Jonine, Chanock, Stephen J., Lissowska, Jolanta, Sherman, Mark E., Hall, Per, Schoof, Nils, Hooning, Maartje, Hollestelle, Antoinette, Oldenburg, Rogier A., Tilanus-Linthorst, Madeleine, Liu, Jianjun, Cox, Angie, Brock, Ian W., Reed, Malcolm W. R., Cross, Simon S., Blot, William, Signorello, Lisa B., Pharoah, Paul D. P., Dunning, Alison M., Shah, Mitul, Kang, Daehee, Noh, Dong-Young, Park, Sue K., Choi, Ji-Yeob, Hartman, Mikael, Miao, Hui, Lim, Wei Yen, Tang, Anthony, Hamann, Ute, Foersti, Asta, Ruediger, Thomas, Ulmer, Hans Ulrich, Jakubowska, Anna, Lubinski, Jan, Jaworska-Bieniek, Katarzyna, Durda, Katarzyna, Sangrajrang, Suleeporn, Gaborieau, Valerie, Brennan, Paul, Mckay, James, Slager, Susan, Toland, Amanda E., Vachon, Celine, Yannoukakos, Drakoulis, Shen, Chen-Yang, Yu, Jyh-Cherng, Huang, Chiun-Sheng, Hou, Ming-Feng, Gonzalez-Neira, Anna, Tessier, Daniel C., Vincent, Daniel, Bacot, Francois, Luccarini, Craig, Dennis, Joe, Michailidou, Kyriaki, Bolla, Manjeet K., Wang, Jean, Easton, Douglas F., Garcia-Closas, Montserrat, Dowsett, Mitch, Ashworth, Alan, Swerdlow, Anthony J., Peto, Julian, Silva, Isabel dos Santos, and Fletcher, Olivia
Abstract: Introduction: We have previously shown that a tag single nucleotide polymorphism (rs10235235), which maps to the CYP3A locus (7q22.1), was associated with a reduction in premenopausal urinary estrone glucuronide levels and a modest reduction in risk of breast cancer in women age <= 50 years. Methods: We further investigated the association of rs10235235 with breast cancer risk in a large case control study of 47,346 cases and 47,570 controls from 52 studies participating in the Breast Cancer Association Consortium. Genotyping of rs10235235 was conducted using a custom Illumina Infinium array. Stratified analyses were conducted to determine whether this association was modified by age at diagnosis, ethnicity, age at menarche or tumor characteristics. Results: We confirmed the association of rs10235235 with breast cancer risk for women of European ancestry but found no evidence that this association differed with age at diagnosis. Heterozygote and homozygote odds ratios (ORs) were OR = 0.98 (95% CI 0.94, 1.01; P = 0.2) and OR = 0.80 (95% CI 0.69, 0.93; P = 0.004), respectively (P-trend = 0.02). There was no evidence of effect modification by tumor characteristics. rs10235235 was, however, associated with age at menarche in controls (P-trend = 0.005) but not cases (P-trend = 0.97). Consequently the association between rs10235235 and breast cancer risk differed according to age at menarche (P-het = 0.02); the rare allele of rs10235235 was associated with a reduction in breast cancer risk for women who had their menarche age >= 15 years (ORhet = 0.84, 95% CI 0.75, 0.94; ORhom = 0.81, 95% CI 0.51, 1.30; P-trend = 0.002) but not for those who had their menarche age <= 11 years (ORhet = 1.06, 95% CI 0.95, 1.19, ORhom = 1.07, 95% CI 0.67, 1.72; P-trend = 0.29). Conclusions: To our knowledge rs10235235 is the first single nucleotide polymorphism to be associated with both breast cancer risk and age at menarche consistent with the well-documented association between later age
Published: 2014

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Publication Year Range

Publication Type

Database

Publisher

84 results on '"Sherman, Mark E"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources