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2. Susceptibility gene mutations in germline and tumors of patients with HER2-negative advanced breast cancer

Author

Fasching, Peter A., Hu, Chunling, Hart, Steven N., Ruebner, Matthias, Polley, Eric C., Gnanaolivu, Rohan D., Hartkopf, Andreas D., Huebner, Hanna, Janni, Wolfgang, Hadji, Peyman, Tesch, Hans, Uhrig, Sabrina, Ettl, Johannes, Lux, Michael P., Lüftner, Diana, Wallwiener, Markus, Wurmthaler, Lena A., Goossens, Chloë, Müller, Volkmar, Beckmann, Matthias W., Hein, Alexander, Anetsberger, Daniel, Belleville, Erik, Wimberger, Pauline, Untch, Michael, Ekici, Arif B., Kolberg, Hans-Christian, Hartmann, Arndt, Taran, Florin-Andrei, Fehm, Tanja N., Wallwiener, Diethelm, Brucker, Sara Y., Schneeweiss, Andreas, Häberle, Lothar, and Couch, Fergus J.

Published
2024
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6. Functional analysis and clinical classification of 462 germline BRCA2 missense variants affecting the DNA binding domain

Author

Hu, Chunling, Huang, Huaizhi, Na, Jie, Lumby, Carolyn, Abozaid, Mohamed, Holdren, Megan A., Rao, Tara J., Karam, Rachid, Pesaran, Tina, Weyandt, Jamie D., Csuy, Christen M., Seelaus, Christina A., Young, Colin C., Fulk, Kelly, Heidari, Zahra, Morais Lyra, Paulo Cilas, Jr., Couch, Ronan E., Persons, Benjamin, Polley, Eric C., Gnanaolivu, Rohan D., Boddicker, Nicholas J., Monteiro, Alvaro N.A., Yadav, Siddhartha, Domchek, Susan M., Richardson, Marcy E., and Couch, Fergus J.

Published
2024
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7. Germline Pathogenic Variants in Cancer Predisposition Genes Among Women With Invasive Lobular Carcinoma of the Breast

Author

Yadav, Siddhartha, Hu, Chunling, Nathanson, Katherine L, Weitzel, Jeffrey N, Goldgar, David E, Kraft, Peter, Gnanaolivu, Rohan D, Na, Jie, Huang, Hongyan, Boddicker, Nicholas J, Larson, Nicole, Gao, Chi, Yao, Song, Weinberg, Clarice, Vachon, Celine M, Trentham-Dietz, Amy, Taylor, Jack A, Sandler, Dale R, Patel, Alpa, Palmer, Julie R, Olson, Janet E, Neuhausen, Susan, Martinez, Elena, Lindstrom, Sara, Lacey, James V, Kurian, Allison W, John, Esther M, Haiman, Christopher, Bernstein, Leslie, Auer, Paul W, Anton-Culver, Hoda, Ambrosone, Christine B, Karam, Rachid, Chao, Elizabeth, Yussuf, Amal, Pesaran, Tina, Dolinsky, Jill S, Hart, Steven N, LaDuca, Holly, Polley, Eric C, Domchek, Susan M, and Couch, Fergus J

Subjects
Breast Cancer, Clinical Research, Genetics, Cancer, 2.1 Biological and endogenous factors, Aetiology, Adolescent, Adult, Aged, Aged, 80 and over, Biomarkers, Tumor, Breast Neoplasms, Carcinoma, Ductal, Breast, Carcinoma, Lobular, Case-Control Studies, Female, Follow-Up Studies, Genetic Predisposition to Disease, Genetic Testing, Germ-Line Mutation, Humans, Middle Aged, Prognosis, Young Adult, Clinical Sciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

PurposeTo determine the contribution of germline pathogenic variants (PVs) in hereditary cancer testing panel genes to invasive lobular carcinoma (ILC) of the breast.Materials and methodsThe study included 2,999 women with ILC from a population-based cohort and 3,796 women with ILC undergoing clinical multigene panel testing (clinical cohort). Frequencies of germline PVs in breast cancer predisposition genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, PALB2, PTEN, RAD51C, RAD51D, and TP53) were compared between women with ILC and unaffected female controls and between women with ILC and infiltrating ductal carcinoma (IDC).ResultsThe frequency of PVs in breast cancer predisposition genes among women with ILC was 6.5% in the clinical cohort and 5.2% in the population-based cohort. In case-control analysis, CDH1 and BRCA2 PVs were associated with high risks of ILC (odds ratio [OR] > 4) and CHEK2, ATM, and PALB2 PVs were associated with moderate (OR = 2-4) risks. BRCA1 PVs and CHEK2 p.Ile157Thr were not associated with clinically relevant risks (OR < 2) of ILC. Compared with IDC, CDH1 PVs were > 10-fold enriched, whereas PVs in BRCA1 were substantially reduced in ILC.ConclusionThe study establishes that PVs in ATM, BRCA2, CDH1, CHEK2, and PALB2 are associated with an increased risk of ILC, whereas BRCA1 PVs are not. The similar overall PV frequencies for ILC and IDC suggest that cancer histology should not influence the decision to proceed with genetic testing. Similar to IDC, multigene panel testing may be appropriate for women with ILC, but CDH1 should be specifically discussed because of low prevalence and gastric cancer risk.

Published
2021

8. A Population-Based Study of Genes Previously Implicated in Breast Cancer

Author

Hu, Chunling, Hart, Steven N, Gnanaolivu, Rohan, Huang, Hongyan, Lee, Kun Y, Na, Jie, Gao, Chi, Lilyquist, Jenna, Yadav, Siddhartha, Boddicker, Nicholas J, Samara, Raed, Klebba, Josh, Ambrosone, Christine B, Anton-Culver, Hoda, Auer, Paul, Bandera, Elisa V, Bernstein, Leslie, Bertrand, Kimberly A, Burnside, Elizabeth S, Carter, Brian D, Eliassen, Heather, Gapstur, Susan M, Gaudet, Mia, Haiman, Christopher, Hodge, James M, Hunter, David J, Jacobs, Eric J, John, Esther M, Kooperberg, Charles, Kurian, Allison W, Le Marchand, Loic, Lindstroem, Sara, Lindstrom, Tricia, Ma, Huiyan, Neuhausen, Susan, Newcomb, Polly A, O'Brien, Katie M, Olson, Janet E, Ong, Irene M, Pal, Tuya, Palmer, Julie R, Patel, Alpa V, Reid, Sonya, Rosenberg, Lynn, Sandler, Dale P, Scott, Christopher, Tamimi, Rulla, Taylor, Jack A, Trentham-Dietz, Amy, Vachon, Celine M, Weinberg, Clarice, Yao, Song, Ziogas, Argyrios, Weitzel, Jeffrey N, Goldgar, David E, Domchek, Susan M, Nathanson, Katherine L, Kraft, Peter, Polley, Eric C, and Couch, Fergus J

Subjects
Breast Cancer, Genetic Testing, Prevention, Cancer, Clinical Research, Genetics, 2.1 Biological and endogenous factors, Aetiology, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, Adult, Aged, Aged, 80 and over, Breast Neoplasms, Case-Control Studies, Female, Genetic Predisposition to Disease, Genetic Variation, Humans, Middle Aged, Mutation, Odds Ratio, Risk, Sequence Analysis, DNA, Young Adult, Medical and Health Sciences, General & Internal Medicine
Abstract

BackgroundPopulation-based estimates of the risk of breast cancer associated with germline pathogenic variants in cancer-predisposition genes are critically needed for risk assessment and management in women with inherited pathogenic variants.MethodsIn a population-based case-control study, we performed sequencing using a custom multigene amplicon-based panel to identify germline pathogenic variants in 28 cancer-predisposition genes among 32,247 women with breast cancer (case patients) and 32,544 unaffected women (controls) from population-based studies in the Cancer Risk Estimates Related to Susceptibility (CARRIERS) consortium. Associations between pathogenic variants in each gene and the risk of breast cancer were assessed.ResultsPathogenic variants in 12 established breast cancer-predisposition genes were detected in 5.03% of case patients and in 1.63% of controls. Pathogenic variants in BRCA1 and BRCA2 were associated with a high risk of breast cancer, with odds ratios of 7.62 (95% confidence interval [CI], 5.33 to 11.27) and 5.23 (95% CI, 4.09 to 6.77), respectively. Pathogenic variants in PALB2 were associated with a moderate risk (odds ratio, 3.83; 95% CI, 2.68 to 5.63). Pathogenic variants in BARD1, RAD51C, and RAD51D were associated with increased risks of estrogen receptor-negative breast cancer and triple-negative breast cancer, whereas pathogenic variants in ATM, CDH1, and CHEK2 were associated with an increased risk of estrogen receptor-positive breast cancer. Pathogenic variants in 16 candidate breast cancer-predisposition genes, including the c.657_661del5 founder pathogenic variant in NBN, were not associated with an increased risk of breast cancer.ConclusionsThis study provides estimates of the prevalence and risk of breast cancer associated with pathogenic variants in known breast cancer-predisposition genes in the U.S. population. These estimates can inform cancer testing and screening and improve clinical management strategies for women in the general population with inherited pathogenic variants in these genes. (Funded by the National Institutes of Health and the Breast Cancer Research Foundation.).

Published
2021

9. Contribution of Germline Predisposition Gene Mutations to Breast Cancer Risk in African American Women

Author

Palmer, Julie R, Polley, Eric C, Hu, Chunling, John, Esther M, Haiman, Christopher, Hart, Steven N, Gaudet, Mia, Pal, Tuya, Anton-Culver, Hoda, Trentham-Dietz, Amy, Bernstein, Leslie, Ambrosone, Christine B, Bandera, Elisa V, Bertrand, Kimberly A, Bethea, Traci N, Gao, Chi, Gnanaolivu, Rohan D, Huang, Hongyan, Lee, Kun Y, LeMarchand, Loic, Na, Jie, Sandler, Dale P, Shah, Payal D, Yadav, Siddhartha, Yang, William, Weitzel, Jeffrey N, Domchek, Susan M, Goldgar, David E, Nathanson, Katherine L, Kraft, Peter, Yao, Song, and Couch, Fergus J

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Prevention, Genetic Testing, Cancer, Breast Cancer, Clinical Research, Genetics, 2.1 Biological and endogenous factors, Aetiology, Adolescent, Adult, Black or African American, Aged, Aged, 80 and over, Breast Neoplasms, Case-Control Studies, Cohort Studies, Female, Genetic Predisposition to Disease, Genotype, Germ-Line Mutation, Humans, Middle Aged, Registries, Risk Factors, Young Adult, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

BackgroundThe risks of breast cancer in African American (AA) women associated with inherited mutations in breast cancer predisposition genes are not well defined. Thus, whether multigene germline hereditary cancer testing panels are applicable to this population is unknown. We assessed associations between mutations in panel-based genes and breast cancer risk in 5054 AA women with breast cancer and 4993 unaffected AA women drawn from 10 epidemiologic studies.MethodsGermline DNA samples were sequenced for mutations in 23 cancer predisposition genes using a QIAseq multiplex amplicon panel. Prevalence of mutations and odds ratios (ORs) for associations with breast cancer risk were estimated with adjustment for study design, age, and family history of breast cancer.ResultsPathogenic mutations were identified in 10.3% of women with estrogen receptor (ER)-negative breast cancer, 5.2% of women with ER-positive breast cancer, and 2.3% of unaffected women. Mutations in BRCA1, BRCA2, and PALB2 were associated with high risks of breast cancer (OR = 47.55, 95% confidence interval [CI] = 10.43 to >100; OR = 7.25, 95% CI = 4.07 to 14.12; OR = 8.54, 95% CI = 3.67 to 24.95, respectively). RAD51D mutations were associated with high risk of ER-negative disease (OR = 7.82, 95% CI = 1.61 to 57.42). Moderate risks were observed for CHEK2, ATM, ERCC3, and FANCC mutations with ER-positive cancer, and RECQL mutations with all breast cancer.ConclusionsThe study identifies genes that predispose to breast cancer in the AA population, demonstrates the validity of current breast cancer testing panels for use in AA women, and provides a basis for increased referral of AA patients for cancer genetic testing.

Published
2020

12. Abstract PR09: Functional and clinical characterization of hypomorphic missense variants in the BRCA2 cancer predisposition gene

Author

Huang, Huaizhi (Gilbert), primary, Hu, Chunling, additional, Na, Jie, additional, Abozaid, Mohamed, additional, Munankarmy, Amik, additional, Rao, Tara, additional, Lumby, Carolyn A. Dunn, additional, Lyra, Paulo Cilas Morais, additional, Couch, Ronan E., additional, Persons, Benjamin R., additional, Polley, Eric C., additional, Karam, Rachid, additional, Pesaran, Tina, additional, Yadav, Siddhartha, additional, Monteiro, Alvaro N.A., additional, Boddicker, Nicholas J., additional, Domchek, Susan M., additional, Richardson, Marcy E., additional, and Couch, Fergus J., additional

Published
2024
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15. Testing the Relative Performance of Data Adaptive Prediction Algorithms: A Generalized Test of Conditional Risk Differences

Author

Goldstein, Benjamin A, Polley, Eric C, Briggs, Farren BS, van der Laan, Mark J, and Hubbard, Alan

Subjects
Mathematical Sciences, Statistics, Genetics, Data Interpretation, Statistical, Genetic Association Studies, Humans, Machine Learning, Models, Statistical, Polymorphism, Single Nucleotide, Risk Assessment, risk prediction, cross-validation, semi-parametric models, machine learning, Statistics & Probability
Abstract

Comparing the relative fit of competing models can be used to address many different scientific questions. In classical statistics one can, if appropriate, use likelihood ratio tests and information based criterion, whereas clinical medicine has tended to rely on comparisons of fit metrics like C-statistics. However, for many data adaptive modelling procedures such approaches are not suitable. In these cases, statisticians have used cross-validation, which can make inference challenging. In this paper we propose a general approach that focuses on the "conditional" risk difference (conditional on the model fits being fixed) for the improvement in prediction risk. Specifically, we derive a Wald-type test statistic and associated confidence intervals for cross-validated test sets utilizing the independent validation within cross-validation in conjunction with a test for multiple comparisons. We show that this test maintains proper Type I Error under the null fit, and can be used as a general test of relative fit for any semi-parametric model alternative. We apply the test to a candidate gene study to test for the association of a set of genes in a genetic pathway.

Published
2016

16. Analytical Data from Targeted Investigational Oncology Agents in the NCI-60: A Phenotypic Systems–based Resource

Author

Morris, Joel, primary, Kunkel, Mark W., primary, White, Stephen L., primary, Wishka, Donn G., primary, Lopez, Omar D., primary, Bowles, Lori, primary, Sellers Brady, Penny, primary, Ramsey, Patricia, primary, Grams, Julie, primary, Rohrer, Tiffany, primary, Martin, Karen, primary, Dexheimer, Thomas S., primary, Coussens, Nathan P., primary, Evans, David, primary, Risbood, Prabhakar, primary, Sonkin, Dmitriy, primary, Williams, John D., primary, Polley, Eric C., primary, Collins, Jerry M., primary, Doroshow, James H., primary, and Teicher, Beverly A., primary

Published
2023
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17. Supplementary Figures 1 and 2 from Targeted Investigational Oncology Agents in the NCI-60: A Phenotypic Systems–based Resource

Author

Morris, Joel, primary, Kunkel, Mark W., primary, White, Stephen L., primary, Wishka, Donn G., primary, Lopez, Omar D., primary, Bowles, Lori, primary, Sellers Brady, Penny, primary, Ramsey, Patricia, primary, Grams, Julie, primary, Rohrer, Tiffany, primary, Martin, Karen, primary, Dexheimer, Thomas S., primary, Coussens, Nathan P., primary, Evans, David, primary, Risbood, Prabhakar, primary, Sonkin, Dmitriy, primary, Williams, John D., primary, Polley, Eric C., primary, Collins, Jerry M., primary, Doroshow, James H., primary, and Teicher, Beverly A., primary

Published
2023
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18. Data from Targeted Investigational Oncology Agents in the NCI-60: A Phenotypic Systems–based Resource

Author

Morris, Joel, primary, Kunkel, Mark W., primary, White, Stephen L., primary, Wishka, Donn G., primary, Lopez, Omar D., primary, Bowles, Lori, primary, Sellers Brady, Penny, primary, Ramsey, Patricia, primary, Grams, Julie, primary, Rohrer, Tiffany, primary, Martin, Karen, primary, Dexheimer, Thomas S., primary, Coussens, Nathan P., primary, Evans, David, primary, Risbood, Prabhakar, primary, Sonkin, Dmitriy, primary, Williams, John D., primary, Polley, Eric C., primary, Collins, Jerry M., primary, Doroshow, James H., primary, and Teicher, Beverly A., primary

Published
2023
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19. Table S1 from Targeted Investigational Oncology Agents in the NCI-60: A Phenotypic Systems–based Resource

Author

Morris, Joel, primary, Kunkel, Mark W., primary, White, Stephen L., primary, Wishka, Donn G., primary, Lopez, Omar D., primary, Bowles, Lori, primary, Sellers Brady, Penny, primary, Ramsey, Patricia, primary, Grams, Julie, primary, Rohrer, Tiffany, primary, Martin, Karen, primary, Dexheimer, Thomas S., primary, Coussens, Nathan P., primary, Evans, David, primary, Risbood, Prabhakar, primary, Sonkin, Dmitriy, primary, Williams, John D., primary, Polley, Eric C., primary, Collins, Jerry M., primary, Doroshow, James H., primary, and Teicher, Beverly A., primary

Published
2023
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20. A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers

Author

Coignard, Juliette, Lush, Michael, Beesley, Jonathan, O’Mara, Tracy A., Dennis, Joe, Tyrer, Jonathan P., Barnes, Daniel R., McGuffog, Lesley, Leslie, Goska, Bolla, Manjeet K., Adank, Muriel A., Agata, Simona, Ahearn, Thomas, Aittomäki, Kristiina, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Arnold, Norbert, Aronson, Kristan J., Arun, Banu K., Augustinsson, Annelie, Azzollini, Jacopo, Barrowdale, Daniel, Baynes, Caroline, Becher, Heiko, Bermisheva, Marina, Bernstein, Leslie, Białkowska, Katarzyna, Blomqvist, Carl, Bojesen, Stig E., Bonanni, Bernardo, Borg, Ake, Brauch, Hiltrud, Brenner, Hermann, Burwinkel, Barbara, Buys, Saundra S., Caldés, Trinidad, Caligo, Maria A., Campa, Daniele, Carter, Brian D., Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chung, Wendy K., Claes, Kathleen B. M., Clarke, Christine L., Collée, J. Margriet, Conroy, Don M., Czene, Kamila, Daly, Mary B., Devilee, Peter, Diez, Orland, Ding, Yuan Chun, Domchek, Susan M., Dörk, Thilo, dos-Santos-Silva, Isabel, Dunning, Alison M., Dwek, Miriam, Eccles, Diana M., Eliassen, A. Heather, Engel, Christoph, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Flyger, Henrik, Fostira, Florentia, Friedman, Eitan, Fritschi, Lin, Frost, Debra, Gago-Dominguez, Manuela, Gapstur, Susan M., Garber, Judy, Garcia-Barberan, Vanesa, García-Closas, Montserrat, García-Sáenz, José A., Gaudet, Mia M., Gayther, Simon A., Gehrig, Andrea, Georgoulias, Vassilios, Giles, Graham G., Godwin, Andrew K., Goldberg, Mark S., Goldgar, David E., González-Neira, Anna, Greene, Mark H., Guénel, Pascal, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Håkansson, Niclas, Hall, Per, Hamann, Ute, Harrington, Patricia A., Hart, Steven N., He, Wei, Hogervorst, Frans B. L., Hollestelle, Antoinette, Hopper, John L., Horcasitas, Darling J., Hulick, Peter J., Hunter, David J., Imyanitov, Evgeny N., Jager, Agnes, Jakubowska, Anna, James, Paul A., Jensen, Uffe Birk, John, Esther M., Jones, Michael E., Kaaks, Rudolf, Kapoor, Pooja Middha, Karlan, Beth Y., Keeman, Renske, Khusnutdinova, Elza, Kiiski, Johanna I., Ko, Yon-Dschun, Kosma, Veli-Matti, Kraft, Peter, Kurian, Allison W., Laitman, Yael, Lambrechts, Diether, Le Marchand, Loic, Lester, Jenny, Lesueur, Fabienne, Lindstrom, Tricia, Lopez-Fernández, Adria, Loud, Jennifer T., Luccarini, Craig, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Martens, John W. M., Mebirouk, Noura, Meindl, Alfons, Miller, Austin, Milne, Roger L., Montagna, Marco, Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Nielsen, Finn C., O’Brien, Katie M., Olopade, Olufunmilayo I., Olson, Janet E., Olsson, Håkan, Osorio, Ana, Ottini, Laura, Park-Simon, Tjoung-Won, Parsons, Michael T., Pedersen, Inge Sokilde, Peshkin, Beth, Peterlongo, Paolo, Peto, Julian, Pharoah, Paul D. P., Phillips, Kelly-Anne, Polley, Eric C., Poppe, Bruce, Presneau, Nadege, Pujana, Miquel Angel, Punie, Kevin, Radice, Paolo, Rantala, Johanna, Rashid, Muhammad U., Rennert, Gad, Rennert, Hedy S., Robson, Mark, Romero, Atocha, Rossing, Maria, Saloustros, Emmanouil, Sandler, Dale P., Santella, Regina, Scheuner, Maren T., Schmidt, Marjanka K., Schmidt, Gunnar, Scott, Christopher, Sharma, Priyanka, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Steinsnyder, Zoe, Stone, Jennifer, Stoppa-Lyonnet, Dominique, Swerdlow, Anthony, Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Terry, Mary Beth, Teulé, Alex, Thull, Darcy L., Tischkowitz, Marc, Toland, Amanda E., Torres, Diana, Trainer, Alison H., Truong, Thérèse, Tung, Nadine, Vachon, Celine M., Vega, Ana, Vijai, Joseph, Wang, Qin, Wappenschmidt, Barbara, Weinberg, Clarice R., Weitzel, Jeffrey N., Wendt, Camilla, Wolk, Alicja, Yadav, Siddhartha, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zheng, Wei, Ziogas, Argyrios, Zorn, Kristin K., Park, Sue K., Thomassen, Mads, Offit, Kenneth, Schmutzler, Rita K., Couch, Fergus J., Simard, Jacques, Chenevix-Trench, Georgia, Easton, Douglas F., Andrieu, Nadine, and Antoniou, Antonis C.

Published
2021
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23. A clinical guide to hereditary cancer panel testing: evaluation of gene-specific cancer associations and sensitivity of genetic testing criteria in a cohort of 165,000 high-risk patients

Author

LaDuca, Holly, Polley, Eric C., Yussuf, Amal, Hoang, Lily, Gutierrez, Stephanie, Hart, Steven N., Yadav, Siddhartha, Hu, Chunling, Na, Jie, Goldgar, David E., Fulk, Kelly, Smith, Laura Panos, Horton, Carolyn, Profato, Jessica, Pesaran, Tina, Gau, Chia-Ling, Pronold, Melissa, Davis, Brigette Tippin, Chao, Elizabeth C., Couch, Fergus J., and Dolinsky, Jill S.

Published
2020
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26. Assessing the use of observational methods and real-world data to emulate ongoing randomized controlled trials

Author

Wallach, Joshua D, primary, Deng, Yihong, additional, Polley, Eric C, additional, Dhruva, Sanket S, additional, Herrin, Jeph, additional, Quinto, Kenneth, additional, Gandotra, Charu, additional, Crown, William, additional, Noseworthy, Peter, additional, Yao, Xiaoxi, additional, Jeffery, Molly Moore, additional, Lyon, Timothy D, additional, Ross, Joseph S, additional, and McCoy, Rozalina G, additional

Published
2023
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27. Targeted Investigational Oncology Agents (IOA) in the NCI60: A Phenotypic Systems-Based Resource

Author

Morris, Joel, primary, Kunkel, Mark W., additional, White, Stephen L., additional, Wishka, Donn G., additional, Lopez, Omar D., additional, Bowles, Lori, additional, Sellers Brady, Penny, additional, Ramsey, Patricia, additional, Grams, Julie, additional, Rohrer, Tiffany, additional, Martin, Karen, additional, Dexheimer, Thomas S., additional, Coussens, Nathan P., additional, Evans, David, additional, Risbood, Prabhakar, additional, Sonkin, Dmitriy, additional, Williams, John D., additional, Polley, Eric C., additional, Collins, Jerry M., additional, Doroshow, James H., additional, and Teicher, Beverly A., additional

Published
2023
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28. Supplementary Materials, Figure S1-S4, Table S1-S9 from Functional and Clinical Characterization of Variants of Uncertain Significance Identifies a Hotspot for Inactivating Missense Variants in RAD51C

Author

Hu, Chunling, primary, Nagaraj, Anil Belur, primary, Shimelis, Hermela, primary, Montalban, Gemma, primary, Lee, Kun Y., primary, Huang, Huaizhi, primary, Lumby, Carolyn A., primary, Na, Jie, primary, Susswein, Lisa R., primary, Roberts, Maegan E., primary, Marshall, Megan L., primary, Hiraki, Susan, primary, LaDuca, Holly, primary, Chao, Elizabeth, primary, Yussuf, Amal, primary, Pesaran, Tina, primary, Neuhausen, Susan L., primary, Haiman, Christopher A., primary, Kraft, Peter, primary, Lindstrom, Sara, primary, Palmer, Julie R., primary, Teras, Lauren R., primary, Vachon, Celine M., primary, Yao, Song, primary, Ong, Irene, primary, Nathanson, Katherine L., primary, Weitzel, Jeffrey N., primary, Boddicker, Nicholas, primary, Gnanaolivu, Rohan, primary, Polley, Eric C., primary, Mer, Georges, primary, Cui, Gaofeng, primary, Karam, Rachid, primary, Richardson, Marcy E., primary, Domchek, Susan M., primary, Yadav, Siddhartha, primary, Hruska, Kathleen S., primary, Dolinsky, Jill, primary, Weroha, S. John, primary, Hart, Steven N., primary, Simard, Jacques, primary, Masson, Jean Yves, primary, Pang, Yuan-Ping, primary, and Couch, Fergus J., primary

Published
2023
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29. Data from Functional and Clinical Characterization of Variants of Uncertain Significance Identifies a Hotspot for Inactivating Missense Variants in RAD51C

Author

Hu, Chunling, primary, Nagaraj, Anil Belur, primary, Shimelis, Hermela, primary, Montalban, Gemma, primary, Lee, Kun Y., primary, Huang, Huaizhi, primary, Lumby, Carolyn A., primary, Na, Jie, primary, Susswein, Lisa R., primary, Roberts, Maegan E., primary, Marshall, Megan L., primary, Hiraki, Susan, primary, LaDuca, Holly, primary, Chao, Elizabeth, primary, Yussuf, Amal, primary, Pesaran, Tina, primary, Neuhausen, Susan L., primary, Haiman, Christopher A., primary, Kraft, Peter, primary, Lindstrom, Sara, primary, Palmer, Julie R., primary, Teras, Lauren R., primary, Vachon, Celine M., primary, Yao, Song, primary, Ong, Irene, primary, Nathanson, Katherine L., primary, Weitzel, Jeffrey N., primary, Boddicker, Nicholas, primary, Gnanaolivu, Rohan, primary, Polley, Eric C., primary, Mer, Georges, primary, Cui, Gaofeng, primary, Karam, Rachid, primary, Richardson, Marcy E., primary, Domchek, Susan M., primary, Yadav, Siddhartha, primary, Hruska, Kathleen S., primary, Dolinsky, Jill, primary, Weroha, S. John, primary, Hart, Steven N., primary, Simard, Jacques, primary, Masson, Jean Yves, primary, Pang, Yuan-Ping, primary, and Couch, Fergus J., primary

Published
2023
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34. Functional and Clinical Characterization of Variants of Uncertain Significance Identifies a Hotspot for Inactivating Missense Variants in RAD51C

Author

Hu, Chunling, primary, Nagaraj, Anil Belur, additional, Shimelis, Hermela, additional, Montalban, Gemma, additional, Lee, Kun Y., additional, Huang, Huaizhi, additional, Lumby, Carolyn A., additional, Na, Jie, additional, Susswein, Lisa R., additional, Roberts, Maegan E., additional, Marshall, Megan L., additional, Hiraki, Susan, additional, LaDuca, Holly, additional, Chao, Elizabeth, additional, Yussuf, Amal, additional, Pesaran, Tina, additional, Neuhausen, Susan L., additional, Haiman, Christopher A., additional, Kraft, Peter, additional, Lindstrom, Sara, additional, Palmer, Julie R., additional, Teras, Lauren R., additional, Vachon, Celine M., additional, Yao, Song, additional, Ong, Irene, additional, Nathanson, Katherine L., additional, Weitzel, Jeffrey N., additional, Boddicker, Nicholas, additional, Gnanaolivu, Rohan, additional, Polley, Eric C., additional, Mer, Georges, additional, Cui, Gaofeng, additional, Karam, Rachid, additional, Richardson, Marcy E., additional, Domchek, Susan M., additional, Yadav, Siddhartha, additional, Hruska, Kathleen S., additional, Dolinsky, Jill, additional, Weroha, S. John, additional, Hart, Steven N., additional, Simard, Jacques, additional, Masson, Jean Yves, additional, Pang, Yuan-Ping, additional, and Couch, Fergus J., additional

Published
2023
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35. Author Correction: Interaction between the microbiome and TP53 in human lung cancer

Author

Greathouse, K. Leigh, White, James R., Vargas, Ashely J., Bliskovsky, Valery V., Beck, Jessica A., von Muhlinen, Natalia, Polley, Eric C., Bowman, Elise D., Khan, Mohammed A., Robles, Ana I., Cooks, Tomer, Ryan, Bríd M., Padgett, Noah, Dzutsev, Amiran H., Trinchieri, Giorgio, Pineda, Marbin A., Bilke, Sven, Meltzer, Paul S., Hokenstad, Alexis N., Stickrod, Tricia M., Walther-Antonio, Marina R., Earl, Joshua P., Mell, Joshua C., Krol, Jaroslaw E., Balashov, Sergey V., Bhat, Archana S., Ehrlich, Garth D., Valm, Alex, Deming, Clayton, Conlan, Sean, Oh, Julia, Segre, Julie A., and Harris, Curtis C.

Published
2020
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36. Association of the CHEK2 c.1100delC variant, radiotherapy, and systemic treatment with contralateral breast cancer risk and breast cancer-specific survival

Author

Morra, Anna, Schreurs, Maartje A C, Andrulis, Irene L, Anton-Culver, Hoda, Augustinsson, Annelie, Beckmann, Matthias W, Behrens, Sabine, Bojesen, Stig E, Bolla, Manjeet K, Brauch, Hiltrud, Broeks, Annegien, Buys, Saundra S, Camp, Nicola J, Castelao, Jose E, Cessna, Melissa H, Chang-Claude, Jenny, Chung, Wendy K, Colonna, Sarah V, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Daly, Mary B, Dennis, Joe, Devilee, Peter, Dörk, Thilo, Dunning, Alison M, Dwek, Miriam, Easton, Douglas F, Eccles, Diana M, Eriksson, Mikael, Evans, D Gareth, Fasching, Peter A, Fehm, Tanja N, Figueroa, Jonine D, Flyger, Henrik, Gabrielson, Marike, Gago-Dominguez, Manuela, García-Closas, Montserrat, García-Sáenz, José A, Genkinger, Jeanine, Grassmann, Felix, Gündert, Melanie, Hahnen, Eric, Haiman, Christopher A, Hamann, Ute, Harrington, Patricia A, Hartikainen, Jaana M, Hoppe, Reiner, Hopper, John L, Houlston, Richard S, Howell, Anthony, Jakubowska, Anna, Janni, Wolfgang, Jernström, Helena, John, Esther M, Johnson, Nichola, Jones, Michael E, Kristensen, Vessela N, Kurian, Allison W, Lambrechts, Diether, Le Marchand, Loic, Lindblom, Annika, Lubiński, Jan, Lux, Michael P, Mannermaa, Arto, Mavroudis, Dimitrios, Mulligan, Anna Marie, Muranen, Taru A, Nevanlinna, Heli, Nevelsteen, Ines, Neven, Patrick, Newman, William G, Obi, Nadia, Offit, Kenneth, Olshan, Andrew F, Park-Simon, Tjoung-Won, Patel, Alpa V, Peterlongo, Paolo, Phillips, Kelly-Anne, Plaseska-Karanfilska, Dijana, Polley, Eric C, Presneau, Nadege, Pylkäs, Katri, Rack, Brigitte, Radice, Paolo, Rashid, Muhammad U, Rhenius, Valerie, Robson, Mark, Romero, Atocha, Saloustros, Emmanouil, Sawyer, Elinor J, Schmutzler, Rita K, Schuetze, Sabine, Scott, Christopher, Shah, Mitul, Smichkoska, Snezhana, Southey, Melissa C, Tapper, William J, Teras, Lauren R, Tollenaar, Rob A E M, Tomczyk, Katarzyna, Tomlinson, Ian, Troester, Melissa A, Vachon, Celine M, van Veen, Elke M, Wang, Qin, Wendt, Camilla, Wildiers, Hans, Winqvist, Robert, Ziogas, Argyrios, Hall, Per, Pharoah, Paul D P, Adank, Muriel A, Hollestelle, Antoinette, Schmidt, Marjanka K, and Hooning, Maartje J

Abstract

BACKGROUND: Breast cancer (BC) patients with a germline CHEK2 c.1100delC variant have an increased risk of contralateral BC (CBC) and worse BC-specific survival (BCSS) compared to non-carriers.AIM: To assessed the associations of CHEK2 c.1100delC, radiotherapy, and systemic treatment with CBC risk and BCSS.METHODS: Analyses were based on 82,701 women diagnosed with a first primary invasive BC including 963 CHEK2 c.1100delC carriers; median follow-up was 9.1 years. Differential associations with treatment by CHEK2 c.1100delC status were tested by including interaction terms in a multivariable Cox regression model. A multi-state model was used for further insight into the relation between CHEK2 c.1100delC status, treatment, CBC risk and death.RESULTS: There was no evidence for differential associations of therapy with CBC risk by CHEK2 c.1100delC status. The strongest association with reduced CBC risk was observed for the combination of chemotherapy and endocrine therapy [HR (95% CI): 0.66 (0.55-0.78)]. No association was observed with radiotherapy. Results from the multi-state model showed shorter BCSS for CHEK2 c.1100delC carriers versus non-carriers also after accounting for CBC occurrence [HR (95% CI): 1.30 (1.09-1.56)].CONCLUSION: Systemic therapy was associated with reduced CBC risk irrespective of CHEK2 c.1100delC status. Moreover, CHEK2 c.1100delC carriers had shorter BCSS, which appears not to be fully explained by their CBC risk.

Published
2023

38. Supplementary Data from Effect of Germline Mutations in Homologous Recombination Repair Genes on Overall Survival of Patients with Pancreatic Adenocarcinoma

Author

Yadav, Siddhartha, primary, Kasi, Pashtoon M., primary, Bamlet, William R., primary, Ho, Thanh P., primary, Polley, Eric C., primary, Hu, Chunling, primary, Hart, Steven N., primary, Rabe, Kari G., primary, Boddicker, Nicholas J., primary, Gnanaolivu, Rohan D., primary, Lee, Kun Y., primary, Lindstrom, Tricia H., primary, Petersen, Gloria M., primary, Couch, Fergus J., primary, and McWilliams, Robert R., primary

Published
2023
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39. Supplementary Data from The NCI Transcriptional Pharmacodynamics Workbench: A Tool to Examine Dynamic Expression Profiling of Therapeutic Response in the NCI-60 Cell Line Panel

Author

Monks, Anne, primary, Zhao, Yingdong, primary, Hose, Curtis, primary, Hamed, Hossein, primary, Krushkal, Julia, primary, Fang, Jianwen, primary, Sonkin, Dmitriy, primary, Palmisano, Alida, primary, Polley, Eric C., primary, Fogli, Laura K., primary, Konaté, Mariam M., primary, Miller, Sarah B., primary, Simpson, Melanie A., primary, Voth, Andrea Regier, primary, Li, Ming-Chung, primary, Harris, Erik, primary, Wu, Xiaolin, primary, Connelly, John W., primary, Rapisarda, Annamaria, primary, Teicher, Beverly A., primary, Simon, Richard, primary, and Doroshow, James H., primary

Published
2023
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40. Data from The NCI Transcriptional Pharmacodynamics Workbench: A Tool to Examine Dynamic Expression Profiling of Therapeutic Response in the NCI-60 Cell Line Panel

Author

Monks, Anne, primary, Zhao, Yingdong, primary, Hose, Curtis, primary, Hamed, Hossein, primary, Krushkal, Julia, primary, Fang, Jianwen, primary, Sonkin, Dmitriy, primary, Palmisano, Alida, primary, Polley, Eric C., primary, Fogli, Laura K., primary, Konaté, Mariam M., primary, Miller, Sarah B., primary, Simpson, Melanie A., primary, Voth, Andrea Regier, primary, Li, Ming-Chung, primary, Harris, Erik, primary, Wu, Xiaolin, primary, Connelly, John W., primary, Rapisarda, Annamaria, primary, Teicher, Beverly A., primary, Simon, Richard, primary, and Doroshow, James H., primary

Published
2023
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41. Supplementary Figure 9 from The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology

Author

Abaan, Ogan D., primary, Polley, Eric C., primary, Davis, Sean R., primary, Zhu, Yuelin J., primary, Bilke, Sven, primary, Walker, Robert L., primary, Pineda, Marbin, primary, Gindin, Yevgeniy, primary, Jiang, Yuan, primary, Reinhold, William C., primary, Holbeck, Susan L., primary, Simon, Richard M., primary, Doroshow, James H., primary, Pommier, Yves, primary, and Meltzer, Paul S., primary

Published
2023
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42. Supplementary Figure 10 from The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology

Author

Abaan, Ogan D., primary, Polley, Eric C., primary, Davis, Sean R., primary, Zhu, Yuelin J., primary, Bilke, Sven, primary, Walker, Robert L., primary, Pineda, Marbin, primary, Gindin, Yevgeniy, primary, Jiang, Yuan, primary, Reinhold, William C., primary, Holbeck, Susan L., primary, Simon, Richard M., primary, Doroshow, James H., primary, Pommier, Yves, primary, and Meltzer, Paul S., primary

Published
2023
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43. Supplementary Table 1 from The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology

Author

Abaan, Ogan D., primary, Polley, Eric C., primary, Davis, Sean R., primary, Zhu, Yuelin J., primary, Bilke, Sven, primary, Walker, Robert L., primary, Pineda, Marbin, primary, Gindin, Yevgeniy, primary, Jiang, Yuan, primary, Reinhold, William C., primary, Holbeck, Susan L., primary, Simon, Richard M., primary, Doroshow, James H., primary, Pommier, Yves, primary, and Meltzer, Paul S., primary

Published
2023
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44. Supplementary Table 2 from The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology

Author

Abaan, Ogan D., primary, Polley, Eric C., primary, Davis, Sean R., primary, Zhu, Yuelin J., primary, Bilke, Sven, primary, Walker, Robert L., primary, Pineda, Marbin, primary, Gindin, Yevgeniy, primary, Jiang, Yuan, primary, Reinhold, William C., primary, Holbeck, Susan L., primary, Simon, Richard M., primary, Doroshow, James H., primary, Pommier, Yves, primary, and Meltzer, Paul S., primary

Published
2023
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45. Supplementary Figure Legend from The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology

Author

Abaan, Ogan D., primary, Polley, Eric C., primary, Davis, Sean R., primary, Zhu, Yuelin J., primary, Bilke, Sven, primary, Walker, Robert L., primary, Pineda, Marbin, primary, Gindin, Yevgeniy, primary, Jiang, Yuan, primary, Reinhold, William C., primary, Holbeck, Susan L., primary, Simon, Richard M., primary, Doroshow, James H., primary, Pommier, Yves, primary, and Meltzer, Paul S., primary

Published
2023
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46. Data from The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology

Author

Abaan, Ogan D., primary, Polley, Eric C., primary, Davis, Sean R., primary, Zhu, Yuelin J., primary, Bilke, Sven, primary, Walker, Robert L., primary, Pineda, Marbin, primary, Gindin, Yevgeniy, primary, Jiang, Yuan, primary, Reinhold, William C., primary, Holbeck, Susan L., primary, Simon, Richard M., primary, Doroshow, James H., primary, Pommier, Yves, primary, and Meltzer, Paul S., primary

Published
2023
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47. Supplementary Figures 1 - 8 from The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology

Author

Abaan, Ogan D., primary, Polley, Eric C., primary, Davis, Sean R., primary, Zhu, Yuelin J., primary, Bilke, Sven, primary, Walker, Robert L., primary, Pineda, Marbin, primary, Gindin, Yevgeniy, primary, Jiang, Yuan, primary, Reinhold, William C., primary, Holbeck, Susan L., primary, Simon, Richard M., primary, Doroshow, James H., primary, Pommier, Yves, primary, and Meltzer, Paul S., primary

Published
2023
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48. Supplementary Table 3 from The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology

Author

Abaan, Ogan D., primary, Polley, Eric C., primary, Davis, Sean R., primary, Zhu, Yuelin J., primary, Bilke, Sven, primary, Walker, Robert L., primary, Pineda, Marbin, primary, Gindin, Yevgeniy, primary, Jiang, Yuan, primary, Reinhold, William C., primary, Holbeck, Susan L., primary, Simon, Richard M., primary, Doroshow, James H., primary, Pommier, Yves, primary, and Meltzer, Paul S., primary

Published
2023
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49. Contralateral Breast Cancer Risk Among Carriers of Germline Pathogenic Variants in ATM, BRCA1, BRCA2, CHEK2, and PALB2

Author

Yadav, Siddhartha, primary, Boddicker, Nicholas J., additional, Na, Jie, additional, Polley, Eric C., additional, Hu, Chunling, additional, Hart, Steven N., additional, Gnanaolivu, Rohan D., additional, Larson, Nicole, additional, Holtegaard, Susan, additional, Huang, Huaizhi, additional, Dunn, Carolyn A., additional, Teras, Lauren R., additional, Patel, Alpa V., additional, Lacey, James V., additional, Neuhausen, Susan L., additional, Martinez, Elena, additional, Haiman, Christopher, additional, Chen, Fei, additional, Ruddy, Kathryn J., additional, Olson, Janet E., additional, John, Esther M., additional, Kurian, Allison W., additional, Sandler, Dale P., additional, O'Brien, Katie M., additional, Taylor, Jack A., additional, Weinberg, Clarice R., additional, Anton-Culver, Hoda, additional, Ziogas, Argyrios, additional, Zirpoli, Gary, additional, Goldgar, David E., additional, Palmer, Julie R., additional, Domchek, Susan M., additional, Weitzel, Jeffrey N., additional, Nathanson, Katherine L., additional, Kraft, Peter, additional, and Couch, Fergus J., additional

Published
2023
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50. Abstract GS4-04: Population-based Estimates of contralateral Breast Cancer Risk among Carriers of Germline Pathogenic Variants in ATM, BRCA1, BRCA2, CHEK2, and PALB2

Author

Yadav, Siddhartha, primary, Boddicker, Nicholas J., additional, Na, Jie, additional, Polley, Eric C., additional, Hu, Chunling, additional, Hart, Steven N., additional, Gnanaolivu, Rohan D., additional, Larson, Nicole, additional, Dunn, Carolyn, additional, Holtegaard, Susan, additional, Huang, Huaizhi, additional, Teras, Lauren R., additional, Patel, Alpa V., additional, Lacey, James V., additional, Neuhausen, Susan, additional, Bernstein, Leslie, additional, Martinez, Elena, additional, Haiman, Christopher, additional, Chen, Fei, additional, Ruddy, Kathryn, additional, Olson, Janet, additional, John, Esther, additional, Kurian, Allison W., additional, Sandler, Dale P., additional, O’Brien, Katie M., additional, Taylor, Jack A., additional, Weinberg, Clarice R., additional, Anton-Culver, Hoda, additional, Ziogas, Argyrios, additional, Zirpoli, Gary R., additional, Goldgar, David E., additional, Nathanson, Katherine L., additional, Domchek, Susan, additional, Palmer, Julie R., additional, Weitzel, Jeffrey, additional, Kraft, Peter, additional, and Couch, Fergus J., additional

Published
2023
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