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6 results on '"Pharoah, Paul D.P."'

1. Multi-Tissue Transcriptome-Wide Association Study Identifies 26 Novel Candidate Susceptibility Genes for High Grade Serous Epithelial Ovarian Cancer

Author

Gusev, Alexander, Lawrenson, Kate, Segato, Felipe, Fonseca, Marcos A.S., Kar, Siddhartha, Vavra, Kevin C., Lee, Janet M, Pejovic, Tanya, Karlan, Beth Y., Freedman, Matthew L., Noushmehr, Houtan, Pharoah, Paul D.P., Pasaniuc, Bogdan, and Gayther, Simon A.

Subjects
Genetics, 0303 health sciences, Biology, 3. Good health, Transcriptome, 03 medical and health sciences, Exon, 0302 clinical medicine, 030220 oncology & carcinogenesis, Expression quantitative trait loci, Gene expression, RNA splicing, Gene, Genotyping, 030304 developmental biology, Genetic association
Abstract

Genome-wide association studies (GWASs) have identified about 30 different susceptibility loci associated with high grade serous ovarian cancer (HGSOC) risk. We sought to identify potential susceptibility genes by integrating the risk variants at these regions with genetic variants impacting gene expression and splicing of nearby genes. We compiled gene expression and genotyping data from 2,169 samples for 6 different HGSOC-relevant tissue types. We integrated these data with GWAS data from 13,037 HGSOC cases and 40,941 controls, and performed a transcriptome-wide association study (TWAS) across >70,000 significantly heritable gene/exon features. We identified 24 transcriptome-wide significant associations for 14 unique genes, plus 90 significant exon-level associations in 20 unique genes. We implicated multiple novel genes at risk loci, e.g.LRRC46at 19q21.32 (TWASP=1×10−9) and aPRC1splicing event (TWASP=9×10−8) which was splice-variant specific and exhibited no eQTL signal. Functional analyses in HGSOC cell lines found evidence of essentiality forGOSR2, INTS1, KANSL1andPRC1; with the latter gene showing levels of essentiality comparable to that ofMYC. Overall, gene expression and splicing events explained 41% of SNP-heritability for HGSOC (s.e. 11%,P=2.5×10−4), implicated at least one target gene for 6/13 distinct genome-wide significant regions and revealed 2 known and 26 novel candidate susceptibility genes for HGSOC.STATEMENT OF SIGNIFICANCEFor many ovarian cancer risk regions, the target genes regulated by germline genetic variants are unknown. Using expression data from >2,100 individuals, this study identified novel associations of genes and splicing variants with ovarian cancer risk; with transcriptional variation now explaining over one-third of the SNP-heritability for this disease.

Published
2018
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2. Germline whole exome sequencing and large-scale replication identifies FANCM as a likely high grade serous ovarian cancer susceptibility gene

Author

Dicks, Ed, Song, Honglin, Ramus, Susan J., Van Oudenhove, Elke, Tyrer, Jonathan P., Intermaggio, Maria P., Kar, Siddhartha, Harrington, Patricia, Bowtell, David D., Study Group, Aocs, Cicek, Mine S., Cunningham, Julie M., Fridley, Brooke L., Alsop, Jennifer, Jimenez-Linan, Mercedes, Piskorz, Anna, Goranova, Teodora, Kent, Emma, Siddiqui, Nadeem, Paul, James, Crawford, Robin, Poblete, Samantha, Lele, Shashi, Sucheston-Campbell, Lara, Moysich, Kirsten B., Sieh, Weiva, McGuire, Valerie, Lester, Jenny, Odunsi, Kunle, Whittemore, Alice S., Bogdanova, Natalia, Dürst, Matthias, Hillemanns, Peter, Karlan, Beth Y., Gentry-Maharaj, Aleksandra, Menon, Usha, Tischkowitz, Marc, Levine, Douglas, Brenton, James D., Dörk, Thilo, Goode, Ellen L., Gayther, Simon A., Pharoah, Paul D.P., Dicks, Ed [0000-0002-0617-0401], Song, Honglin [0000-0001-5076-7371], Tyrer, Jonathan [0000-0003-3724-4757], Tischkowitz, Marc [0000-0002-7880-0628], Brenton, James [0000-0002-5738-6683], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, DNA repair, Oncology and Carcinogenesis, Genome-wide association study, VARIANTS, Biology, BREAST, Germline, 03 medical and health sciences, 0302 clinical medicine, Rare Diseases, Clinical Research, Medicine and Health Sciences, LOCUS, Genetics, CONFER SUSCEPTIBILITY, 2.1 Biological and endogenous factors, FANCL, susceptibility genes, FANCM, Genetic Testing, GENOME-WIDE ASSOCIATION, Mutation frequency, Aetiology, Exome sequencing, Cancer, next generation sequencing, RAD51C, MUTATIONS, Prevention, Human Genome, BRCA2, RISKS, 3. Good health, 030104 developmental biology, Good Health and Well Being, ovarian cancer, Oncology, 030220 oncology & carcinogenesis, Cancer research
Abstract

We analyzed whole exome sequencing data in germline DNA from 412 high grade serous ovarian cancer (HGSOC) cases from The Cancer Genome Atlas Project and identified 5,517 genes harboring a predicted deleterious germline coding mutation in at least one HGSOC case. Gene-set enrichment analysis showed enrichment for genes involved in DNA repair (p = 1.8x10(-3)). Twelve DNA repair genes - APEX1, APLF, ATX, EME1, FANCL, FANCM, MAD2L2, PARP2, PARP3, POLN, RAD54L and SMUG1 - were prioritized for targeted sequencing in up to 3,107 HGSOC cases, 1,491 cases of other epithelial ovarian cancer (EOC) subtypes and 3,368 unaffected controls of European origin. We estimated mutation prevalence for each gene and tested for associations with disease risk. Mutations were identified in both cases and controls in all genes except MAD2L2, where we found no evidence of mutations in controls. In FANCM we observed a higher mutation frequency in HGSOC cases compared to controls (29/3,107 cases, 0.96 percent; 13/3,368 controls, 0.38 percent; P = 0.008) with little evidence for association with other subtypes (6/1,491, 0.40 percent; P = 0.82). The relative risk of HGSOC associated with deleterious FANCM mutations was estimated to be 2.5 (95% CI 1.3 - 5.0; P = 0.006). In summary, whole exome sequencing of EOC cases with large-scale replication in case-control studies has identified FANCM as a likely novel susceptibility gene for HGSOC, with mutations associated with a moderate increase in risk. These data may have clinical implications for risk prediction and prevention approaches for high-grade serous ovarian cancer in the future and a significant impact on reducing disease mortality.

Published
2017
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3. Genome-wide Analysis Identifies Novel Loci Associated with Ovarian Cancer Outcomes: Findings from the Ovarian Cancer Association Consortium

Author

Johnatty, Sharon E., Tyrer, Jonathan P., Kar, Siddhartha, Beesley, Jonathan, Lu, Yi, Gao, Bo, Fasching, Peter A., Hein, Alexander, Ekici, Arif B., Beckmann, Matthias W., Lambrechts, Diether, Nieuwenhuysen, Els Van, Vergote, Ignace, Lambrechts, Sandrina, Rossing, Mary Anne, Doherty, Jennifer A., Chang-Claude, Jenny, Modugno, Francesmary, Ness, Roberta B., Moysich, Kirsten B., Levine, Douglas A., Kiemeney, Lambertus A., Massuger, Leon F.A.G., Gronwald, Jacek, Lubiński, Jan, Jakubowska, Anna, Cybulski, Cezary, Brinton, Louise, Lissowska, Jolanta, Wentzensen, Nicolas, Song, Honglin, Rhenius, Valerie, Campbell, Ian, Eccles, Diana, Sieh, Weiva, Whittemore, Alice S., McGuire, Valerie, Rothstein, Joseph H., Sutphen, Rebecca, Anton-Culver, Hoda, Ziogas, Argyrios, Gayther, Simon A., Gentry-Maharaj, Aleksandra, Menon, Usha, Ramus, Susan J., Pearce, Celeste L, Pike, Malcolm C, Stram, Daniel O., Wu, Anna H., Kupryjanczyk, Jolanta, Dansonka-Mieszkowska, Agnieszka, Rzepecka, Iwona K., Spiewankiewicz, Beata, Goodman, Marc T., Wilkens, Lynne R., Carney, Michael E., Thompson, Pamela J, Heitz, Florian, du Bois, Andreas, Schwaab, Ira, Harter, Philipp, Pisterer, Jacobus, Hillemanns, Peter, Karlan, Beth Y., Walsh, Christine, Lester, Jenny, Orsulic, Sandra, Winham, Stacey J, Earp, Madalene, Larson, Melissa C., Fogarty, Zachary C., Høgdall, Estrid, Jensen, Allan, Kjaer, Susanne Kruger, Fridley, Brooke L., Cunningham, Julie M., Vierkant, Robert A., Schildkraut, Joellen M., Iversen, Edwin S., Terry, Kathryn L., Cramer, Daniel W., Bandera, Elisa V., Orlow, Irene, Pejovic, Tanja, Bean, Yukie, Høgdall, Claus, Lundvall, Lene, McNeish, Ian, Paul, James, Carty, Karen, Siddiqui, Nadeem, Glasspool, Rosalind, Sellers, Thomas, Kennedy, Catherine, Chiew, Yoke-Eng, Berchuck, Andrew, MacGregor, Stuart, deFazio, Anna, Pharoah, Paul D.P., Goode, Ellen L., Webb, Penelope M., and Chenevix-Trench, Georgia

Subjects
Oncology, Cancer Research, Genome-wide association study, AGO Study Group, Kaplan-Meier Estimate, Carcinoma, Ovarian Epithelial, Bioinformatics, chemistry.chemical_compound, Neoplasms, Ovarian Epithelial, 2.1 Biological and endogenous factors, Neoplasms, Glandular and Epithelial, Aetiology, Cancer, Ovarian Neoplasms, Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17], Glandular and Epithelial, Single Nucleotide, Prognosis, Ovarian Cancer, Urological cancers Radboud Institute for Health Sciences [Radboudumc 15], Female, Australian Ovarian Cancer Study Group, medicine.medical_specialty, Genotype, Quantitative Trait Loci, Oncology and Carcinogenesis, Single-nucleotide polymorphism, Polymorphism, Single Nucleotide, Article, Rare Diseases, Meta-Analysis as Topic, Clinical Research, Internal medicine, Carcinoma, medicine, Genetics, SNP, Humans, Progression-free survival, Oncology & Carcinogenesis, Polymorphism, Alleles, business.industry, Human Genome, Computational Biology, medicine.disease, Carboplatin, Patient Outcome Assessment, Regimen, Orphan Drug, chemistry, Ovarian cancer, business, Genome-Wide Association Study
Abstract

Purpose: Chemotherapy resistance remains a major challenge in the treatment of ovarian cancer. We hypothesize that germline polymorphisms might be associated with clinical outcome. Experimental Design: We analyzed approximately 2.8 million genotyped and imputed SNPs from the iCOGS experiment for progression-free survival (PFS) and overall survival (OS) in 2,901 European epithelial ovarian cancer (EOC) patients who underwent first-line treatment of cytoreductive surgery and chemotherapy regardless of regimen, and in a subset of 1,098 patients treated with ≥4 cycles of paclitaxel and carboplatin at standard doses. We evaluated the top SNPs in 4,434 EOC patients, including patients from The Cancer Genome Atlas. In addition, we conducted pathway analysis of all intragenic SNPs and tested their association with PFS and OS using gene set enrichment analysis. Results: Five SNPs were significantly associated (P ≤ 1.0 × 10−5) with poorer outcomes in at least one of the four analyses, three of which, rs4910232 (11p15.3), rs2549714 (16q23), and rs6674079 (1q22), were located in long noncoding RNAs (lncRNAs) RP11-179A10.1, RP11-314O13.1, and RP11-284F21.8, respectively (P ≤ 7.1 × 10−6). ENCODE ChIP-seq data at 1q22 for normal ovary show evidence of histone modification around RP11-284F21.8, and rs6674079 is perfectly correlated with another SNP within the super-enhancer MEF2D, expression levels of which were reportedly associated with prognosis in another solid tumor. YAP1- and WWTR1 (TAZ)-stimulated gene expression and high-density lipoprotein (HDL)-mediated lipid transport pathways were associated with PFS and OS, respectively, in the cohort who had standard chemotherapy (pGSEA ≤6 × 10−3). Conclusions: We have identified SNPs in three lncRNAs that might be important targets for novel EOC therapies. Clin Cancer Res; 21(23); 5264–76. ©2015 AACR.

Published
2015

4. Common non-synonymous snps associated with breast cancer susceptibility: findings from the breast cancer association consortium

Author

Milne, Roger L., Burwinkel, Barbara, Michailidou, Kyriaki, Arias-Perez, Jose-Ignacio, Zamora, M. Pilar, Menéndez-Rodríguez, Primitiva, Hardisson, David, Mendiola, Marta, González-Neira, Anna, Pita, Guillermo, Alonso, M. Rosario, Dennis, Joe, Wang, Qin, Bolla, Manjeet K., Swerdlow, Anthony, Ashworth, Alan, Orr, Nick, Schoemaker, Minouk, Ko, Yon-Dschun, Brauch, Hiltrud, Hamann, Ute, Andrulis, Irene L., Knight, Julia A., Glendon, Gord, Tchatchou, Sandrine, Matsuo, Keitaro, Ito, Hidemi, Iwata, Hiroji, Tajima, Kazuo, Li, Jingmei, Brand, Judith S., Brenner, Hermann, Dieffenbach, Aida Karina, Arndt, Volker, Stegmaier, Christa, Lambrechts, Diether, Peuteman, Gilian, Christiaens, Marie-Rose, Smeets, Ann, Jakubowska, Anna, Lubinski, Jan, Jaworska-Bieniek, Katarzyna, Durda, Katazyna, Hartman, Mikael, Hui, Miao, Yen Lim, Wei, Wan Chan, Ching, Marme, Federick, Yang, Rongxi, Bugert, Peter, Lindblom, Annika, Margolin, Sara, García-Closas, Montserrat, Chanock, Stephen J., Lissowska, Jolanta, Figueroa, Jonine D., Bojesen, Stig E., Nordestgaard, Børge G., Flyger, Henrik, Hooning, Maartje J., Kriege, Mieke, van den Ouweland, Ans M.W., Koppert, Linetta B., Fletcher, Olivia, Johnson, Nichola, dos-Santos-Silva, Isabel, Peto, Julian, Zheng, Wei, Deming-Halverson, Sandra, Shrubsole, Martha J., Long, Jirong, Chang-Claude, Jenny, Rudolph, Anja, Seibold, Petra, Flesch-Janys, Dieter, Winqvist, Robert, Pylkäs, Katri, Jukkola-Vuorinen, Arja, Grip, Mervi, Cox, Angela, Cross, Simon S., Reed, Malcolm W.R., Schmidt, Marjanka K., Broeks, Annegien, Cornelissen, Sten, Braaf, Linde, Kang, Daehee, Choi, Ji-Yeob, Park, Sue K., Noh, Dong-Young, Simard, Jacques, Dumont, Martine, Goldberg, Mark S., Labrèche, France, Fasching, Peter A., Hein, Alexander, Ekici, Arif B., Beckmann, Matthias W., Radice, Paolo, Peterlongo, Paolo, Azzollini, Jacopo, Barile, Monica, Sawyer, Elinor, Tomlinson, Ian, Kerin, Michael, Miller, Nicola, Hopper, John L., Schmidt, Daniel F., Makalic, Enes, Southey, Melissa C., Hwang Teo, Soo, Har Yip, Cheng, Sivanandan, Kavitta, Tay, Wan-Ting, Shen, Chen-Yang, Hsiung, Chia-Ni, Yu, Jyh-Cherng, Hou, Ming-Feng, Guénel, Pascal, Truong, Therese, Sanchez, Marie, Mulot, Claire, Blot, William, Cai, Qiuyin, Nevanlinna, Heli, Muranen, Taru A., Aittomäki, Kristiina, Blomqvist, Carl, Wu, Anna H., Tseng, Chiu-Chen, Van Den Berg, David, Stram, Daniel O., Bogdanova, Natalia, Dörk, Thilo, Muir, Kenneth, Lophatananon, Artitaya, Stewart-Brown, Sarah, Siriwanarangsan, Pornthep, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M., Shu, Xiao-Ou, Lu, Wei, Gao, Yu-Tang, Zhang, Ben, Couch, Fergus J., Toland, Amanda E., Yannoukakos, Drakoulis, Sangrajrang, Suleeporn, McKay, James, Wang, Xianshu, Olson, Janet E., Vachon, Celine, Purrington, Kristen, Severi, Gianluca, Baglietto, Laura, Haiman, Christopher A., Henderson, Brian E., Schumacher, Fredrick, Le Marchand, Loic, Devilee, Peter, Tollenaar, Robert A.E.M., Seynaeve, Caroline, Czene, Kamila, Eriksson, Mikael, Humphreys, Keith, Darabi, Hatef, Ahmed, Shahana, Shah, Mitul, Pharoah, Paul D.P., Hall, Per, Giles, Graham G., Benítez, Javier, Dunning, Alison M., Chenevix-Trench, Georgia, Easton, Douglas F., Berchuck, Andrew, Eeles, Rosalind A., Olama, Ali Amin Al, Kote-Jarai, Zsofia, Benlloch, Sara, Antoniou, Antonis, McGuffog, Lesley, Offit, Ken, Lee, Andrew, Dicks, Ed, Luccarini, Craig, Tessier, Daniel C., Bacot, Francois, Vincent, Daniel, LaBoissière, Sylvie, Robidoux, Frederic, Nielsen, Sune F., Cunningham, Julie M., Windebank, Sharon A., Hilker, Christopher A., Meyer, Jeffrey, Angelakos, Maggie, Maskiell, Judi, van der Schoot, Ellen, Rutgers, Emiel, Verhoef, Senno, Hogervorst, Frans, Boonyawongviroj, Prat, Siriwanarungsan, Pornthep, Schrauder, Michael, Rübner, Matthias, Oeser, Sonja, Landrith, Silke, Williams, Eileen, Ryder-Mills, Elaine, Sargus, Kara, McInerney, Niall, Colleran, Gabrielle, Rowan, Andrew, Jones, Angela, Sohn, Christof, Schneeweiß, Andeas, Álvarez, Núria, Lacey, James, Wang, Sophia, Ma, Huiyan, Lu, Yani, Deapen, Dennis, Pinder, Rich, Lee, Eunjung, Schumacher, Fred, Horn-Ross, Pam, Reynolds, Peggy, Nelson, David, Ziegler, Hartwig, Wolf, Sonja, Hermann, Volker, Lo, Wing-Yee, Justenhoven, Christina, Baisch, Christian, Fischer, Hans-Peter, Brüning, Thomas, Pesch, Beate, Rabstein, Sylvia, Lotz, Anne, Harth, Volker, Heikkinen, Tuomas, Erkkilä, Irja, Aaltonen, Kirsimari, von Smitten, Karl, Antonenkova, Natalia, Hillemanns, Peter, Christiansen, Hans, Myöhänen, Eija, Kemiläinen, Helena, Thorne, Heather, Niedermayr, Eveline, Bowtell, D, Chenevix-Trench, G, deFazio, A, Gertig, D, Green, A, Webb, P, Green, A., Parsons, P., Hayward, N., Webb, P., Whiteman, D., Fung, Annie, Yashiki, June, Smeets, Dominiek, Brussel, Thomas Van, Corthouts, Kathleen, Obi, Nadia, Heinz, Judith, Behrens, Sabine, Eilber, Ursula, Celik, Muhabbet, Olchers, Til, Manoukian, Siranoush, Peissel, Bernard, Scuvera, Giulietta, Zaffaroni, Daniela, Bonanni, Bernardo, Feroce, Irene, Maniscalco, Angela, Rossi, Alessandra, Bernard, Loris, Tranchant, Martine, Valois, Marie-France, Turgeon, Annie, Heguy, Lea, Sze Yee, Phuah, Kang, Peter, Nee, Kang In, Mariapun, Shivaani, Sook-Yee, Yoon, Lee, Daphne, Ching, Teh Yew, Taib, Nur Aishah Mohd, Otsukka, Meeri, Mononen, Kari, Selander, Teresa, Weerasooriya, Nayana, staff, OFBCR, Krol-Warmerdam, E., Molenaar, J., Blom, J., Brinton, Louise, Szeszenia-Dabrowska, Neonila, Peplonska, Beata, Zatonski, Witold, Chao, Pei, Stagner, Michael, Bos, Petra, Blom, Jannet, Crepin, Ellen, Nieuwlaat, Anja, Heemskerk, Annette, Higham, Sue, Cross, Simon, Cramp, Helen, Connley, Dan, Balasubramanian, Sabapathy, Brock, Ian, Conroy, Don, Baynes, Caroline, and Chua, Kimberley

Subjects
Adult, A Kinase Anchor Proteins, Alleles, Ataxin-7, Breast Neoplasms, Case-Control Studies, Cytoskeletal Proteins, Female, Genome-Wide Association Study, Humans, Middle Aged, Nerve Tissue Proteins, Protein-Serine-Threonine Kinases, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Molecular Biology, Genetics, Genetics (clinical), Protein Serine-Threonine Kinases, Medizinische Fakultät, NIMA-Related Kinases, ddc:610, Polymorphism, risk, variants, Association Studies Articles, identifies 2, Single Nucleotide, confer susceptibility, 5p12, loci, alleles, genome-wide association, metaanalysis
Abstract

Candidate variant association studies have been largely unsuccessful in identifying common breast cancer susceptibility variants, although most studies have been underpowered to detect associations of a realistic magnitude. We assessed 41 common non-synonymous single-nucleotide polymorphisms (nsSNPs) for which evidence of association with breast cancer risk had been previously reported. Case-control data were combined from 38 studies of white European women (46 450 cases and 42 600 controls) and analyzed using unconditional logistic regression. Strong evidence of association was observed for three nsSNPs: ATXN7-K264R at 3p21 [rs1053338, per allele OR = 1.07, 95% confidence interval (CI) = 1.04-1.10, P = 2.9 × 10(-6)], AKAP9-M463I at 7q21 (rs6964587, OR = 1.05, 95% CI = 1.03-1.07, P = 1.7 × 10(-6)) and NEK10-L513S at 3p24 (rs10510592, OR = 1.10, 95% CI = 1.07-1.12, P = 5.1 × 10(-17)). The first two associations reached genome-wide statistical significance in a combined analysis of available data, including independent data from nine genome-wide association studies (GWASs): for ATXN7-K264R, OR = 1.07 (95% CI = 1.05-1.10, P = 1.0 × 10(-8)); for AKAP9-M463I, OR = 1.05 (95% CI = 1.04-1.07, P = 2.0 × 10(-10)). Further analysis of other common variants in these two regions suggested that intronic SNPs nearby are more strongly associated with disease risk. We have thus identified a novel susceptibility locus at 3p21, and confirmed previous suggestive evidence that rs6964587 at 7q21 is associated with risk. The third locus, rs10510592, is located in an established breast cancer susceptibility region; the association was substantially attenuated after adjustment for the known GWAS hit. Thus, each of the associated nsSNPs is likely to be a marker for another, non-coding, variant causally related to breast cancer risk. Further fine-mapping and functional studies are required to identify the underlying risk-modifying variants and the genes through which they act.

Published
2014

5. Identification of a BRCA2-Specific Modifier Locus at 6p24 Related to Breast Cancer Risk

Author

Gaudet, Mia M., Kuchenbaecker, Karoline B., Vijai, Joseph, Klein, Robert J., Kirchhoff, Tomas, McGuffog, Lesley, Barrowdale, Daniel, Dunning, Alison M., Lee, Andrew, Dennis, Joe, Healey, Sue, Dicks, Ed, Soucy, Penny, Sinilnikova, Olga M., Pankratz, Vernon S., Wang, Xianshu, Eldridge, Ronald C., Tessier, Daniel C., Vincent, Daniel, Bacot, Francois, Hogervorst, Frans B.L., Peock, Susan, Stoppa-Lyonnet, Dominique, Coulet, Florence, Colas, Chrystelle, Soubrier, Florent, Peterlongo, Paolo, Schmutzler, Rita K., Nathanson, Katherine L., Piedmonte, Marion, Singer, Christian F., Thomassen, Mads, Sokolowska, Johanna, Bronner, Myriam, Hansen, Thomas V.O., Neuhausen, Susan L., Blanco, Ignacio, Greene, Mark H., Garber, Judith, Weitzel, Jeffrey N., Andrulis, Irene L., Goldgar, David E., D'Andrea, Emma, Caldes, Trinidad, Nevanlinna, Heli, Osorio, Ana, van Rensburg, Elizabeth J., Arason, Adalgeir, Rennert, Gad, van den Ouweland, Ans M.W., van der Hout, Annemarie H., Kets, Carolien M., Aalfs, Cora M., Wijnen, Juul T., Ausems, Margreet G.E.M., Frost, Debra, Ellis, Steve, Fineberg, Elena, Platte, Radka, Evans, D. Gareth, Jacobs, Chris, Adlard, Julian, Tischkowitz, Marc, Porteous, Mary, Damiola, Francesca, Golmard, Lisa, Barjhoux, Laure, Longy, Michel, Belotti, Muriel, Ferrer, Sandra Fert, Mazoyer, Sylvie, Spurdle, Amanda B., Manoukian, Siranoush, Barile, Monica, Genuardi, Maurizio, Arnold, Norbert, Meindl, Alfons, Sutter, Christian, Wappenschmidt, Barbara, Domchek, Susan M., Pfeiler, Georg, Friedman, Eitan, Jensen, Uffe Birk, Robson, Mark, Shah, Sohela, Lazaro, Conxi, Mai, Phuong L., Benitez, Javier, Southey, Melissa C., Schmidt, M. K., Fasching, Peter A., Peto, Julian, Humphreys, Manjeet K., Wang, Qin, Michailidou, Kyriaki, Sawyer, Elinor J., Burwinkel, Barbara, Guénel, Pascal, Bojesen, Stig E., Milne, Roger L., Brenner, Hermann, Lochmann, Magdalena, Brauch, Hiltrud, Ko, Yon Dschun, Baisch, Christian, Fischer, Hand Peter, Bruening, Thomas, Pesch, Beate, Rabstein, Sylvia, Spickenheuer, Anne, Aittomäki, Kristiina, Dörk, Thilo, Margolin, Sara, Mannermaa, Arto, Lambrechts, Diether, Chang-Claude, Jenny, Radice, Paolo, Giles, Graham G., Haiman, Christopher A., Winqvist, Robert, Devillee, Peter, García-Closas, Montserrat, Schoof, Nils, Hooning, M. J., Cox, Angela, Pharoah, Paul D.P., Jakubowska, Anna, Orr, Nick, González-Neira, Anna, Pita, Guillermo, Alonso, M. Rosario, Hall, Per, Couch, Fergus J., Simard, Jacques, Altshuler, David, Easton, Douglas F., Chenevix-Trench, Georgia, Antoniou, Antonis C., Offit, Kenneth, Rookus, M. A., van Leeuwen, F. E., Verhoef, S., de Lange, J. L., Collée, J. M., Seynaeve, C., van Deurzen, C. H.M., van Asperen, C. J., Tollenaar, R. A., Devilee, P., van Cronenburg, T. C.T.E.F., Mensenkamp, A. R., van der Luijt, R. B., van Os, T. A.M., Gille, J. J.P., Waisfisz, Q., Meijers-Heijboer, H. E.J., Gómez-Garcia, E. B., Blok, M. J., Oosterwijk, J. C., Mourits, M. J., de Bock, G. H., Vasen, H. F., Miedzybrodzka, Zosia, Gregory, Helen, Morrison, Patrick, Jeffers, Lisa, Cole, Trevor, Ong, Kai ren, Hoffman, Jonathan, Donaldson, Alan, James, Margaret, Paterson, Joan, Taylor, Amy, Murray, Alexandra, Rogers, Mark T., McCann, Emma, Kennedy, M. John, Barton, David, Drummond, Sarah, Brewer, Carole, Kivuva, Emma, Searle, Anne, Goodman, Selina, Hill, Kathryn, Davidson, Rosemarie, Murday, Victoria, Bradshaw, Nicola, Snadden, Lesley, Longmuir, Mark, Watt, Catherine, Gibson, Sarah, Haque, Eshika, Tobias, Ed, Duncan, Alexis, Izatt, Louise, Langman, Caroline, Brady, Angela, Dorkins, Huw, Melville, Athalie, Randhawa, Kashmir, Barwell, Julian, Serra-Feliu, Gemma, Ellis, Ian, Houghton, Catherine, Lalloo, Fiona, Taylor, Jane, Side, Lucy, Male, Alison, Berlin, Cheryl, Eason, Jacqueline, Douglas, Fiona, Claber, Oonagh, Collier, Rebecca, Jobson, Irene, Walker, Lisa, McLeod, Diane, Durell, Sarah, Stayner, Barbara, Eeles, Rosalind A., Shanley, Susan, Rahman, Nazneen, Houlston, Richard, Bancroft, Elizabeth, Page, Elizabeth, Ardern-Jones, Audrey, Kohut, Kelly, Wiggins, Jennifer, Castro, Elena, Killick, Emma, Martin, Sue, Rea, Gillian, Kulkarni, Anjana, Cook, Jackie, Quarrell, Oliver, Bardsley, Cathryn, Hodgson, Shirley, Goff, Sheila, Brice, Glen, Winchester, Lizzie, Eddy, Charlotte, Tripathi, Vishakha, Attard, Virginia, Lehmann, Anna, Eccles, Diana, Lucassen, Anneke, Crawford, Gillian, McBride, Donna, Smalley, Sarah, Sinilnikova, Olga, Verny-Pierre, Carole, Giraud, Sophie, Léone, Mélanie, Gauthier-Villars, Marion, Buecher, Bruno, Houdayer, Claude, Moncoutier, Virginie, Tirapo, Carole, de Pauw, Antoine, Bressac-de-Paillerets, Brigitte, Caron, Olivier, Bignon, Yves Jean, Uhrhammer, Nancy, Lasset, Christine, Bonadona, Valérie, Handallou, Sandrine, Hardouin, Agnés, Berthet, Pascaline, Sobol, Hagay, Bourdon, Violaine, Noguchi, Tetsuro, Remenieras, Audrey, Coupier, Isabelle, Pujol, Pascal, Peyrat, Jean Philippe, Fournier, Joëlle, Révillion, Françoise, Vennin, Philippe, Adenis, Claude, Rouleau, Etienne, Lidereau, Rosette, Demange, Liliane, Nogues, Catherine, Muller, Danièle, Fricker, Jean Pierre, Barouk-Simonet, Emmanuelle, Bonnet, Françoise, Bubien, Virginie, Sevenet, Nicolas, Toulas, Christine, Guimbaud, Rosine, Gladieff, Laurence, Feillel, Viviane, Dreyfus, Hélène, Rebischung, Christine, Peysselon, Magalie, Coron, Fanny, Faivre, Laurence, Prieur, Fabienne, Lebrun, Marine, Kientz, Caroline, Frénay, Marc, Vénat-Bouvet, Laurence, Delnatte, Capucine, Mortemousque, Isabelle, Lynch, Henry T., Snyder, Carrie L., Clinical Genetics, Medical Oncology, Human Genetics, Human genetics, EMGO - Quality of care, Anesthesiology, CCA - Oncogenesis, CCA - Cancer biology and immunology, Epidemiology and Data Science, Department of Obstetrics and Gynecology, Clinicum, and Department of Medical and Clinical Genetics

Subjects
Cancer Research, SUSCEPTIBILITY ALLELES, Genome-wide association study, Aetiology, screening and detection [ONCOL 5], QH426-470, Settore MED/03 - GENETICA MEDICA, Genoma humà, SUBTYPES, Breast cancer, 0302 clinical medicine, Risk Factors, CDKN2A, Genotype, BRCA2 MUTATION CARRIERS, Malalties hereditàries, GWAS, skin and connective tissue diseases, Genetics (clinical), POPULATION, 2. Zero hunger, Genetics, 0303 health sciences, education.field_of_study, BRCA1 Protein, COMMON VARIANTS, genetic modifiers, BRCA2, cancer risk, Middle Aged, 3. Good health, 030220 oncology & carcinogenesis, Chromosomes, Human, Pair 6, Female, Genetic diseases, Adult, Heterozygote, Medizinische Fakultät -ohne weitere Spezifikation, education, Population, Breast Neoplasms, Single-nucleotide polymorphism, Locus (genetics), Human chromosomes, Biology, Polymorphism, Single Nucleotide, OVARIAN-CANCER, BRCA2-specific modifier locus at 6p24, Càncer de mama, 03 medical and health sciences, TRANSCRIPTION FACTOR AP-2, SDG 3 - Good Health and Well-being, medicine, Humans, Genetic Predisposition to Disease, ddc:610, Allele, GENOME-WIDE ASSOCIATION, Molecular Biology, Alleles, Ecology, Evolution, Behavior and Systematics, Aged, 030304 developmental biology, BRCA2 Protein, Cromosomes humans, Human genome, Hereditary cancer and cancer-related syndromes [ONCOL 1], CONSORTIUM, medicine.disease, Mutation, 3111 Biomedicine, ZNF365, Genome-Wide Association Study
Abstract

Contains fulltext : 118578.pdf (Publisher’s version ) (Open Access) Common genetic variants contribute to the observed variation in breast cancer risk for BRCA2 mutation carriers; those known to date have all been found through population-based genome-wide association studies (GWAS). To comprehensively identify breast cancer risk modifying loci for BRCA2 mutation carriers, we conducted a deep replication of an ongoing GWAS discovery study. Using the ranked P-values of the breast cancer associations with the imputed genotype of 1.4 M SNPs, 19,029 SNPs were selected and designed for inclusion on a custom Illumina array that included a total of 211,155 SNPs as part of a multi-consortial project. DNA samples from 3,881 breast cancer affected and 4,330 unaffected BRCA2 mutation carriers from 47 studies belonging to the Consortium of Investigators of Modifiers of BRCA1/2 were genotyped and available for analysis. We replicated previously reported breast cancer susceptibility alleles in these BRCA2 mutation carriers and for several regions (including FGFR2, MAP3K1, CDKN2A/B, and PTHLH) identified SNPs that have stronger evidence of association than those previously published. We also identified a novel susceptibility allele at 6p24 that was inversely associated with risk in BRCA2 mutation carriers (rs9348512; per allele HR = 0.85, 95% CI 0.80-0.90, P = 3.9x10(-8)). This SNP was not associated with breast cancer risk either in the general population or in BRCA1 mutation carriers. The locus lies within a region containing TFAP2A, which encodes a transcriptional activation protein that interacts with several tumor suppressor genes. This report identifies the first breast cancer risk locus specific to a BRCA2 mutation background. This comprehensive update of novel and previously reported breast cancer susceptibility loci contributes to the establishment of a panel of SNPs that modify breast cancer risk in BRCA2 mutation carriers. This panel may have clinical utility for women with BRCA2 mutations weighing options for medical prevention of breast cancer.

Published
2013
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6. No association between SNPs regulating TGF-β1 secretion and late radiotherapy toxicity to the breast: Results from the RAPPER study

Author

Barnett, Gillian C., Coles, Charlotte E., Burnet, Neil G., Pharoah, Paul D.P., Wilkinson, Jennifer, West, Catharine M.L., Elliott, Rebecca M., Baynes, Caroline, and Dunning, Alison M.

Subjects
*GENETIC polymorphisms, *TRANSFORMING growth factors-beta, *SECRETION, *BREAST cancer treatment, *CANCER radiotherapy complications, *FIBROSIS, *GENETICS
Abstract

Abstract: Background and purpose: Several small studies have reported associations between TGFB1 single nucleotide polymorphisms (SNPs), considered to increase secretion of TGF-β1, and greater than 3-fold increases in incidence of fibrosis – an indicator of late toxicity after radiotherapy in breast cancer patients. Materials and methods: Two SNPs in TGFB1, C-509T (rs1800469) and L10P (rs1800470), were genotyped in 778 breast cancer patients who had received radiotherapy to the breast. Late radiotherapy toxicity was assessed two years after radiotherapy using a validated photographic technique, clinical assessment and patient questionnaires. Results: On photographic assessment, 210 (27%) patients showed some degree of breast shrinkage, whilst 45 (6%) patients showed marked breast shrinkage. There was no significant association of genotype at either of the TGFB1 SNPs with any measure of late radiation toxicity. Conclusion: This adequately powered trial failed to confirm previously reported increases in fibrosis with TGFB1 genotype – any increase greater than 1.36 can be excluded with 95% confidence. Similar frequent failures to replicate associations with candidate genes have been resolved using genome-wide association scans: this methodology detects common, low risk alleles but requires even larger patient numbers for adequate statistical power. [ABSTRACT FROM AUTHOR]

Published
2010
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