Citations 2
A Likelihood Ratio Approach for Utilizing Case-Control Data in the Clinical Classification of Rare Sequence Variants: Application to BRCA1 and BRCA2
Zanti, Maria , O'Mahony, Denise G , Li, Hongyan , Aittomäkkiki, Kristiina, Andrulis, Irene L. , Aronson, Kristan J. , Bolla, Manjeet K. , Brenner, Hermann , Caputo, Sandrine M. , Chang‐Claude, Jenny , Collaborators, GC-HBOC study, Daly, Mary B., Nicolo, Arcangela De , Eccles, Diana M., Engel, Christoph , Evans, D. Gareth , Fasching, Peter A. , Giele, Willemina R. R. Geurts -, Glendon, Gord , Goldberg, Mark S. , Gómez, E. , Güendert, Melanie, Hahnen, Eric , Haiman, Christopher A. , Hamann, Ute, Harkness, Elaine F. , Hogervorst, Frans B.L., Hoppe, Reiner , Houdayer, Claude , Houlston, Richard S. , Howell, Anthony , Investigators, ABCTB, Jakimovska, Milena , John, Esther M. , Kristensen, Vessela N. , Lambrechts, Diether , Léone, Mélanie, Lindblom, Annika , Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush , Menon, Usha , Offit, Kenneth, Park, Sue K. , Peto, Julian , Plaseska‐Karanfilska, Dijana , Romero, Atocha , Schmutzler, Rita K. , Stone, Jennifer , Tapper, William , Teo, Soo‐Hwang , Thomassen, Mads , Vachon, Celine M. , Vega, Ana , Wang, Qin , Wappenschmidt, Barbara , Zheng, Wei , Easton, Douglas F. , Goldgar, David E., Eccles, Diana , Lambrechts, Diether , Houdayer, Claude , Lambrechts, Diether , Teo, Soo H , Eccles, Diana , Menon, Usha , Houlston, Richard S , Vega, Ana , Evans, D Gareth , John, Esther M , Lambrechts, Diether , Brenner, Hermann , Romero, Atocha , Engel, Christoph , Zheng, Wei , Stone, Jennifer , Gómez-García, Encarna B , De Nicolo, Arcangela , Manoukian, Siranoush , Lindblom, Annika , Plaseska-Karanfilska, Dijana , Parsons, Michael T. , Dennis, Joe , Anton‐Culver, Hoda , Augustinsson, Annelie , Becher, Heiko , Bojesen, Stig E. , Brown, Melissa A. , Buys, Saundra S. , Canzian, Federico , Castelao, Jose E. , Czene, Kamila , Devilee, Peter , Dörk, Thilo , Dunning, Alison M. , Dwek, Miriam , Gago-Domínguez, Manuela , García‐Closas, Montserrat , García-Sáenz, José Á. , Gentry‐Maharaj, Aleksandra , Geurts-Giele, Willemina R.R. , Giles, Graham G. , Guénel, Pascal , Hall, Per N , Hollestelle, Antoinette , Hopper, John L. , Jakubowska, Anna , Jernström, Helena , Kaaks, Rudolf , Kitahara, Cari M. , Koutros, Stella , Kraft, Peter , Lacey, James V. , Léoné, Mélanie, Lubiński, Jan , Lush, Michael J. , Mannermaa, Arto, Margolin, Sara , Martı́nez, Marı́a Elena , Milne, Roger L. , Monteiro, Álvaro N.A. , Murphy, Rachel A. , Neuhausen, Susan L. , Nevanlinna, Heli , Newman, William G. , James, Paul A. , Peterlongo, Paolo , Punie, Kevin , Radice, Paolo , Rashid, Muhammad Usman , Rennert, Gad , Rosenberg, Efraim H. , Saloustros, Emmanouil , Sandler, Dale P. , Schmidt, Marjanka K. , Shu, Xiao‐Ou , Simard, Jacques , Southey, Melissa C. , Stoppa‐Lyonnet, Dominique , Tamimi, Rulla M. , Taylor, Jack A. , Teras, Lauren R. , Terry, Mary Beth , Troester, Melissa A. , Vachon, Celine M. , Vreeswijk, Maaike P.G. , Weinberg, Clarice R. , Wolk, Alicja , Feng, Bing , Couch, Fergus J. , Spurdle, Amanda B. , Michailidou, Kyriaki
Human Mutation | September 15, 2023 | Volume: 2023 | Issue: No issue available | Pages: 1-17
A large number of variants identified through clinical genetic testing in disease susceptibility genes are of uncertain significance (VUS). Following the recommendations of the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP), the frequency in case-control datasets (PS4 criterion) can inform their interpretation. We present a novel case-control likelihood ratio-based method that incorporates gene-specific age-related penetrance. We demonstrate the utility of this method in the analysis of simulated and real datasets. In the analysis of simulated data, the likelihood ratio method was more powerful compared to other methods. Likelihood ratios were calculated for a case-control dataset of BRCA1 and BRCA2 variants from the Breast Cancer Association Consortium (BCAC) and compared with logistic regression results. A larger number of variants reached evidence in favor of pathogenicity, and a substantial number of variants had evidence against pathogenicity—findings that would not have been reached using other case-control analysis methods. Our novel method provides greater power to classify rare variants compared with classical case-control methods. As an initiative from the ENIGMA Analytical Working Group, we provide user-friendly scripts and preformatted Excel calculators for implementation of the method for rare variants in BRCA1, BRCA2, and other high-risk genes with known penetrance.
Common Variants at the 19p13.1 and ZNF365 Loci Are Associated with ER Subtypes of Breast Cancer and Ovarian Cancer Risk in BRCA1 and BRCA2
Gaudet, Mia M. , Antoniou, Antonis C. , Ramus, Susan J. , Kuchenbaecker, Karoline , Soucy, Penny, Chen, Xiaoqing, Kirchhoff, Tomas , McGuffog, Lesley, Barrowdale, Daniel , Healey, Sue, Sinilnikova, Olga M., Andrulis, Irene L. , Özçelik, Hilmi, Mulligan, Anna Marie , Thomassen, Mads , Gerdes, Anne‐Marie , Jensen, Uffe Birk , Skytte, Anne‐Bine , Kruse, Torben A., Caligo, Maria A. , Wachenfeldt, Anna von , Barbany, Gisela , Loman, Niklas, Soller, Maria , Ehrencrona, Hans , Karlsson, Per , Nathanson, Katherine L. , Rebbeck, Timothy R., Jakubowska, Anna , Lubiński, Jan , Jaworska, Katarzyna, Durda, Katarzyna, Złowocka, Elżbieta, Huzarski, Tomasz , Byrski, Tomasz , Cybulski, Cezary, Górski, Bohdan , Osório, Ana , Durán, M. , Tejada, María‐Isabel , Hamann, Ute, Hogervorst, Frans B.L., Os, Theo A. van, Leeuwen, Flora E. van , Meijers‐Heijboer, Hanne , Blok, Marinus J. , Kets, Marleen, Hooning, Maartje J. , Oldenburg, Rogier A., Ausems, Margreet G.E.M. , Peock, Susan, Frost, Debra, Ellis, Steve D., Platte, Radka, Fineberg, Elena, Evans, D. Gareth , Jacobs, Chris , Eeles, Rosalind A. , Adlard, Julian , Davidson, Rosemarie, Eccles, Diana M., Cole, Trevor, Paterson, Joan, Brewer, Carole, Douglas, Fiona, Hodgson, Shirley V. , Walker, Lisa, Porteous, Mary, Kennedy, M. John, Side, Lucy, Bove, Betsy, Fassy-Colcombet, Marion, Castéra, Laurent , Cornelis, François, Mazoyer, Sylvie , Léoné, Mélanie, Boutry‐Kryza, Nadia, Paillerets, Brigitte Bressac–de , Coupier, Isabelle, Delnatte, Capucine, Akloul, Linda, Lynch, Henry T., Snyder, Carrie, Daly, Mary B., Terry, Mary Beth , John, Esther M. , Miron, Alexander, Southey, Melissa C. , Goldgar, David E., Singer, Christian F., Rappaport, Christine , Tea, Muy‐Kheng M., Fink-Retter, Anneliese, Hansen, Thomas van Overeem , Nielsen, Finn C., Arason, Aðalgeir , Vijai, Joseph , Shah, Sohela, Sarrel, Kara , Piedmonte, Marion, Phillips, Kelly, Basil, Jack, Rubinstein, Wendy S. , Boggess, John F., Wakeley, Katie, Montagna, Marco , Imyanitov, Evgeny N., Janavičius, Ramūnas , Lázaro, Conxi , Blanco, Ignacio , Feliubadaló, Lídia , Brunet, Joan , Gayther, Simon A. , Odunsi, Kunle , Walsh, Christine , Oláh, Edith , Teo, Soo‐Hwang , Ganz, Patricia A. , Beattie, Mary, Rensburg, Elizabeth J. van , Dorfling, Cecelia M., Dı́ez, Orland , Kwong, Ava , Schmutzler, Rita K., Wappenschmidt, Barbara, Engel, Christoph , Meindl, Alfons , Ditsch, Nina , Arnold, Norbert , Heidemann, Simone , Niederacher, Dieter , Preisler‐Adams, Sabine, Gadzicki, Dorothea, Varon-Mateeva, Raymonda, Deißler, Helmut , Gehrig, Andrea, Sutter, Christian , Kast, Karin, Fiebig, Britta, Heinritz, Wolfram, Caldes, Trinidad, Hoya, Miguel de la , Muranen, Taru , Nevanlinna, Heli , Spurdle, Amanda B. , Ding, Yuan Chun , Lindor, Noralane M. , Fredericksen, Zachary, Pankratz, V. Shane , Peterlongo, Paolo , Manoukian, Siranoush , Peissel, Bernard , Zaffaroni, Daniela , Barile, Monica, Bernard, Loris, Viel, Alessandra , Giannini, Giuseppe , Varesco, Liliana , Radice, Paolo , Greene, Mark H. , Mai, Phuong L., Easton, Douglas F., Chenevix‐Trench, Georgia , Offit, Kenneth, Simard, Jacques , Durocher, Francine , Eccles, Diana , Thorne, Heather , Phillips, Kelly‐Anne , Couch, Fergus J. , Beesley, Jonathan , Chen, Xiaoqing, Wang, Xianshu , Lee, Andrew , Domchek, Susan M. , Gronwald, Jacek , Benı́tez, Javier , Wijnen, Juul , Eccles, Diana M., Cook, Jackie A , Morrison, Patrick J. , Kennedy, M. John, Godwin, Andrew K. , Stoppa‐Lyonnet, Dominique , Caron, Olivier , Pujol, Pascal , Buys, Saundra S. , Chung, Wendy K. , Hopper, John L. , Singer, Christian F. , Robson, Mark E. , Phillips, Kelly, Toland, Amanda Ewart , Agata, Simona , Isaacs, Claudine , Pharoah, Paul D.P. , Karlan, Beth Y. , Meindl, Alfons , Varon-Mateeva, Raymonda, Caldes, Trinidad, Tischkowitz, Marc D. , Neuhausen, Susan L. , Mai, Phuong L., Nevanlinna, H , Caligo, Maria A , Peterlongo, Paolo , Ramus, Susan J , Spurdle, Amanda B , Teo, Soo H , van Rensburg, Elizabeth J , Eccles, Diana , de la Hoya, Miguel , Diez, Orland , Radice, Paolo , Adlard, Julian , Arnold, Norbert , Brunet, Joan , Eeles, Rosalind A , Ehrencrona, Hans , Evans, D Gareth , John, Esther M , Joseph, Vijai , Southey, Melissa C , Jakubowska, Anna , Muranen, Taru A , Nathanson, Katherine L , Arason, Adalgeir , Barrowdale, Daniel , Engel, Christoph , Lazaro, Conxi , Montagna, Marco , Viel, Alessandra , Simard, Jacques , Chenevix-Trench, Georgia , Huzarski, Tomasz , Feliubadaló, Lidia , Hansen, Thomas van Overeem , Manoukian, Siranoush , Lubinski, Jan , Phillips, Kelly-Anne , Terry, Mary Beth , Kwong, Ava
Cancer Epidemiology, Biomarkers & Prevention | March 29, 2012 | Volume: 21 | Issue: 4 | Pages: 645-657
Abstract Background: Genome-wide association studies (GWAS) identified variants at 19p13.1 and ZNF365 (10q21.2) as risk factors for breast cancer among BRCA1 and BRCA2 mutation carriers, respectively. We explored associations with ovarian cancer and with breast cancer by tumor histopathology for these variants in mutation carriers from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Methods: Genotyping data for 12,599 BRCA1 and 7,132 BRCA2 mutation carriers from 40 studies were combined. Results: We confirmed associations between rs8170 at 19p13.1 and breast cancer risk for BRCA1 mutation carriers [HR, 1.17; 95% confidence interval (CI), 1.07–1.27; P = 7.42 × 10−4] and between rs16917302 at ZNF365 (HR, 0.84; 95% CI, 0.73–0.97; P = 0.017) but not rs311499 at 20q13.3 (HR, 1.11; 95% CI, 0.94–1.31; P = 0.22) and breast cancer risk for BRCA2 mutation carriers. Analyses based on tumor histopathology showed that 19p13 variants were predominantly associated with estrogen receptor (ER)-negative breast cancer for both BRCA1 and BRCA2 mutation carriers, whereas rs16917302 at ZNF365 was mainly associated with ER-positive breast cancer for both BRCA1 and BRCA2 mutation carriers. We also found for the first time that rs67397200 at 19p13.1 was associated with an increased risk of ovarian cancer for BRCA1 (HR, 1.16; 95% CI, 1.05–1.29; P = 3.8 × 10−4) and BRCA2 mutation carriers (HR, 1.30; 95% CI, 1.10–1.52; P = 1.8 × 10−3). Conclusions: 19p13.1 and ZNF365 are susceptibility loci for ovarian cancer and ER subtypes of breast cancer among BRCA1 and BRCA2 mutation carriers. Impact: These findings can lead to an improved understanding of tumor development and may prove useful for breast and ovarian cancer risk prediction for BRCA1 and BRCA2 mutation carriers. Cancer Epidemiol Biomarkers Prev; 21(4); 645–57. ©2012 AACR.