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1. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes

Author

Chen, Zhishan, Guo, Xingyi, Tao, Ran, Huyghe, Jeroen R., Law, Philip J., Fernandez-Rozadilla, Ceres, Ping, Jie, Jia, Guochong, Long, Jirong, Li, Chao, Shen, Quanhu, Xie, Yuhan, Timofeeva, Maria N., Thomas, Minta, Schmit, Stephanie L., Díez-Obrero, Virginia, Devall, Matthew, Moratalla-Navarro, Ferran, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah E. W., Svinti, Victoria, Donnelly, Kevin, Farrington, Susan M., Blackmur, James, Vaughan-Shaw, Peter G., Shu, Xiao-Ou, Lu, Yingchang, Broderick, Peter, Studd, James, Harrison, Tabitha A., Conti, David V., Schumacher, Fredrick R., Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John L., Jenkins, Mark A., Win, Aung Ko, Pai, Rish K., Figueiredo, Jane C., Haile, Robert W., Gallinger, Steven, Woods, Michael O., Newcomb, Polly A., Duggan, David, Cheadle, Jeremy P., Kaplan, Richard, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Jukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri A., Rissanen, Harri, Pukkala, Eero, Eriksson, Johan G., Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie J., Ruiz-Narvaez, Edward, Palmer, Julie R., Buchanan, Daniel D., Platz, Elizabeth A., Visvanathan, Kala, Ulrich, Cornelia M., Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter T., Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha L., Potter, John D., Tsilidis, Kostas K., Schulze, Matthias B., Gunter, Marc J., Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Bishop, D. Timothy, Giles, Graham G., Southey, Melissa C., Idos, Gregory E., McDonnell, Kevin J., Abu-Ful, Zomoroda, Greenson, Joel K., Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope O., van Guelpen, Bethany, Hudson, Thomas J., Hampel, Heather, Pearlman, Rachel, Berndt, Sonja I., Hayes, Richard B., Martinez, Marie Elena, Thomas, Sushma S., Pharoah, Paul D. P., Larsson, Susanna C., Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly F., Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew T., Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David J., Joshi, Amit D., Schafmayer, Clemens, Scacheri, Peter C., Kundaje, Anshul, Schoen, Robert E., Hampe, Jochen, Stadler, Zsofia K., Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Edlund, Christopher K., Gauderman, W. James, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen J., van Duijnhoven, Franzel, Feskens, Edith J. M., Sakoda, Lori C., Gago-Dominguez, Manuela, Wolk, Alicja, Pardini, Barbara, FitzGerald, Liesel M., Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie A., Kooperberg, Charles, Li, Christopher I., Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Le Marchand, Loic, Wu, Anna H., Qu, Chenxu, McNeil, Caroline E., Coetzee, Gerhard, Hayward, Caroline, Deary, Ian J., Harris, Sarah E., Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Lau, Ken S., Zhao, Hongyu, Hsu, Li, Cai, Qiuyin, Dunlop, Malcolm G., Gruber, Stephen B., Houlston, Richard S., Moreno, Victor, Casey, Graham, Peters, Ulrike, Tomlinson, Ian, and Zheng, Wei

Published
2024
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3. Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

Author

Fernandez-Rozadilla, Ceres, Timofeeva, Maria, Chen, Zhishan, Law, Philip, Thomas, Minta, Schmit, Stephanie, Díez-Obrero, Virginia, Hsu, Li, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah, Svinti, Victoria, Donnelly, Kevin, Farrington, Susan, Blackmur, James, Vaughan-Shaw, Peter, Shu, Xiao-ou, Long, Jirong, Cai, Qiuyin, Guo, Xingyi, Lu, Yingchang, Broderick, Peter, Studd, James, Huyghe, Jeroen, Harrison, Tabitha, Conti, David, Dampier, Christopher, Devall, Mathew, Schumacher, Fredrick, Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Moratalla-Navarro, Ferran, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John, Jenkins, Mark, Win, Aung Ko, Pai, Rish, Figueiredo, Jane, Haile, Robert, Gallinger, Steven, Woods, Michael, Newcomb, Polly, Duggan, David, Cheadle, Jeremy, Kaplan, Richard, Maughan, Timothy, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Lukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri, Rissanen, Harri, Pukkala, Eero, Eriksson, Johan, Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Zanke, Brent, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie, Ruiz-Narvaez, Edward, Palmer, Julie, Buchanan, Daniel, Platz, Elizabeth, Visvanathan, Kala, Ulrich, Cornelia, Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter, Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha, Potter, John, Tsilidis, Konstantinos, Schulze, Matthias, Gunter, Marc, Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Stern, Mariana, Pardamean, Bens, Bishop, Timothy, Giles, Graham, Southey, Melissa, Idos, Gregory, McDonnell, Kevin, Abu-Ful, Zomoroda, Greenson, Joel, Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope, van Guelpen, Bethany, Hudson, Thomas, Hampel, Heather, Pearlman, Rachel, Berndt, Sonja, Hayes, Richard, Martinez, Marie Elena, Thomas, Sushma, Corley, Douglas, Pharoah, Paul, Larsson, Susanna, Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly, Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew, Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David, Joshi, Amit, Schafmayer, Clemens, Scacheri, Peter, Kundaje, Anshul, Nickerson, Deborah, Schoen, Robert, Hampe, Jochen, Stadler, Zsofia, Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Papadopoulos, Nickolas, Edlund, Chistopher, Gauderman, William, Thomas, Duncan, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen, van Duijnhoven, Franzel, Feskens, Edith, Sakoda, Lori, Gago-Dominguez, Manuela, Wolk, Alicja, Naccarati, Alessio, Pardini, Barbara, FitzGerald, Liesel, Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie, Kooperberg, Charles, Li, Christopher, Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Tangen, Catherine, Mardis, Elaine, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Haiman, Christopher, Le Marchand, Loic, Wu, Anna, Qu, Chenxu, McNeil, Caroline, Coetzee, Gerhard, Hayward, Caroline, Deary, Ian, Harris, Sarah, Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Moreno, Victor, Casey, Graham, Gruber, Stephen, Tomlinson, Ian, Zheng, Wei, Dunlop, Malcolm, Houlston, Richard, and Peters, Ulrike

Published
2023
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5. Functional analysis and fine mapping of the 9p22.2 ovarian cancer susceptibility locus

Author

Buckley, Melissa A, Woods, Nicholas T, Tyrer, Jonathan P, Mendoza-Fandiño, Gustavo, Lawrenson, Kate, Hazelett, Dennis J, Najafabadi, Hamed S, Gjyshi, Anxhela, Carvalho, Renato S, Lyra, Paulo C, Coetzee, Simon G, Shen, Howard C, Yang, Ally W, Earp, Madalene A, Yoder, Sean J, Risch, Harvey, Chenevix-Trench, Georgia, Ramus, Susan J, Phelan, Catherine M, Coetzee, Gerhard A, Noushmehr, Houtan, Hughes, Timothy R, Sellers, Thomas A, Goode, Ellen L, Pharoah, Paul D, Gayther, Simon A, and Monteiro, Alvaro NA

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetics, Human Genome, Ovarian Cancer, Women's Health, Rare Diseases, Prevention, Biotechnology, Cancer, 2.1 Biological and endogenous factors, Base Sequence, Carcinoma, Ovarian Epithelial, Cell Cycle Proteins, Cell Line, Tumor, Chromosome Mapping, Chromosomes, Human, Pair 9, Cystadenocarcinoma, Serous, DNA, Neoplasm, DNA-Binding Proteins, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, HEK293 Cells, Humans, Linkage Disequilibrium, Ovarian Neoplasms, Polymorphism, Single Nucleotide, Ovarian Cancer Association Consortium, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

Genome-wide association studies have identified 40 ovarian cancer risk loci. However, the mechanisms underlying these associations remain elusive. In this study, we conducted a two-pronged approach to identify candidate causal SNPs and assess underlying biological mechanisms at chromosome 9p22.2, the first and most statistically significant associated locus for ovarian cancer susceptibility. Three transcriptional regulatory elements with allele-specific effects and a scaffold/matrix attachment region were characterized and, through physical DNA interactions, BNC2 was established as the most likely target gene. We determined the consensus binding sequence for BNC2 in vitro, verified its enrichment in BNC2 ChIP-seq regions, and validated a set of its downstream target genes. Fine-mapping by dense regional genotyping in over 15,000 ovarian cancer cases and 30,000 controls identified SNPs in the scaffold/matrix attachment region as among the most likely causal variants. This study reveals a comprehensive regulatory landscape at 9p22.2 and proposes a likely mechanism of susceptibility to ovarian cancer. SIGNIFICANCE: Mapping the 9p22.2 ovarian cancer risk locus identifies BNC2 as an ovarian cancer risk gene.See related commentary by Choi and Brown, p. 439.

Published
2019

6. Novel Common Genetic Susceptibility Loci for Colorectal Cancer

Author

Schmit, Stephanie L, Edlund, Christopher K, Schumacher, Fredrick R, Gong, Jian, Harrison, Tabitha A, Huyghe, Jeroen R, Qu, Chenxu, Melas, Marilena, Van Den Berg, David J, Wang, Hansong, Tring, Stephanie, Plummer, Sarah J, Albanes, Demetrius, Alonso, M Henar, Amos, Christopher I, Anton, Kristen, Aragaki, Aaron K, Arndt, Volker, Barry, Elizabeth L, Berndt, Sonja I, Bezieau, Stéphane, Bien, Stephanie, Bloomer, Amanda, Boehm, Juergen, Boutron-Ruault, Marie-Christine, Brenner, Hermann, Brezina, Stefanie, Buchanan, Daniel D, Butterbach, Katja, Caan, Bette J, Campbell, Peter T, Carlson, Christopher S, Castelao, Jose E, Chan, Andrew T, Chang-Claude, Jenny, Chanock, Stephen J, Cheng, Iona, Cheng, Ya-Wen, Chin, Lee Soo, Church, James M, Church, Timothy, Coetzee, Gerhard A, Cotterchio, Michelle, Correa, Marcia Cruz, Curtis, Keith R, Duggan, David, Easton, Douglas F, English, Dallas, Feskens, Edith JM, Fischer, Rocky, FitzGerald, Liesel M, Fortini, Barbara K, Fritsche, Lars G, Fuchs, Charles S, Gago-Dominguez, Manuela, Gala, Manish, Gallinger, Steven J, Gauderman, W James, Giles, Graham G, Giovannucci, Edward L, Gogarten, Stephanie M, Gonzalez-Villalpando, Clicerio, Gonzalez-Villalpando, Elena M, Grady, William M, Greenson, Joel K, Gsur, Andrea, Gunter, Marc, Haiman, Christopher A, Hampe, Jochen, Harlid, Sophia, Harju, John F, Hayes, Richard B, Hofer, Philipp, Hoffmeister, Michael, Hopper, John L, Huang, Shu-Chen, Huerta, Jose Maria, Hudson, Thomas J, Hunter, David J, Idos, Gregory E, Iwasaki, Motoki, Jackson, Rebecca D, Jacobs, Eric J, Jee, Sun Ha, Jenkins, Mark A, Jia, Wei-Hua, Jiao, Shuo, Joshi, Amit D, Kolonel, Laurence N, Kono, Suminori, Kooperberg, Charles, Krogh, Vittorio, Kuehn, Tilman, Küry, Sébastien, LaCroix, Andrea, Laurie, Cecelia A, Lejbkowicz, Flavio, Lemire, Mathieu, Lenz, Heinz-Josef, and Levine, David

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Digestive Diseases, Human Genome, Prevention, Colo-Rectal Cancer, Clinical Research, Genetics, Cancer, 2.1 Biological and endogenous factors, Case-Control Studies, Colorectal Neoplasms, Ethnicity, Follow-Up Studies, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Polymorphism, Single Nucleotide, Prognosis, United States, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

BackgroundPrevious genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk.MethodsWe conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided.ResultsThe discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0.ConclusionsThis study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.

Published
2019

7. Author Correction: Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

Author

Fernandez-Rozadilla, Ceres, Timofeeva, Maria, Chen, Zhishan, Law, Philip, Thomas, Minta, Schmit, Stephanie, Díez-Obrero, Virginia, Hsu, Li, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah, Svinti, Victoria, Donnelly, Kevin, Farrington, Susan, Blackmur, James, Vaughan-Shaw, Peter, Shu, Xiao-ou, Long, Jirong, Cai, Qiuyin, Guo, Xingyi, Lu, Yingchang, Broderick, Peter, Studd, James, Huyghe, Jeroen, Harrison, Tabitha, Conti, David, Dampier, Christopher, Devall, Mathew, Schumacher, Fredrick, Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Moratalla-Navarro, Ferran, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John, Jenkins, Mark, Win, Aung Ko, Pai, Rish, Figueiredo, Jane, Haile, Robert, Gallinger, Steven, Woods, Michael, Newcomb, Polly, Duggan, David, Cheadle, Jeremy, Kaplan, Richard, Maughan, Timothy, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Lukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri, Rissanen, Harri, Pukkala, Eero, Eriksson, Johan, Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Zanke, Brent, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie, Ruiz-Narvaez, Edward, Palmer, Julie, Buchanan, Daniel, Platz, Elizabeth, Visvanathan, Kala, Ulrich, Cornelia, Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter, Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha, Potter, John, Tsilidis, Konstantinos, Schulze, Matthias, Gunter, Marc, Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Stern, Mariana, Pardamean, Bens, Bishop, Timothy, Giles, Graham, Southey, Melissa, Idos, Gregory, McDonnell, Kevin, Abu-Ful, Zomoroda, Greenson, Joel, Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope, van Guelpen, Bethany, Hudson, Thomas, Hampel, Heather, Pearlman, Rachel, Berndt, Sonja, Hayes, Richard, Martinez, Marie Elena, Thomas, Sushma, Corley, Douglas, Pharoah, Paul, Larsson, Susanna, Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly, Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew, Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David, Joshi, Amit, Schafmayer, Clemens, Scacheri, Peter, Kundaje, Anshul, Nickerson, Deborah, Schoen, Robert, Hampe, Jochen, Stadler, Zsofia, Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Papadopoulos, Nickolas, Edlund, Chistopher, Gauderman, William, Thomas, Duncan, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen, van Duijnhoven, Franzel, Feskens, Edith, Sakoda, Lori, Gago-Dominguez, Manuela, Wolk, Alicja, Naccarati, Alessio, Pardini, Barbara, FitzGerald, Liesel, Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie, Kooperberg, Charles, Li, Christopher, Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Tangen, Catherine, Mardis, Elaine, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Haiman, Christopher, Le Marchand, Loic, Wu, Anna, Qu, Chenxu, McNeil, Caroline, Coetzee, Gerhard, Hayward, Caroline, Deary, Ian, Harris, Sarah, Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Moreno, Victor, Casey, Graham, Gruber, Stephen, Tomlinson, Ian, Zheng, Wei, Dunlop, Malcolm, Houlston, Richard, and Peters, Ulrike

Published
2023
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8. Prostate Cancer Susceptibility in Men of African Ancestry at 8q24

Author

Han, Ying, Rand, Kristin A, Hazelett, Dennis J, Ingles, Sue A, Kittles, Rick A, Strom, Sara S, Rybicki, Benjamin A, Nemesure, Barbara, Isaacs, William B, Stanford, Janet L, Zheng, Wei, Schumacher, Fredrick R, Berndt, Sonja I, Wang, Zhaoming, Xu, Jianfeng, Rohland, Nadin, Reich, David, Tandon, Arti, Pasaniuc, Bogdan, Allen, Alex, Quinque, Dominique, Mallick, Swapan, Notani, Dimple, Rosenfeld, Michael G, Jayani, Ranveer Singh, Kolb, Suzanne, Gapstur, Susan M, Stevens, Victoria L, Pettaway, Curtis A, Yeboah, Edward D, Tettey, Yao, Biritwum, Richard B, Adjei, Andrew A, Tay, Evelyn, Truelove, Ann, Niwa, Shelley, Chokkalingam, Anand P, John, Esther M, Murphy, Adam B, Signorello, Lisa B, Carpten, John, Leske, M Cristina, Wu, Suh-Yuh, Hennis, Anslem JM, Neslund-Dudas, Christine, Hsing, Ann W, Chu, Lisa, Goodman, Phyllis J, Klein, Eric A, Zheng, S Lilly, Witte, John S, Casey, Graham, Lubwama, Alex, Pooler, Loreall C, Sheng, Xin, Coetzee, Gerhard A, Cook, Michael B, Chanock, Stephen J, Stram, Daniel O, Watya, Stephen, Blot, William J, Conti, David V, Henderson, Brian E, and Haiman, Christopher A

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Clinical Research, Cancer, Prostate Cancer, Aging, Urologic Diseases, Human Genome, Prevention, Genetics, Aetiology, 2.1 Biological and endogenous factors, Black or African American, Aged, Aged, 80 and over, Case-Control Studies, Chromosomes, Human, Pair 8, Genetic Predisposition to Disease, Humans, Male, Middle Aged, Polymorphism, Single Nucleotide, Prostatic Neoplasms, RNA, Long Noncoding, United States, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

The 8q24 region harbors multiple risk variants for distinct cancers, including >8 for prostate cancer. In this study, we conducted fine mapping of the 8q24 risk region (127.8-128.8Mb) in search of novel associations with common and rare variation in 4853 prostate cancer case patients and 4678 control subjects of African ancestry. All statistical tests were two-sided. We identified three independent associations at P values of less than 5.00×10(-8), all of which were replicated in studies from Ghana and Uganda (combined sample = 5869 case patients, 5615 control subjects; rs114798100: risk allele frequency [RAF] = 0.04, per-allele odds ratio [OR] = 2.31, 95% confidence interval [CI] = 2.04 to 2.61, P = 2.38×10(-40); rs72725879: RAF = 0.33, OR = 1.37, 95% CI = 1.30 to 1.45, P = 3.04×10(-27); and rs111906932: RAF = 0.03, OR = 1.79, 95% CI = 1.53 to 2.08, P = 1.39×10(-13)). Risk variants rs114798100 and rs111906923 are only found in men of African ancestry, with rs111906923 representing a novel association signal. The three variants are located within or near a number of prostate cancer-associated long noncoding RNAs (lncRNAs), including PRNCR1, PCAT1, and PCAT2. These findings highlight ancestry-specific risk variation and implicate prostate-specific lncRNAs at the 8q24 prostate cancer susceptibility region.

Published
2016

9. Fine-mapping analysis including over 254 000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes

Author

Chen, Zhishan, Guo, Xingyi, Tao, Ran, Huyghe, Jeroen R., Law, Philip J., Fernandez-Rozadilla, Ceres, Ping, Jie, Jia, Guochong, Long, Jirong, Li, Chao, Shen, Quanhu, Xie, Yuhan, Timofeeva, Maria N., Thomas, Minta, Schmit, Stephanie L., Díez-Obrero, Virginia, Devall, Matthew, Moratalla-Navarro, Ferran, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah E. W., Svinti, Victoria, Donnelly, Kevin, Farrington, Susan M., Blackmur, James, Vaughan-Shaw, Peter G., Shu, Xiao-Ou, Lu, Yingchang, Broderick, Peter, Studd, James, Harrison, Tabitha A., Conti, David V., Schumacher, Fredrick R., Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John L., Jenkins, Mark A., Win, Aung Ko, Pai, Rish K., Figueiredo, Jane C., Haile, Robert W., Gallinger, Steven, Woods, Michael O., Newcomb, Polly A., Duggan, David, Cheadle, Jeremy P., Kaplan, Richard, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Jukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri A., Rissanen, Harri, Pukkala, Eero, Eriksson, Johan G., Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie J., Ruiz-Narvaez, Edward, Palmer, Julie R., Buchanan, Daniel D., Platz, Elizabeth A., Visvanathan, Kala, Ulrich, Cornelia M., Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter T., Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha L., Potter, John D., Tsilidis, Kostas K., Schulze, Matthias B., Gunter, Marc J., Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Bishop, D. Timothy, Giles, Graham G., Southey, Melissa C., Idos, Gregory E., McDonnell, Kevin J., Abu-Ful, Zomoroda, Greenson, Joel K., Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope O., van Guelpen, Bethany, Hudson, Thomas J., Hampel, Heather, Pearlman, Rachel, Berndt, Sonja I., Hayes, Richard B., Martinez, Marie Elena, Thomas, Sushma S., Pharoah, Paul D. P., Larsson, Susanna C., Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly F., Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew T., Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David J., Joshi, Amit D., Schafmayer, Clemens, Scacheri, Peter C., Kundaje, Anshul, Schoen, Robert E., Hampe, Jochen, Stadler, Zsofia K., Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Edlund, Christopher K., Gauderman, W. James, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen J., van Duijnhoven, Franzel, Feskens, Edith J. M., Sakoda, Lori C., Gago-Dominguez, Manuela, Wolk, Alicja, Pardini, Barbara, FitzGerald, Liesel M., Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie A., Kooperberg, Charles, Li, Christopher I., Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Le Marchand, Loic, Wu, Anna H., Qu, Chenxu, McNeil, Caroline E., Coetzee, Gerhard, Hayward, Caroline, Deary, Ian J., Harris, Sarah E., Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Lau, Ken S., Zhao, Hongyu, Hsu, Li, Cai, Qiuyin, Dunlop, Malcolm G., Gruber, Stephen B., Houlston, Richard S., Moreno, Victor, Casey, Graham, Peters, Ulrike, Tomlinson, Ian, Zheng, Wei, Chen, Zhishan, Guo, Xingyi, Tao, Ran, Huyghe, Jeroen R., Law, Philip J., Fernandez-Rozadilla, Ceres, Ping, Jie, Jia, Guochong, Long, Jirong, Li, Chao, Shen, Quanhu, Xie, Yuhan, Timofeeva, Maria N., Thomas, Minta, Schmit, Stephanie L., Díez-Obrero, Virginia, Devall, Matthew, Moratalla-Navarro, Ferran, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah E. W., Svinti, Victoria, Donnelly, Kevin, Farrington, Susan M., Blackmur, James, Vaughan-Shaw, Peter G., Shu, Xiao-Ou, Lu, Yingchang, Broderick, Peter, Studd, James, Harrison, Tabitha A., Conti, David V., Schumacher, Fredrick R., Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John L., Jenkins, Mark A., Win, Aung Ko, Pai, Rish K., Figueiredo, Jane C., Haile, Robert W., Gallinger, Steven, Woods, Michael O., Newcomb, Polly A., Duggan, David, Cheadle, Jeremy P., Kaplan, Richard, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Jukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri A., Rissanen, Harri, Pukkala, Eero, Eriksson, Johan G., Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie J., Ruiz-Narvaez, Edward, Palmer, Julie R., Buchanan, Daniel D., Platz, Elizabeth A., Visvanathan, Kala, Ulrich, Cornelia M., Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter T., Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha L., Potter, John D., Tsilidis, Kostas K., Schulze, Matthias B., Gunter, Marc J., Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Bishop, D. Timothy, Giles, Graham G., Southey, Melissa C., Idos, Gregory E., McDonnell, Kevin J., Abu-Ful, Zomoroda, Greenson, Joel K., Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope O., van Guelpen, Bethany, Hudson, Thomas J., Hampel, Heather, Pearlman, Rachel, Berndt, Sonja I., Hayes, Richard B., Martinez, Marie Elena, Thomas, Sushma S., Pharoah, Paul D. P., Larsson, Susanna C., Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly F., Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew T., Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David J., Joshi, Amit D., Schafmayer, Clemens, Scacheri, Peter C., Kundaje, Anshul, Schoen, Robert E., Hampe, Jochen, Stadler, Zsofia K., Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Edlund, Christopher K., Gauderman, W. James, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen J., van Duijnhoven, Franzel, Feskens, Edith J. M., Sakoda, Lori C., Gago-Dominguez, Manuela, Wolk, Alicja, Pardini, Barbara, FitzGerald, Liesel M., Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie A., Kooperberg, Charles, Li, Christopher I., Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Le Marchand, Loic, Wu, Anna H., Qu, Chenxu, McNeil, Caroline E., Coetzee, Gerhard, Hayward, Caroline, Deary, Ian J., Harris, Sarah E., Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Lau, Ken S., Zhao, Hongyu, Hsu, Li, Cai, Qiuyin, Dunlop, Malcolm G., Gruber, Stephen B., Houlston, Richard S., Moreno, Victor, Casey, Graham, Peters, Ulrike, Tomlinson, Ian, and Zheng, Wei

Abstract

Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.

Published
2024
Full Text
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11. The PsychENCODE project

Author

Akbarian, Schahram, Liu, Chunyu, Knowles, James A, Vaccarino, Flora M, Farnham, Peggy J, Crawford, Gregory E, Jaffe, Andrew E, Pinto, Dalila, Dracheva, Stella, Geschwind, Daniel H, Mill, Jonathan, Nairn, Angus C, Abyzov, Alexej, Pochareddy, Sirisha, Prabhakar, Shyam, Weissman, Sherman, Sullivan, Patrick F, State, Matthew W, Weng, Zhiping, Peters, Mette A, White, Kevin P, Gerstein, Mark B, Amiri, Anahita, Armoskus, Chris, Ashley-Koch, Allison E, Bae, Taejeong, Beckel-Mitchener, Andrea, Berman, Benjamin P, Coetzee, Gerhard A, Coppola, Gianfilippo, Francoeur, Nancy, Fromer, Menachem, Gao, Robert, Grennan, Kay, Herstein, Jennifer, Kavanagh, David H, Ivanov, Nikolay A, Jiang, Yan, Kitchen, Robert R, Kozlenkov, Alexey, Kundakovic, Marija, Li, Mingfeng, Li, Zhen, Liu, Shuang, Mangravite, Lara M, Mattei, Eugenio, Markenscoff-Papadimitriou, Eirene, Navarro, Fábio CP, North, Nicole, Omberg, Larsson, Panchision, David, Parikshak, Neelroop, Poschmann, Jeremie, Price, Amanda J, Purcaro, Michael, Reddy, Timothy E, Roussos, Panos, Schreiner, Shannon, Scuderi, Soraya, Sebra, Robert, Shibata, Mikihito, Shieh, Annie W, Skarica, Mario, Sun, Wenjie, Swarup, Vivek, Thomas, Amber, Tsuji, Junko, van Bakel, Harm, Wang, Daifeng, Wang, Yongjun, Wang, Kai, Werling, Donna M, Willsey, A Jeremy, Witt, Heather, Won, Hyejung, Wong, Chloe CY, Wray, Gregory A, Wu, Emily Y, Xu, Xuming, Yao, Lijing, Senthil, Geetha, Lehner, Thomas, Sklar, Pamela, and Sestan, Nenad

Subjects
Biotechnology, Human Genome, Brain Disorders, Genetics, Mental Health, Serious Mental Illness, Neurosciences, Schizophrenia, Intellectual and Developmental Disabilities (IDD), Autism, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Underpinning research, Aetiology, Mental health, Animals, Brain, Chromosome Mapping, Epigenesis, Genetic, Genetic Code, Humans, Mental Disorders, Transcriptome, PsychENCODE Consortium, Psychology, Cognitive Sciences, Neurology & Neurosurgery
Abstract

Recent research on disparate psychiatric disorders has implicated rare variants in genes involved in global gene regulation and chromatin modification, as well as many common variants located primarily in regulatory regions of the genome. Understanding precisely how these variants contribute to disease will require a deeper appreciation for the mechanisms of gene regulation in the developing and adult human brain. The PsychENCODE project aims to produce a public resource of multidimensional genomic data using tissue- and cell type–specific samples from approximately 1,000 phenotypically well-characterized, high-quality healthy and disease-affected human post-mortem brains, as well as functionally characterize disease-associated regulatory elements and variants in model systems. We are beginning with a focus on autism spectrum disorder, bipolar disorder and schizophrenia, and expect that this knowledge will apply to a wide variety of psychiatric disorders. This paper outlines the motivation and design of PsychENCODE.

Published
2015

12. Corrigendum: genome-wide association study of colorectal cancer identifies six new susceptibility loci.

Author

Schumacher, Fredrick R, Schmit, Stephanie L, Jiao, Shuo, Edlund, Christopher K, Wang, Hansong, Zhang, Ben, Hsu, Li, Huang, Shu-Chen, Fischer, Christopher P, Harju, John F, Idos, Gregory E, Lejbkowicz, Flavio, Manion, Frank J, McDonnell, Kevin, McNeil, Caroline E, Melas, Marilena, Rennert, Hedy S, Shi, Wei, Thomas, Duncan C, Van Den Berg, David J, Hutter, Carolyn M, Aragaki, Aaron K, Butterbach, Katja, Caan, Bette J, Carlson, Christopher S, Chanock, Stephen J, Curtis, Keith R, Fuchs, Charles S, Gala, Manish, Giovannucci, Edward L, Gogarten, Stephanie M, Hayes, Richard B, Henderson, Brian, Hunter, David J, Jackson, Rebecca D, Kolonel, Laurence N, Kooperberg, Charles, Küry, Sébastien, LaCroix, Andrea, Laurie, Cathy C, Laurie, Cecelia A, Lemire, Mathieu, Levine, David, Ma, Jing, Makar, Karen W, Qu, Conghui, Taverna, Darin, Ulrich, Cornelia M, Wu, Kana, Kono, Suminori, West, Dee W, Berndt, Sonja I, Bezieau, Stephane, Brenner, Hermann, Campbell, Peter T, Chan, Andrew T, Chang-Claude, Jenny, Coetzee, Gerhard A, Conti, David V, Duggan, David, Figueiredo, Jane C, Fortini, Barbara K, Gallinger, Steven J, Gauderman, W James, Giles, Graham, Green, Roger, Haile, Robert, Harrison, Tabitha A, Hoffmeister, Michael, Hopper, John L, Hudson, Thomas J, Jacobs, Eric, Iwasaki, Motoki, Jee, Sun Ha, Jenkins, Mark, Jia, Wei-Hua, Joshi, Amit, Li, Li, Lindor, Noralene M, Matsuo, Keitaro, Moreno, Victor, Mukherjee, Bhramar, Newcomb, Polly A, Potter, John D, Raskin, Leon, Rennert, Gad, Rosse, Stephanie, Severi, Gianluca, Schoen, Robert E, Seminara, Daniela, Shu, Xiao-Ou, Slattery, Martha L, Tsugane, Shoichiro, White, Emily, Xiang, Yong-Bing, Zanke, Brent W, Zheng, Wei, Le Marchand, Loic, Casey, Graham, and Gruber, Stephen B

Subjects
MD Multidisciplinary
Published
2015

13. Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions

Author

Han, Ying, Hazelett, Dennis J, Wiklund, Fredrik, Schumacher, Fredrick R, Stram, Daniel O, Berndt, Sonja I, Wang, Zhaoming, Rand, Kristin A, Hoover, Robert N, Machiela, Mitchell J, Yeager, Merideth, Burdette, Laurie, Chung, Charles C, Hutchinson, Amy, Yu, Kai, Xu, Jianfeng, Travis, Ruth C, Key, Timothy J, Siddiq, Afshan, Canzian, Federico, Takahashi, Atsushi, Kubo, Michiaki, Stanford, Janet L, Kolb, Suzanne, Gapstur, Susan M, Diver, W Ryan, Stevens, Victoria L, Strom, Sara S, Pettaway, Curtis A, Olama, Ali Amin Al, Kote-Jarai, Zsofia, Eeles, Rosalind A, Yeboah, Edward D, Tettey, Yao, Biritwum, Richard B, Adjei, Andrew A, Tay, Evelyn, Truelove, Ann, Niwa, Shelley, Chokkalingam, Anand P, Isaacs, William B, Chen, Constance, Lindstrom, Sara, Le Marchand, Loic, Giovannucci, Edward L, Pomerantz, Mark, Long, Henry, Li, Fugen, Ma, Jing, Stampfer, Meir, John, Esther M, Ingles, Sue A, Kittles, Rick A, Murphy, Adam B, Blot, William J, Signorello, Lisa B, Zheng, Wei, Albanes, Demetrius, Virtamo, Jarmo, Weinstein, Stephanie, Nemesure, Barbara, Carpten, John, Leske, M Cristina, Wu, Suh-Yuh, Hennis, Anselm JM, Rybicki, Benjamin A, Neslund-Dudas, Christine, Hsing, Ann W, Chu, Lisa, Goodman, Phyllis J, Klein, Eric A, Zheng, S Lilly, Witte, John S, Casey, Graham, Riboli, Elio, Li, Qiyuan, Freedman, Matthew L, Hunter, David J, Gronberg, Henrik, Cook, Michael B, Nakagawa, Hidewaki, Kraft, Peter, Chanock, Stephen J, Easton, Douglas F, Henderson, Brian E, Coetzee, Gerhard A, Conti, David V, and Haiman, Christopher A

Subjects
Cancer, Human Genome, Biotechnology, Genetics, Urologic Diseases, Prostate Cancer, 2.1 Biological and endogenous factors, Aetiology, Asian People, Black People, Chromosome Mapping, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Hispanic or Latino, Humans, Linkage Disequilibrium, Male, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Prostatic Neoplasms, Quantitative Trait Loci, White People, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Interpretation of biological mechanisms underlying genetic risk associations for prostate cancer is complicated by the relatively large number of risk variants (n = 100) and the thousands of surrogate SNPs in linkage disequilibrium. Here, we combined three distinct approaches: multiethnic fine-mapping, putative functional annotation (based upon epigenetic data and genome-encoded features), and expression quantitative trait loci (eQTL) analyses, in an attempt to reduce this complexity. We examined 67 risk regions using genotyping and imputation-based fine-mapping in populations of European (cases/controls: 8600/6946), African (cases/controls: 5327/5136), Japanese (cases/controls: 2563/4391) and Latino (cases/controls: 1034/1046) ancestry. Markers at 55 regions passed a region-specific significance threshold (P-value cutoff range: 3.9 × 10(-4)-5.6 × 10(-3)) and in 30 regions we identified markers that were more significantly associated with risk than the previously reported variants in the multiethnic sample. Novel secondary signals (P < 5.0 × 10(-6)) were also detected in two regions (rs13062436/3q21 and rs17181170/3p12). Among 666 variants in the 55 regions with P-values within one order of magnitude of the most-associated marker, 193 variants (29%) in 48 regions overlapped with epigenetic or other putative functional marks. In 11 of the 55 regions, cis-eQTLs were detected with nearby genes. For 12 of the 55 regions (22%), the most significant region-specific, prostate-cancer associated variant represented the strongest candidate functional variant based on our annotations; the number of regions increased to 20 (36%) and 27 (49%) when examining the 2 and 3 most significantly associated variants in each region, respectively. These results have prioritized subsets of candidate variants for downstream functional evaluation.

Published
2015

14. Erratum: Corrigendum: Genome-wide association study of colorectal cancer identifies six new susceptibility loci

Author

Schumacher, Fredrick R, Schmit, Stephanie L, Jiao, Shuo, Edlund, Christopher K, Wang, Hansong, Zhang, Ben, Hsu, Li, Huang, Shu-Chen, Fischer, Christopher P, Harju, John F, Idos, Gregory E, Lejbkowicz, Flavio, Manion, Frank J, McDonnell, Kevin, McNeil, Caroline E, Melas, Marilena, Rennert, Hedy S, Shi, Wei, Thomas, Duncan C, Van Den Berg, David J, Hutter, Carolyn M, Aragaki, Aaron K, Butterbach, Katja, Caan, Bette J, Carlson, Christopher S, Chanock, Stephen J, Curtis, Keith R, Fuchs, Charles S, Gala, Manish, Giovannucci, Edward L, Gogarten, Stephanie M, Hayes, Richard B, Henderson, Brian, Hunter, David J, Jackson, Rebecca D, Kolonel, Laurence N, Kooperberg, Charles, Küry, Sébastien, LaCroix, Andrea, Laurie, Cathy C, Laurie, Cecelia A, Lemire, Mathieu, Levine, David, Ma, Jing, Makar, Karen W, Qu, Conghui, Taverna, Darin, Ulrich, Cornelia M, Wu, Kana, Kono, Suminori, West, Dee W, Berndt, Sonja I, Bezieau, Stephane, Brenner, Hermann, Campbell, Peter T, Chan, Andrew T, Chang-Claude, Jenny, Coetzee, Gerhard A, Conti, David V, Duggan, David, Figueiredo, Jane C, Fortini, Barbara K, Gallinger, Steven J, Gauderman, W James, Giles, Graham, Green, Roger, Haile, Robert, Harrison, Tabitha A, Hoffmeister, Michael, Hopper, John L, Hudson, Thomas J, Jacobs, Eric, Iwasaki, Motoki, Jee, Sun Ha, Jenkins, Mark, Jia, Wei-Hua, Joshi, Amit, Li, Li, Lindor, Noralene M, Matsuo, Keitaro, Moreno, Victor, Mukherjee, Bhramar, Newcomb, Polly A, Potter, John D, Raskin, Leon, Rennert, Gad, Rosse, Stephanie, Severi, Gianluca, Schoen, Robert E, Seminara, Daniela, Shu, Xiao-Ou, Slattery, Martha L, Tsugane, Shoichiro, White, Emily, Xiang, Yong-Bing, Zanke, Brent W, Zheng, Wei, Le Marchand, Loic, Casey, Graham, and Gruber, Stephen B

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Digestive Diseases, Human Genome, Genetics, Cancer, Cancer Genomics, Colo-Rectal Cancer
Published
2015

15. Genome-wide association study of colorectal cancer identifies six new susceptibility loci.

Author

Schumacher, Fredrick R, Schmit, Stephanie L, Jiao, Shuo, Edlund, Christopher K, Wang, Hansong, Zhang, Ben, Hsu, Li, Huang, Shu-Chen, Fischer, Christopher P, Harju, John F, Idos, Gregory E, Lejbkowicz, Flavio, Manion, Frank J, McDonnell, Kevin, McNeil, Caroline E, Melas, Marilena, Rennert, Hedy S, Shi, Wei, Thomas, Duncan C, Van Den Berg, David J, Hutter, Carolyn M, Aragaki, Aaron K, Butterbach, Katja, Caan, Bette J, Carlson, Christopher S, Chanock, Stephen J, Curtis, Keith R, Fuchs, Charles S, Gala, Manish, Giovannucci, Edward L, Gogarten, Stephanie M, Hayes, Richard B, Henderson, Brian, Hunter, David J, Jackson, Rebecca D, Kolonel, Laurence N, Kooperberg, Charles, Küry, Sébastien, LaCroix, Andrea, Laurie, Cathy C, Laurie, Cecelia A, Lemire, Mathieu, Levine, David, Ma, Jing, Makar, Karen W, Qu, Conghui, Taverna, Darin, Ulrich, Cornelia M, Wu, Kana, Kono, Suminori, West, Dee W, Berndt, Sonja I, Bezieau, Stéphane, Brenner, Hermann, Campbell, Peter T, Chan, Andrew T, Chang-Claude, Jenny, Coetzee, Gerhard A, Conti, David V, Duggan, David, Figueiredo, Jane C, Fortini, Barbara K, Gallinger, Steven J, Gauderman, W James, Giles, Graham, Green, Roger, Haile, Robert, Harrison, Tabitha A, Hoffmeister, Michael, Hopper, John L, Hudson, Thomas J, Jacobs, Eric, Iwasaki, Motoki, Jee, Sun Ha, Jenkins, Mark, Jia, Wei-Hua, Joshi, Amit, Li, Li, Lindor, Noralene M, Matsuo, Keitaro, Moreno, Victor, Mukherjee, Bhramar, Newcomb, Polly A, Potter, John D, Raskin, Leon, Rennert, Gad, Rosse, Stephanie, Severi, Gianluca, Schoen, Robert E, Seminara, Daniela, Shu, Xiao-Ou, Slattery, Martha L, Tsugane, Shoichiro, White, Emily, Xiang, Yong-Bing, Zanke, Brent W, and Zheng, Wei

Subjects
Humans, Colorectal Neoplasms, Genetic Predisposition to Disease, Odds Ratio, Case-Control Studies, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Genetics, Digestive Diseases, Prevention, Cancer, Human Genome, Colo-Rectal Cancer, 2.1 Biological and endogenous factors, MD Multidisciplinary
Abstract

Genetic susceptibility to colorectal cancer is caused by rare pathogenic mutations and common genetic variants that contribute to familial risk. Here we report the results of a two-stage association study with 18,299 cases of colorectal cancer and 19,656 controls, with follow-up of the most statistically significant genetic loci in 4,725 cases and 9,969 controls from two Asian consortia. We describe six new susceptibility loci reaching a genome-wide threshold of P

Published
2015

16. Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci

Author

Coetzee, Simon G, Shen, Howard C, Hazelett, Dennis J, Lawrenson, Kate, Kuchenbaecker, Karoline, Tyrer, Jonathan, Rhie, Suhn K, Levanon, Keren, Karst, Alison, Drapkin, Ronny, Ramus, Susan J, Consortium, The Consortium of Investigators of Modifiers of BRCA1 2 The Ovarian Cancer Association, Couch, Fergus J, Offit, Kenneth, Chenevix-Trench, Georgia, Monteiro, Alvaro NA, Antoniou, Antonis, Freedman, Matthew, Coetzee, Gerhard A, Pharoah, Paul DP, Noushmehr, Houtan, Gayther, Simon A, Anton-Culver, Hoda, Antonenkova, Natalia, Baker, Helen, Bandera, Elisa V, Bean, Yukie, Beckmann, Matthias W, Berchuck, Andrew, Bisogna, Maria, Bjorge, Line, Bogdanova, Natalia, Brinton, Louise A, Brooks-Wilson, Angela, Bruinsma, Fiona, Butzow, Ralf, Campbell, Ian G, Carty, Karen, Chang-Claude, Jenny, Chen, Ann, Chen, Zhihua, Cook, Linda S, Cramer, Daniel W, Cunningham, Julie M, Cybulski, Cezary, Dansonka-Mieszkowska, Agnieszka, Dennis, Joe, Dicks, Ed, Doherty, Jennifer A, Dörk, Thilo, du Bois, Andreas, Dürst, Matthias, Eccles, Diana, Easton, Douglas F, Edwards, Robert P, Eilber, Ursula, Ekici, Arif B, Fasching, Peter A, Fridley, Brooke L, Gao, Yu-Tang, Gentry-Maharaj, Aleksandra, Giles, Graham G, Glasspool, Rosalind, Goode, Ellen L, Goodman, Marc T, Grownwald, Jacek, Harrington, Patricia, Harter, Philipp, Hasmad, Hanis Nazihah, Hein, Alexander, Heitz, Florian, Hildebrandt, Michelle AT, Hillemanns, Peter, Hogdall, Estrid, Hogdall, Claus, Hosono, Satoyo, Iversen, Edwin S, Jakubowska, Anna, James, Paul, Jensen, Allan, Ji, Bu-Tian, Karlan, Beth Y, Kjaer, Susanne Kruger, Kelemen, Linda E, Kellar, Melissa, Kelley, Joseph L, Kiemeney, Lambertus A, Krakstad, Camilla, Kupryjanczyk, Jolanta, Lambrechts, Diether, Lambrechts, Sandrina, Le, Nhu D, Lele, Shashi, Leminen, Arto, Lester, Jenny, Levine, Douglas A, Liang, Dong, and Lissowska, Jolanta

Subjects
Biological Sciences, Genetics, Rare Diseases, Women's Health, Cancer Genomics, Ovarian Cancer, Human Genome, Cancer, Prevention, 2.1 Biological and endogenous factors, Chromatin, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Histones, Humans, Organ Specificity, Ovarian Neoplasms, Polymorphism, Single Nucleotide, Regulatory Sequences, Nucleic Acid, Ovarian Cancer Association Consortium, The Consortium of Investigators of Modifiers of BRCA1/2, Ovarian Cancer Association Consortium The Consortium of Investigators of Modifiers of BRCA1/2, Medical and Health Sciences, Genetics & Heredity
Abstract

Understanding the regulatory landscape of the human genome is a central question in complex trait genetics. Most single-nucleotide polymorphisms (SNPs) associated with cancer risk lie in non-protein-coding regions, implicating regulatory DNA elements as functional targets of susceptibility variants. Here, we describe genome-wide annotation of regions of open chromatin and histone modification in fallopian tube and ovarian surface epithelial cells (FTSECs, OSECs), the debated cellular origins of high-grade serous ovarian cancers (HGSOCs) and in endometriosis epithelial cells (EECs), the likely precursor of clear cell ovarian carcinomas (CCOCs). The regulatory architecture of these cell types was compared with normal human mammary epithelial cells and LNCaP prostate cancer cells. We observed similar positional patterns of global enhancer signatures across the three different ovarian cancer precursor cell types, and evidence of tissue-specific regulatory signatures compared to non-gynecological cell types. We found significant enrichment for risk-associated SNPs intersecting regulatory biofeatures at 17 known HGSOC susceptibility loci in FTSECs (P = 3.8 × 10(-30)), OSECs (P = 2.4 × 10(-23)) and HMECs (P = 6.7 × 10(-15)) but not for EECs (P = 0.45) or LNCaP cells (P = 0.88). Hierarchical clustering of risk SNPs conditioned on the six different cell types indicates FTSECs and OSECs are highly related (96% of samples using multi-scale bootstrapping) suggesting both cell types may be precursors of HGSOC. These data represent the first description of regulatory catalogues of normal precursor cells for different ovarian cancer subtypes, and provide unique insights into the tissue specific regulatory variation with respect to the likely functional targets of germline genetic susceptibility variants for ovarian cancer.

Published
2015

18. A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry

Author

Monda, Keri L, Chen, Gary K, Taylor, Kira C, Palmer, Cameron, Edwards, Todd L, Lange, Leslie A, Ng, Maggie CY, Adeyemo, Adebowale A, Allison, Matthew A, Bielak, Lawrence F, Chen, Guanjie, Graff, Mariaelisa, Irvin, Marguerite R, Rhie, Suhn K, Li, Guo, Liu, Yongmei, Liu, Youfang, Lu, Yingchang, Nalls, Michael A, Sun, Yan V, Wojczynski, Mary K, Yanek, Lisa R, Aldrich, Melinda C, Ademola, Adeyinka, Amos, Christopher I, Bandera, Elisa V, Bock, Cathryn H, Britton, Angela, Broeckel, Ulrich, Cai, Quiyin, Caporaso, Neil E, Carlson, Chris S, Carpten, John, Casey, Graham, Chen, Wei-Min, Chen, Fang, Chen, Yii-Der I, Chiang, Charleston WK, Coetzee, Gerhard A, Demerath, Ellen, Deming-Halverson, Sandra L, Driver, Ryan W, Dubbert, Patricia, Feitosa, Mary F, Feng, Ye, Freedman, Barry I, Gillanders, Elizabeth M, Gottesman, Omri, Guo, Xiuqing, Haritunians, Talin, Harris, Tamara, Harris, Curtis C, Hennis, Anselm JM, Hernandez, Dena G, McNeill, Lorna H, Howard, Timothy D, Howard, Barbara V, Howard, Virginia J, Johnson, Karen C, Kang, Sun J, Keating, Brendan J, Kolb, Suzanne, Kuller, Lewis H, Kutlar, Abdullah, Langefeld, Carl D, Lettre, Guillaume, Lohman, Kurt, Lotay, Vaneet, Lyon, Helen, Manson, JoAnn E, Maixner, William, Meng, Yan A, Monroe, Kristine R, Morhason-Bello, Imran, Murphy, Adam B, Mychaleckyj, Josyf C, Nadukuru, Rajiv, Nathanson, Katherine L, Nayak, Uma, N'Diaye, Amidou, Nemesure, Barbara, Wu, Suh-Yuh, Leske, M Cristina, Neslund-Dudas, Christine, Neuhouser, Marian, Nyante, Sarah, Ochs-Balcom, Heather, Ogunniyi, Adesola, Ogundiran, Temidayo O, Ojengbede, Oladosu, Olopade, Olufunmilayo I, Palmer, Julie R, Ruiz-Narvaez, Edward A, Palmer, Nicholette D, Press, Michael F, Rampersaud, Evandine, Rasmussen-Torvik, Laura J, Rodriguez-Gil, Jorge L, Salako, Babatunde, and Schadt, Eric E

Subjects
Biological Sciences, Genetics, Human Genome, Black or African American, Body Mass Index, Case-Control Studies, Gene Frequency, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Linkage Disequilibrium, Obesity, Polymorphism, Single Nucleotide, NABEC Consortium, UKBEC Consortium, BioBank Japan Project, AGEN Consortium, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Genome-wide association studies (GWAS) have identified 36 loci associated with body mass index (BMI), predominantly in populations of European ancestry. We conducted a meta-analysis to examine the association of >3.2 million SNPs with BMI in 39,144 men and women of African ancestry and followed up the most significant associations in an additional 32,268 individuals of African ancestry. We identified one new locus at 5q33 (GALNT10, rs7708584, P = 3.4 × 10(-11)) and another at 7p15 when we included data from the GIANT consortium (MIR148A-NFE2L3, rs10261878, P = 1.2 × 10(-10)). We also found suggestive evidence of an association at a third locus at 6q16 in the African-ancestry sample (KLHL32, rs974417, P = 6.9 × 10(-8)). Thirty-two of the 36 previously established BMI variants showed directionally consistent effect estimates in our GWAS (binomial P = 9.7 × 10(-7)), five of which reached genome-wide significance. These findings provide strong support for shared BMI loci across populations, as well as for the utility of studying ancestrally diverse populations.

Published
2013

19. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer.

Author

Antonenkova, Natalia, Armasu, Sebastian, Baglietto, Laura, Bandera, Elisa, Beckmann, Matthias, Birrer, Michael, Bloom, Greg, Bogdanova, Natalia, Brenton, James, Brinton, Louise, Brooks-Wilson, Angela, Brown, Robert, Butzow, Ralf, Campbell, Ian, Carney, Michael, Carvalho, Renato, Chang-Claude, Jenny, Chen, Y, Chen, Zhihua, Chow, Wong-Ho, Cicek, Mine, Coetzee, Gerhard, Cook, Linda, Cramer, Daniel, Cybulski, Cezary, Dansonka-Mieszkowska, Agnieszka, Despierre, Evelyn, Doherty, Jennifer, Dörk, Thilo, du Bois, Andreas, Dürst, Matthias, Eccles, Diana, Edwards, Robert, Ekici, Arif, Fasching, Peter, Fenstermacher, David, Flanagan, James, Gao, Yu-Tang, Garcia-Closas, Montserrat, Gentry-Maharaj, Aleksandra, Giles, Graham, Gjyshi, Anxhela, Gore, Martin, Gronwald, Jacek, Guo, Qi, Halle, Mari, Harter, Philipp, Hein, Alexander, Heitz, Florian, Hillemanns, Peter, Hoatlin, Maureen, Høgdall, Estrid, Høgdall, Claus, Hosono, Satoyo, Jakubowska, Anna, Jensen, Allan, Kalli, Kimberly, Krakstad, Camilla, Kupryjanczyk, Jolanta, Lambrechts, Diether, Lambrechts, Sandrina, Le, Nhu, Lee, Nathan, Lee, Janet, Leminen, Arto, Lim, Boon, Lissowska, Jolanta, Lubiński, Jan, Lundvall, Lene, Lurie, Galina, Massuger, Leon, Matsuo, Keitaro, McGuire, Valerie, McLaughlin, John, Menon, Usha, Modugno, Francesmary, Moysich, Kirsten, Nakanishi, Toru, Narod, Steven, Ness, Roberta, Nevanlinna, Heli, Nickels, Stefan, Noushmehr, Houtan, Odunsi, Kunle, Olson, Sara, Orlow, Irene, Paul, James, Pejovic, Tanja, Pelttari, Liisa, Permuth-Wey, Jenny, Pike, Malcolm, Poole, Elizabeth, Qu, Xiaotao, Risch, Harvey, Rodriguez-Rodriguez, Lorna, Rossing, Mary, Rudolph, Anja, Runnebaum, Ingo, Rzepecka, Iwona, and Salvesen, Helga

Subjects
Case-Control Studies, Cooperative Behavior, Cystadenocarcinoma, Serous, Female, Gene-Environment Interaction, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Meta-Analysis as Topic, Neoplasm Invasiveness, Ovarian Neoplasms, Polymorphism, Single Nucleotide, Risk Factors
Abstract

Genome-wide association studies (GWAS) have identified four susceptibility loci for epithelial ovarian cancer (EOC), with another two suggestive loci reaching near genome-wide significance. We pooled data from a GWAS conducted in North America with another GWAS from the UK. We selected the top 24,551 SNPs for inclusion on the iCOGS custom genotyping array. We performed follow-up genotyping in 18,174 individuals with EOC (cases) and 26,134 controls from 43 studies from the Ovarian Cancer Association Consortium. We validated the two loci at 3q25 and 17q21 that were previously found to have associations close to genome-wide significance and identified three loci newly associated with risk: two loci associated with all EOC subtypes at 8q21 (rs11782652, P = 5.5 × 10(-9)) and 10p12 (rs1243180, P = 1.8 × 10(-8)) and another locus specific to the serous subtype at 17q12 (rs757210, P = 8.1 × 10(-10)). An integrated molecular analysis of genes and regulatory regions at these loci provided evidence for functional mechanisms underlying susceptibility and implicated CHMP4C in the pathogenesis of ovarian cancer.

Published
2013

20. Identification of Genetic Susceptibility Loci for Colorectal Tumors in a Genome-Wide Meta-analysis

Author

Peters, Ulrike, Jiao, Shuo, Schumacher, Fredrick R, Hutter, Carolyn M, Aragaki, Aaron K, Baron, John A, Berndt, Sonja I, Bézieau, Stéphane, Brenner, Hermann, Butterbach, Katja, Caan, Bette J, Campbell, Peter T, Carlson, Christopher S, Casey, Graham, Chan, Andrew T, Chang–Claude, Jenny, Chanock, Stephen J, Chen, Lin S, Coetzee, Gerhard A, Coetzee, Simon G, Conti, David V, Curtis, Keith R, Duggan, David, Edwards, Todd, Fuchs, Charles S, Gallinger, Steven, Giovannucci, Edward L, Gogarten, Stephanie M, Gruber, Stephen B, Haile, Robert W, Harrison, Tabitha A, Hayes, Richard B, Henderson, Brian E, Hoffmeister, Michael, Hopper, John L, Hudson, Thomas J, Hunter, David J, Jackson, Rebecca D, Jee, Sun Ha, Jenkins, Mark A, Jia, Wei–Hua, Kolonel, Laurence N, Kooperberg, Charles, Küry, Sébastien, LaCroix, Andrea Z, Laurie, Cathy C, Laurie, Cecelia A, Le Marchand, Loic, Lemire, Mathieu, Levine, David, Lindor, Noralane M, Liu, Yan, Ma, Jing, Makar, Karen W, Matsuo, Keitaro, Newcomb, Polly A, Potter, John D, Prentice, Ross L, Qu, Conghui, Rohan, Thomas, Rosse, Stephanie A, Schoen, Robert E, Seminara, Daniela, Shrubsole, Martha, Shu, Xiao–Ou, Slattery, Martha L, Taverna, Darin, Thibodeau, Stephen N, Ulrich, Cornelia M, White, Emily, Xiang, Yongbing, Zanke, Brent W, Zeng, Yi–Xin, Zhang, Ben, Zheng, Wei, Hsu, Li, and Registry, Genetics and Epidemiology of Colorectal Cancer Consortium Colon Cancer Family

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Nutrition and Dietetics, Digestive Diseases, Prevention, Genetics, Cancer, Colo-Rectal Cancer, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Age Distribution, Aged, Aged, 80 and over, Colorectal Neoplasms, Cyclin D2, DNA-Binding Proteins, Female, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Incidence, Laminin, Male, Middle Aged, Polymorphism, Single Nucleotide, Prognosis, Risk Assessment, Sex Distribution, T-Box Domain Proteins, Colon Cancer Family Registry and the Genetics and Epidemiology of Colorectal Cancer Consortium, Neurosciences, Paediatrics and Reproductive Medicine, Gastroenterology & Hepatology, Clinical sciences, Nutrition and dietetics
Abstract

Background & aimsHeritable factors contribute to the development of colorectal cancer. Identifying the genetic loci associated with colorectal tumor formation could elucidate the mechanisms of pathogenesis.MethodsWe conducted a genome-wide association study that included 14 studies, 12,696 cases of colorectal tumors (11,870 cancer, 826 adenoma), and 15,113 controls of European descent. The 10 most statistically significant, previously unreported findings were followed up in 6 studies; these included 3056 colorectal tumor cases (2098 cancer, 958 adenoma) and 6658 controls of European and Asian descent.ResultsBased on the combined analysis, we identified a locus that reached the conventional genome-wide significance level at less than 5.0 × 10(-8): an intergenic region on chromosome 2q32.3, close to nucleic acid binding protein 1 (most significant single nucleotide polymorphism: rs11903757; odds ratio [OR], 1.15 per risk allele; P = 3.7 × 10(-8)). We also found evidence for 3 additional loci with P values less than 5.0 × 10(-7): a locus within the laminin gamma 1 gene on chromosome 1q25.3 (rs10911251; OR, 1.10 per risk allele; P = 9.5 × 10(-8)), a locus within the cyclin D2 gene on chromosome 12p13.32 (rs3217810 per risk allele; OR, 0.84; P = 5.9 × 10(-8)), and a locus in the T-box 3 gene on chromosome 12q24.21 (rs59336; OR, 0.91 per risk allele; P = 3.7 × 10(-7)).ConclusionsIn a large genome-wide association study, we associated polymorphisms close to nucleic acid binding protein 1 (which encodes a DNA-binding protein involved in DNA repair) with colorectal tumor risk. We also provided evidence for an association between colorectal tumor risk and polymorphisms in laminin gamma 1 (this is the second gene in the laminin family to be associated with colorectal cancers), cyclin D2 (which encodes for cyclin D2), and T-box 3 (which encodes a T-box transcription factor and is a target of Wnt signaling to β-catenin). The roles of these genes and their products in cancer pathogenesis warrant further investigation.

Published
2013

21. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer.

Author

Pharoah, Paul DP, Tsai, Ya-Yu, Ramus, Susan J, Phelan, Catherine M, Goode, Ellen L, Lawrenson, Kate, Buckley, Melissa, Fridley, Brooke L, Tyrer, Jonathan P, Shen, Howard, Weber, Rachel, Karevan, Rod, Larson, Melissa C, Song, Honglin, Tessier, Daniel C, Bacot, François, Vincent, Daniel, Cunningham, Julie M, Dennis, Joe, Dicks, Ed, Australian Cancer Study, Australian Ovarian Cancer Study Group, Aben, Katja K, Anton-Culver, Hoda, Antonenkova, Natalia, Armasu, Sebastian M, Baglietto, Laura, Bandera, Elisa V, Beckmann, Matthias W, Birrer, Michael J, Bloom, Greg, Bogdanova, Natalia, Brenton, James D, Brinton, Louise A, Brooks-Wilson, Angela, Brown, Robert, Butzow, Ralf, Campbell, Ian, Carney, Michael E, Carvalho, Renato S, Chang-Claude, Jenny, Chen, Y Anne, Chen, Zhihua, Chow, Wong-Ho, Cicek, Mine S, Coetzee, Gerhard, Cook, Linda S, Cramer, Daniel W, Cybulski, Cezary, Dansonka-Mieszkowska, Agnieszka, Despierre, Evelyn, Doherty, Jennifer A, Dörk, Thilo, du Bois, Andreas, Dürst, Matthias, Eccles, Diana, Edwards, Robert, Ekici, Arif B, Fasching, Peter A, Fenstermacher, David, Flanagan, James, Gao, Yu-Tang, Garcia-Closas, Montserrat, Gentry-Maharaj, Aleksandra, Giles, Graham, Gjyshi, Anxhela, Gore, Martin, Gronwald, Jacek, Guo, Qi, Halle, Mari K, Harter, Philipp, Hein, Alexander, Heitz, Florian, Hillemanns, Peter, Hoatlin, Maureen, Høgdall, Estrid, Høgdall, Claus K, Hosono, Satoyo, Jakubowska, Anna, Jensen, Allan, Kalli, Kimberly R, Karlan, Beth Y, Kelemen, Linda E, Kiemeney, Lambertus A, Kjaer, Susanne Krüger, Konecny, Gottfried E, Krakstad, Camilla, Kupryjanczyk, Jolanta, Lambrechts, Diether, Lambrechts, Sandrina, Le, Nhu D, Lee, Nathan, Lee, Janet, Leminen, Arto, Lim, Boon Kiong, Lissowska, Jolanta, Lubiński, Jan, Lundvall, Lene, Lurie, Galina, and Massuger, Leon FAG

Subjects
Australian Cancer Study, Australian Ovarian Cancer Study Group, Humans, Cystadenocarcinoma, Serous, Ovarian Neoplasms, Neoplasm Invasiveness, Genetic Predisposition to Disease, Risk Factors, Case-Control Studies, Cooperative Behavior, Genotype, Polymorphism, Single Nucleotide, Female, Meta-Analysis as Topic, Genome-Wide Association Study, Genetic Loci, Gene-Environment Interaction, Cancer, Human Genome, Prevention, Genetics, Rare Diseases, Ovarian Cancer, Aetiology, 2.1 Biological and endogenous factors, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Genome-wide association studies (GWAS) have identified four susceptibility loci for epithelial ovarian cancer (EOC), with another two suggestive loci reaching near genome-wide significance. We pooled data from a GWAS conducted in North America with another GWAS from the UK. We selected the top 24,551 SNPs for inclusion on the iCOGS custom genotyping array. We performed follow-up genotyping in 18,174 individuals with EOC (cases) and 26,134 controls from 43 studies from the Ovarian Cancer Association Consortium. We validated the two loci at 3q25 and 17q21 that were previously found to have associations close to genome-wide significance and identified three loci newly associated with risk: two loci associated with all EOC subtypes at 8q21 (rs11782652, P = 5.5 × 10(-9)) and 10p12 (rs1243180, P = 1.8 × 10(-8)) and another locus specific to the serous subtype at 17q12 (rs757210, P = 8.1 × 10(-10)). An integrated molecular analysis of genes and regulatory regions at these loci provided evidence for functional mechanisms underlying susceptibility and implicated CHMP4C in the pathogenesis of ovarian cancer.

Published
2013

22. Identification and molecular characterization of a new ovarian cancer susceptibility locus at 17q21.31

Author

Permuth-Wey, Jennifer, Lawrenson, Kate, Shen, Howard C, Velkova, Aneliya, Tyrer, Jonathan P, Chen, Zhihua, Lin, Hui-Yi, Ann Chen, Y, Tsai, Ya-Yu, Qu, Xiaotao, Ramus, Susan J, Karevan, Rod, Lee, Janet, Lee, Nathan, Larson, Melissa C, Aben, Katja K, Anton-Culver, Hoda, Antonenkova, Natalia, Antoniou, Antonis C, Armasu, Sebastian M, Bacot, François, Baglietto, Laura, Bandera, Elisa V, Barnholtz-Sloan, Jill, Beckmann, Matthias W, Birrer, Michael J, Bloom, Greg, Bogdanova, Natalia, Brinton, Louise A, Brooks-Wilson, Angela, Brown, Robert, Butzow, Ralf, Cai, Qiuyin, Campbell, Ian, Chang-Claude, Jenny, Chanock, Stephen, Chenevix-Trench, Georgia, Cheng, Jin Q, Cicek, Mine S, Coetzee, Gerhard A, Cook, Linda S, Couch, Fergus J, Cramer, Daniel W, Cunningham, Julie M, Dansonka-Mieszkowska, Agnieszka, Despierre, Evelyn, Doherty, Jennifer A, Dörk, Thilo, du Bois, Andreas, Dürst, Matthias, Easton, Douglas F, Eccles, Diana, Edwards, Robert, Ekici, Arif B, Fasching, Peter A, Fenstermacher, David A, Flanagan, James M, Garcia-Closas, Montserrat, Gentry-Maharaj, Aleksandra, Giles, Graham G, Glasspool, Rosalind M, Gonzalez-Bosquet, Jesus, Goodman, Marc T, Gore, Martin, Górski, Bohdan, Gronwald, Jacek, Hall, Per, Halle, Mari K, Harter, Philipp, Heitz, Florian, Hillemanns, Peter, Hoatlin, Maureen, Høgdall, Claus K, Høgdall, Estrid, Hosono, Satoyo, Jakubowska, Anna, Jensen, Allan, Jim, Heather, Kalli, Kimberly R, Karlan, Beth Y, Kaye, Stanley B, Kelemen, Linda E, Kiemeney, Lambertus A, Kikkawa, Fumitaka, Konecny, Gottfried E, Krakstad, Camilla, Krüger Kjaer, Susanne, Kupryjanczyk, Jolanta, Lambrechts, Diether, Lambrechts, Sandrina, Lancaster, Johnathan M, Le, Nhu D, Leminen, Arto, Levine, Douglas A, Liang, Dong, Kiong Lim, Boon, Lin, Jie, Lissowska, Jolanta, Lu, Karen H, and Lubiński, Jan

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Prevention, Cancer, Ovarian Cancer, Biotechnology, Human Genome, Genetic Testing, Rare Diseases, Women's Health, Clinical Research, 2.1 Biological and endogenous factors, Carcinoma, Ovarian Epithelial, Chromosomes, Human, Pair 17, Female, Genetic Predisposition to Disease, Humans, Neoplasms, Glandular and Epithelial, Ovarian Neoplasms, Polymorphism, Single Nucleotide, Australian Cancer Study, Australian Ovarian Cancer Study, Consortium of Investigators of Modifiers of BRCA1/2
Abstract

Epithelial ovarian cancer (EOC) has a heritable component that remains to be fully characterized. Most identified common susceptibility variants lie in non-protein-coding sequences. We hypothesized that variants in the 3' untranslated region at putative microRNA (miRNA)-binding sites represent functional targets that influence EOC susceptibility. Here, we evaluate the association between 767 miRNA-related single-nucleotide polymorphisms (miRSNPs) and EOC risk in 18,174 EOC cases and 26,134 controls from 43 studies genotyped through the Collaborative Oncological Gene-environment Study. We identify several miRSNPs associated with invasive serous EOC risk (odds ratio=1.12, P=10(-8)) mapping to an inversion polymorphism at 17q21.31. Additional genotyping of non-miRSNPs at 17q21.31 reveals stronger signals outside the inversion (P=10(-10)). Variation at 17q21.31 is associated with neurological diseases, and our collaboration is the first to report an association with EOC susceptibility. An integrated molecular analysis in this region provides evidence for ARHGAP27 and PLEKHM1 as candidate EOC susceptibility genes.

Published
2013

23. A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11

Author

Siddiq, Afshan, Couch, Fergus J, Chen, Gary K, Lindström, Sara, Eccles, Diana, Millikan, Robert C, Michailidou, Kyriaki, Stram, Daniel O, Beckmann, Lars, Rhie, Suhn Kyong, Ambrosone, Christine B, Aittomäki, Kristiina, Amiano, Pilar, Apicella, Carmel, Investigators, Australian Breast Cancer Tissue Bank, Baglietto, Laura, Bandera, Elisa V, Beckmann, Matthias W, Berg, Christine D, Bernstein, Leslie, Blomqvist, Carl, Brauch, Hiltrud, Brinton, Louise, Bui, Quang M, Buring, Julie E, Buys, Saundra S, Campa, Daniele, Carpenter, Jane E, Chasman, Daniel I, Chang-Claude, Jenny, Chen, Constance, Clavel-Chapelon, Françoise, Cox, Angela, Cross, Simon S, Czene, Kamila, Deming, Sandra L, Diasio, Robert B, Diver, W Ryan, Dunning, Alison M, Durcan, Lorraine, Ekici, Arif B, Fasching, Peter A, Study, Familial Breast Cancer, Feigelson, Heather Spencer, Fejerman, Laura, Figueroa, Jonine D, Fletcher, Olivia, Flesch-Janys, Dieter, Gaudet, Mia M, Consortium, The GENICA, Gerty, Susan M, Rodriguez-Gil, Jorge L, Giles, Graham G, van Gils, Carla H, Godwin, Andrew K, Graham, Nikki, Greco, Dario, Hall, Per, Hankinson, Susan E, Hartmann, Arndt, Hein, Rebecca, Heinz, Judith, Hoover, Robert N, Hopper, John L, Hu, Jennifer J, Huntsman, Scott, Ingles, Sue A, Irwanto, Astrid, Isaacs, Claudine, Jacobs, Kevin B, John, Esther M, Justenhoven, Christina, Kaaks, Rudolf, Kolonel, Laurence N, Coetzee, Gerhard A, Lathrop, Mark, Le Marchand, Loic, Lee, Adam M, Lee, I-Min, Lesnick, Timothy, Lichtner, Peter, Liu, Jianjun, Lund, Eiliv, Makalic, Enes, Martin, Nicholas G, McLean, Catriona A, Meijers-Heijboer, Hanne, Meindl, Alfons, Miron, Penelope, Monroe, Kristine R, Montgomery, Grant W, Müller-Myhsok, Bertram, Nickels, Stefan, Nyante, Sarah J, Olswold, Curtis, Overvad, Kim, Palli, Domenico, Park, Daniel J, Palmer, Julie R, and Pathak, Harsh

Subjects
Biological Sciences, Genetics, Human Genome, Cancer Genomics, Cancer, Aging, Prevention, Women's Health, Breast Cancer, 2.1 Biological and endogenous factors, Breast Neoplasms, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide, Receptors, Estrogen, Australian Breast Cancer Tissue Bank Investigators, Familial Breast Cancer Study, GENICA Consortium, Medical and Health Sciences, Genetics & Heredity
Abstract

Genome-wide association studies (GWAS) of breast cancer defined by hormone receptor status have revealed loci contributing to susceptibility of estrogen receptor (ER)-negative subtypes. To identify additional genetic variants for ER-negative breast cancer, we conducted the largest meta-analysis of ER-negative disease to date, comprising 4754 ER-negative cases and 31 663 controls from three GWAS: NCI Breast and Prostate Cancer Cohort Consortium (BPC3) (2188 ER-negative cases; 25 519 controls of European ancestry), Triple Negative Breast Cancer Consortium (TNBCC) (1562 triple negative cases; 3399 controls of European ancestry) and African American Breast Cancer Consortium (AABC) (1004 ER-negative cases; 2745 controls). We performed in silico replication of 86 SNPs at P ≤ 1 × 10(-5) in an additional 11 209 breast cancer cases (946 with ER-negative disease) and 16 057 controls of Japanese, Latino and European ancestry. We identified two novel loci for breast cancer at 20q11 and 6q14. SNP rs2284378 at 20q11 was associated with ER-negative breast cancer (combined two-stage OR = 1.16; P = 1.1 × 10(-8)) but showed a weaker association with overall breast cancer (OR = 1.08, P = 1.3 × 10(-6)) based on 17 869 cases and 43 745 controls and no association with ER-positive disease (OR = 1.01, P = 0.67) based on 9965 cases and 22 902 controls. Similarly, rs17530068 at 6q14 was associated with breast cancer (OR = 1.12; P = 1.1 × 10(-9)), and with both ER-positive (OR = 1.09; P = 1.5 × 10(-5)) and ER-negative (OR = 1.16, P = 2.5 × 10(-7)) disease. We also confirmed three known loci associated with ER-negative (19p13) and both ER-negative and ER-positive breast cancer (6q25 and 12p11). Our results highlight the value of large-scale collaborative studies to identify novel breast cancer risk loci.

Published
2012

24. Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

Author

Tewari, Alok K, Yardimci, Galip, Shibata, Yoichiro, Sheffield, Nathan C, Song, Lingyun, Taylor, Barry S, Georgiev, Stoyan G, Coetzee, Gerhard A, Ohler, Uwe, Furey, Terrence S, Crawford, Gregory E, and Febbo, Phillip G

Abstract

Abstract Background Epigenetic mechanisms such as chromatin accessibility impact transcription factor binding to DNA and transcriptional specificity. The androgen receptor (AR), a master regulator of the male phenotype and prostate cancer pathogenesis, acts primarily through ligand-activated transcription of target genes. Although several determinants of AR transcriptional specificity have been elucidated, our understanding of the interplay between chromatin accessibility and AR function remains incomplete. Results We used deep sequencing to assess chromatin structure via DNase I hypersensitivity and mRNA abundance, and paired these datasets with three independent AR ChIP-seq datasets. Our analysis revealed qualitative and quantitative differences in chromatin accessibility that corresponded to both AR binding and an enrichment of motifs for potential collaborating factors, one of which was identified as SP1. These quantitative differences were significantly associated with AR-regulated mRNA transcription across the genome. Base-pair resolution of the DNase I cleavage profile revealed three distinct footprinting patterns associated with the AR-DNA interaction, suggesting multiple modes of AR interaction with the genome. Conclusions In contrast with other DNA-binding factors, AR binding to the genome does not only target regions that are accessible to DNase I cleavage prior to hormone induction. AR binding is invariably associated with an increase in chromatin accessibility and, consequently, changes in gene expression. Furthermore, we present the first in vivo evidence that a significant fraction of AR binds only to half of the full AR DNA motif. These findings indicate a dynamic quantitative relationship between chromatin structure and AR-DNA binding that impacts AR transcriptional specificity.

Published
2012

28. Supplementary Table S3 from Characterizing Genetic Susceptibility to Breast Cancer in Women of African Ancestry

Author

Feng, Ye, primary, Rhie, Suhn Kyong, primary, Huo, Dezheng, primary, Ruiz-Narvaez, Edward A., primary, Haddad, Stephen A., primary, Ambrosone, Christine B., primary, John, Esther M., primary, Bernstein, Leslie, primary, Zheng, Wei, primary, Hu, Jennifer J., primary, Ziegler, Regina G., primary, Nyante, Sarah, primary, Bandera, Elisa V., primary, Ingles, Sue A., primary, Press, Michael F., primary, Deming, Sandra L., primary, Rodriguez-Gil, Jorge L., primary, Zheng, Yonglan, primary, Yao, Song, primary, Han, Yoo-Jeong, primary, Ogundiran, Temidayo O., primary, Rebbeck, Timothy R., primary, Adebamowo, Clement, primary, Ojengbede, Oladosu, primary, Falusi, Adeyinka G., primary, Hennis, Anselm, primary, Nemesure, Barbara, primary, Ambs, Stefan, primary, Blot, William, primary, Cai, Qiuyin, primary, Signorello, Lisa, primary, Nathanson, Katherine L., primary, Lunetta, Kathryn L., primary, Sucheston-Campbell, Lara E., primary, Bensen, Jeannette T., primary, Chanock, Stephen J., primary, Marchand, Loic Le, primary, Olshan, Andrew F., primary, Kolonel, Laurence N., primary, Conti, David V., primary, Coetzee, Gerhard A., primary, Stram, Daniel O., primary, Olopade, Olufunmilayo I., primary, Palmer, Julie R., primary, and Haiman, Christopher A., primary

Published
2023
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29. Supplementary Methods and Tables from The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers

Author

Amos, Christopher I., primary, Dennis, Joe, primary, Wang, Zhaoming, primary, Byun, Jinyoung, primary, Schumacher, Fredrick R., primary, Gayther, Simon A., primary, Casey, Graham, primary, Hunter, David J., primary, Sellers, Thomas A., primary, Gruber, Stephen B., primary, Dunning, Alison M., primary, Michailidou, Kyriaki, primary, Fachal, Laura, primary, Doheny, Kimberly, primary, Spurdle, Amanda B., primary, Li, Yafang, primary, Xiao, Xiangjun, primary, Romm, Jane, primary, Pugh, Elizabeth, primary, Coetzee, Gerhard A., primary, Hazelett, Dennis J., primary, Bojesen, Stig E., primary, Caga-Anan, Charlisse, primary, Haiman, Christopher A., primary, Kamal, Ahsan, primary, Luccarini, Craig, primary, Tessier, Daniel, primary, Vincent, Daniel, primary, Bacot, François, primary, Van Den Berg, David J., primary, Nelson, Stefanie, primary, Demetriades, Stephen, primary, Goldgar, David E., primary, Couch, Fergus J., primary, Forman, Judith L., primary, Giles, Graham G., primary, Conti, David V., primary, Bickeböller, Heike, primary, Risch, Angela, primary, Waldenberger, Melanie, primary, Brüske-Hohlfeld, Irene, primary, Hicks, Belynda D., primary, Ling, Hua, primary, McGuffog, Lesley, primary, Lee, Andrew, primary, Kuchenbaecker, Karoline, primary, Soucy, Penny, primary, Manz, Judith, primary, Cunningham, Julie M., primary, Butterbach, Katja, primary, Kote-Jarai, Zsofia, primary, Kraft, Peter, primary, FitzGerald, Liesel, primary, Lindström, Sara, primary, Adams, Marcia, primary, McKay, James D., primary, Phelan, Catherine M., primary, Benlloch, Sara, primary, Kelemen, Linda E., primary, Brennan, Paul, primary, Riggan, Marjorie, primary, O'Mara, Tracy A., primary, Shen, Hongbing, primary, Shi, Yongyong, primary, Thompson, Deborah J., primary, Goodman, Marc T., primary, Nielsen, Sune F., primary, Berchuck, Andrew, primary, Laboissiere, Sylvie, primary, Schmit, Stephanie L., primary, Shelford, Tameka, primary, Edlund, Christopher K., primary, Taylor, Jack A., primary, Field, John K., primary, Park, Sue K., primary, Offit, Kenneth, primary, Thomassen, Mads, primary, Schmutzler, Rita, primary, Ottini, Laura, primary, Hung, Rayjean J., primary, Marchini, Jonathan, primary, Amin Al Olama, Ali, primary, Peters, Ulrike, primary, Eeles, Rosalind A., primary, Seldin, Michael F., primary, Gillanders, Elizabeth, primary, Seminara, Daniela, primary, Antoniou, Antonis C., primary, Pharoah, Paul D.P., primary, Chenevix-Trench, Georgia, primary, Chanock, Stephen J., primary, Simard, Jacques, primary, and Easton, Douglas F., primary

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2023
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30. Supplementary Fig Leg from Characterizing Genetic Susceptibility to Breast Cancer in Women of African Ancestry

Author

Feng, Ye, primary, Rhie, Suhn Kyong, primary, Huo, Dezheng, primary, Ruiz-Narvaez, Edward A., primary, Haddad, Stephen A., primary, Ambrosone, Christine B., primary, John, Esther M., primary, Bernstein, Leslie, primary, Zheng, Wei, primary, Hu, Jennifer J., primary, Ziegler, Regina G., primary, Nyante, Sarah, primary, Bandera, Elisa V., primary, Ingles, Sue A., primary, Press, Michael F., primary, Deming, Sandra L., primary, Rodriguez-Gil, Jorge L., primary, Zheng, Yonglan, primary, Yao, Song, primary, Han, Yoo-Jeong, primary, Ogundiran, Temidayo O., primary, Rebbeck, Timothy R., primary, Adebamowo, Clement, primary, Ojengbede, Oladosu, primary, Falusi, Adeyinka G., primary, Hennis, Anselm, primary, Nemesure, Barbara, primary, Ambs, Stefan, primary, Blot, William, primary, Cai, Qiuyin, primary, Signorello, Lisa, primary, Nathanson, Katherine L., primary, Lunetta, Kathryn L., primary, Sucheston-Campbell, Lara E., primary, Bensen, Jeannette T., primary, Chanock, Stephen J., primary, Marchand, Loic Le, primary, Olshan, Andrew F., primary, Kolonel, Laurence N., primary, Conti, David V., primary, Coetzee, Gerhard A., primary, Stram, Daniel O., primary, Olopade, Olufunmilayo I., primary, Palmer, Julie R., primary, and Haiman, Christopher A., primary

Published
2023
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31. Supplementary Table 5 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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32. Supplementary Figures 1-4 and extended methods from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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33. Supplementary Table 3 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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34. Supplementary Figure S2 from Characterizing Genetic Susceptibility to Breast Cancer in Women of African Ancestry

Author

Feng, Ye, primary, Rhie, Suhn Kyong, primary, Huo, Dezheng, primary, Ruiz-Narvaez, Edward A., primary, Haddad, Stephen A., primary, Ambrosone, Christine B., primary, John, Esther M., primary, Bernstein, Leslie, primary, Zheng, Wei, primary, Hu, Jennifer J., primary, Ziegler, Regina G., primary, Nyante, Sarah, primary, Bandera, Elisa V., primary, Ingles, Sue A., primary, Press, Michael F., primary, Deming, Sandra L., primary, Rodriguez-Gil, Jorge L., primary, Zheng, Yonglan, primary, Yao, Song, primary, Han, Yoo-Jeong, primary, Ogundiran, Temidayo O., primary, Rebbeck, Timothy R., primary, Adebamowo, Clement, primary, Ojengbede, Oladosu, primary, Falusi, Adeyinka G., primary, Hennis, Anselm, primary, Nemesure, Barbara, primary, Ambs, Stefan, primary, Blot, William, primary, Cai, Qiuyin, primary, Signorello, Lisa, primary, Nathanson, Katherine L., primary, Lunetta, Kathryn L., primary, Sucheston-Campbell, Lara E., primary, Bensen, Jeannette T., primary, Chanock, Stephen J., primary, Marchand, Loic Le, primary, Olshan, Andrew F., primary, Kolonel, Laurence N., primary, Conti, David V., primary, Coetzee, Gerhard A., primary, Stram, Daniel O., primary, Olopade, Olufunmilayo I., primary, Palmer, Julie R., primary, and Haiman, Christopher A., primary

Published
2023
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35. Data from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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36. Supplementary Table 1 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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37. Supplementary Table 2 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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38. Supplementary Table 4 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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39. Data from Androgen Receptor Inhibits Estrogen Receptor-α Activity and Is Prognostic in Breast Cancer

Author

Peters, Amelia A., primary, Buchanan, Grant, primary, Ricciardelli, Carmela, primary, Bianco-Miotto, Tina, primary, Centenera, Margaret M., primary, Harris, Jonathan M., primary, Jindal, Shalini, primary, Segara, Davendra, primary, Jia, Li, primary, Moore, Nicole L., primary, Henshall, Susan M., primary, Birrell, Stephen N., primary, Coetzee, Gerhard A., primary, Sutherland, Robert L., primary, Butler, Lisa M., primary, and Tilley, Wayne D., primary

Published
2023
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40. Data from Control of Androgen Receptor Signaling in Prostate Cancer by the Cochaperone Small Glutamine–Rich Tetratricopeptide Repeat Containing Protein α

Author

Buchanan, Grant, primary, Ricciardelli, Carmela, primary, Harris, Jonathan M., primary, Prescott, Jennifer, primary, Yu, Zoe Chiao-Li, primary, Jia, Li, primary, Butler, Lisa M., primary, Marshall, Villis R., primary, Scher, Howard I., primary, Gerald, William L., primary, Coetzee, Gerhard A., primary, and Tilley, Wayne D., primary

Published
2023
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41. Supplementary Tables 1-3 from Androgen Receptor Inhibits Estrogen Receptor-α Activity and Is Prognostic in Breast Cancer

Author

Peters, Amelia A., primary, Buchanan, Grant, primary, Ricciardelli, Carmela, primary, Bianco-Miotto, Tina, primary, Centenera, Margaret M., primary, Harris, Jonathan M., primary, Jindal, Shalini, primary, Segara, Davendra, primary, Jia, Li, primary, Moore, Nicole L., primary, Henshall, Susan M., primary, Birrell, Stephen N., primary, Coetzee, Gerhard A., primary, Sutherland, Robert L., primary, Butler, Lisa M., primary, and Tilley, Wayne D., primary

Published
2023
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42. Supplementary Data 1-4 from Control of Androgen Receptor Signaling in Prostate Cancer by the Cochaperone Small Glutamine–Rich Tetratricopeptide Repeat Containing Protein α

Author

Buchanan, Grant, primary, Ricciardelli, Carmela, primary, Harris, Jonathan M., primary, Prescott, Jennifer, primary, Yu, Zoe Chiao-Li, primary, Jia, Li, primary, Butler, Lisa M., primary, Marshall, Villis R., primary, Scher, Howard I., primary, Gerald, William L., primary, Coetzee, Gerhard A., primary, and Tilley, Wayne D., primary

Published
2023
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44. Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

Author

Fernandez-Rozadilla, Ceres, primary, Timofeeva, Maria, additional, Chen, Zhishan, additional, Law, Philip, additional, Thomas, Minta, additional, Schmit, Stephanie, additional, Díez-Obrero, Virginia, additional, Hsu, Li, additional, Fernandez-Tajes, Juan, additional, Palles, Claire, additional, Sherwood, Kitty, additional, Briggs, Sarah, additional, Svinti, Victoria, additional, Donnelly, Kevin, additional, Farrington, Susan, additional, Blackmur, James, additional, Vaughan-Shaw, Peter, additional, Shu, Xiao-ou, additional, Long, Jirong, additional, Cai, Qiuyin, additional, Guo, Xingyi, additional, Lu, Yingchang, additional, Broderick, Peter, additional, Studd, James, additional, Huyghe, Jeroen, additional, Harrison, Tabitha, additional, Conti, David, additional, Dampier, Christopher, additional, Devall, Mathew, additional, Schumacher, Fredrick, additional, Melas, Marilena, additional, Rennert, Gad, additional, Obón-Santacana, Mireia, additional, Martín-Sánchez, Vicente, additional, Moratalla-Navarro, Ferran, additional, Oh, Jae Hwan, additional, Kim, Jeongseon, additional, Jee, Sun Ha, additional, Jung, Keum Ji, additional, Kweon, Sun-Seog, additional, Shin, Min-Ho, additional, Shin, Aesun, additional, Ahn, Yoon-Ok, additional, Kim, Dong-Hyun, additional, Oze, Isao, additional, Wen, Wanqing, additional, Matsuo, Keitaro, additional, Matsuda, Koichi, additional, Tanikawa, Chizu, additional, Ren, Zefang, additional, Gao, Yu-Tang, additional, Jia, Wei-Hua, additional, Hopper, John, additional, Jenkins, Mark, additional, Win, Aung Ko, additional, Pai, Rish, additional, Figueiredo, Jane, additional, Haile, Robert, additional, Gallinger, Steven, additional, Woods, Michael, additional, Newcomb, Polly, additional, Duggan, David, additional, Cheadle, Jeremy, additional, Kaplan, Richard, additional, Maughan, Timothy, additional, Kerr, Rachel, additional, Kerr, David, additional, Kirac, Iva, additional, Böhm, Jan, additional, Mecklin, Lukka-Pekka, additional, Jousilahti, Pekka, additional, Knekt, Paul, additional, Aaltonen, Lauri, additional, Rissanen, Harri, additional, Pukkala, Eero, additional, Eriksson, Johan, additional, Cajuso, Tatiana, additional, Hänninen, Ulrika, additional, Kondelin, Johanna, additional, Palin, Kimmo, additional, Tanskanen, Tomas, additional, Renkonen-Sinisalo, Laura, additional, Zanke, Brent, additional, Männistö, Satu, additional, Albanes, Demetrius, additional, Weinstein, Stephanie, additional, Ruiz-Narvaez, Edward, additional, Palmer, Julie, additional, Buchanan, Daniel, additional, Platz, Elizabeth, additional, Visvanathan, Kala, additional, Ulrich, Cornelia, additional, Siegel, Erin, additional, Brezina, Stefanie, additional, Gsur, Andrea, additional, Campbell, Peter, additional, Chang-Claude, Jenny, additional, Hoffmeister, Michael, additional, Brenner, Hermann, additional, Slattery, Martha, additional, Potter, John, additional, Tsilidis, Konstantinos, additional, Schulze, Matthias, additional, Gunter, Marc, additional, Murphy, Neil, additional, Castells, Antoni, additional, Castellví-Bel, Sergi, additional, Moreira, Leticia, additional, Arndt, Volker, additional, Shcherbina, Anna, additional, Stern, Mariana, additional, Pardamean, Bens, additional, Bishop, Timothy, additional, Giles, Graham, additional, Southey, Melissa, additional, Idos, Gregory, additional, McDonnell, Kevin, additional, Abu-Ful, Zomoroda, additional, Greenson, Joel, additional, Shulman, Katerina, additional, Lejbkowicz, Flavio, additional, Offit, Kenneth, additional, Su, Yu-Ru, additional, Steinfelder, Robert, additional, Keku, Temitope, additional, van Guelpen, Bethany, additional, Hudson, Thomas, additional, Hampel, Heather, additional, Pearlman, Rachel, additional, Berndt, Sonja, additional, Hayes, Richard, additional, Martinez, Marie Elena, additional, Thomas, Sushma, additional, Corley, Douglas, additional, Pharoah, Paul, additional, Larsson, Susanna, additional, Yen, Yun, additional, Lenz, Heinz-Josef, additional, White, Emily, additional, Li, Li, additional, Doheny, Kimberly, additional, Pugh, Elizabeth, additional, Shelford, Tameka, additional, Chan, Andrew, additional, Cruz-Correa, Marcia, additional, Lindblom, Annika, additional, Hunter, David, additional, Joshi, Amit, additional, Schafmayer, Clemens, additional, Scacheri, Peter, additional, Kundaje, Anshul, additional, Nickerson, Deborah, additional, Schoen, Robert, additional, Hampe, Jochen, additional, Stadler, Zsofia, additional, Vodicka, Pavel, additional, Vodickova, Ludmila, additional, Vymetalkova, Veronika, additional, Papadopoulos, Nickolas, additional, Edlund, Chistopher, additional, Gauderman, William, additional, Thomas, Duncan, additional, Shibata, David, additional, Toland, Amanda, additional, Markowitz, Sanford, additional, Kim, Andre, additional, Chanock, Stephen, additional, van Duijnhoven, Franzel, additional, Feskens, Edith, additional, Sakoda, Lori, additional, Gago-Dominguez, Manuela, additional, Wolk, Alicja, additional, Naccarati, Alessio, additional, Pardini, Barbara, additional, FitzGerald, Liesel, additional, Lee, Soo Chin, additional, Ogino, Shuji, additional, Bien, Stephanie, additional, Kooperberg, Charles, additional, Li, Christopher, additional, Lin, Yi, additional, Prentice, Ross, additional, Qu, Conghui, additional, Bézieau, Stéphane, additional, Tangen, Catherine, additional, Mardis, Elaine, additional, Yamaji, Taiki, additional, Sawada, Norie, additional, Iwasaki, Motoki, additional, Haiman, Christopher, additional, Le Marchand, Loic, additional, Wu, Anna, additional, Qu, Chenxu, additional, McNeil, Caroline, additional, Coetzee, Gerhard, additional, Hayward, Caroline, additional, Deary, Ian, additional, Harris, Sarah, additional, Theodoratou, Evropi, additional, Reid, Stuart, additional, Walker, Marion, additional, Ooi, Li Yin, additional, Moreno, Victor, additional, Casey, Graham, additional, Gruber, Stephen, additional, Tomlinson, Ian, additional, Zheng, Wei, additional, Dunlop, Malcolm, additional, Houlston, Richard, additional, and Peters, Ulrike, additional

Published
2022
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