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1. A PSA SNP associates with cellular function and clinical outcome in men with prostate cancer

Author: Srilakshmi Srinivasan, Thomas Kryza, Nathalie Bock, Brian W. C. Tse, Kamil A. Sokolowski, Panchadsaram Janaththani, Achala Fernando, Leire Moya, Carson Stephens, Ying Dong, Joan Röhl, Saeid Alinezhad, Ian Vela, Joanna L. Perry-Keene, Katie Buzacott, Robert Nica, The IMPACT Study, Manuela Gago-Dominguez, The PROFILE Study Steering Committee, Johanna Schleutker, Christiane Maier, Kenneth Muir, Catherine M. Tangen, Henrik Gronberg, Nora Pashayan, Demetrius Albanes, Alicja Wolk, Janet L. Stanford, Sonja I. Berndt, Lorelei A. Mucci, Stella Koutros, Olivier Cussenot, Karina Dalsgaard Sorensen, Eli Marie Grindedal, Ruth C. Travis, Christopher A. Haiman, Robert J. MacInnis, Ana Vega, Fredrik Wiklund, David E. Neal, Manolis Kogevinas, Kathryn L. Penney, Børge G. Nordestgaard, Hermann Brenner, Esther M. John, Marija Gamulin, Frank Claessens, Olle Melander, Anders Dahlin, Pär Stattin, Göran Hallmans, Christel Häggström, Robert Johansson, Elin Thysell, Ann-Charlotte Rönn, Weiqiang Li, Nigel Brown, Goce Dimeski, Benjamin Shepherd, Tokhir Dadaev, Mark N. Brook, Amanda B. Spurdle, Ulf-Håkan Stenman, Hannu Koistinen, Zsofia Kote-Jarai, Robert J. Klein, Hans Lilja, Rupert C. Ecker, Rosalind Eeles, The Practical Consortium, The Australian Prostate Cancer BioResource, Judith Clements, and Jyotsna Batra
Subjects: Science
Abstract: Abstract Genetic variation at the 19q13.3 KLK locus is linked with prostate cancer susceptibility in men. The non-synonymous KLK3 single nucleotide polymorphism (SNP), rs17632542 (c.536 T > C; Ile163Thr-substitution in PSA) is associated with reduced prostate cancer risk, however, the functional relevance is unknown. Here, we identify that the SNP variant-induced change in PSA biochemical activity mediates prostate cancer pathogenesis. The ‘Thr’ PSA variant leads to small subcutaneous tumours, supporting reduced prostate cancer risk. However, ‘Thr’ PSA also displays higher metastatic potential with pronounced osteolytic activity in an experimental metastasis in-vivo model. Biochemical characterisation of this PSA variant demonstrates markedly reduced proteolytic activity that correlates with differences in in-vivo tumour burden. The SNP is associated with increased risk for aggressive disease and prostate cancer-specific mortality in three independent cohorts, highlighting its critical function in mediating metastasis. Carriers of this SNP allele have reduced serum total PSA and a higher free/total PSA ratio that could contribute to late biopsy decisions and delay in diagnosis. Our results provide a molecular explanation for the prominent 19q13.3 KLK locus, rs17632542 SNP, association with a spectrum of prostate cancer clinical outcomes.
Published: 2024
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2. Detection of differentially methylated CpGs between tumour and adjacent benign cells in diagnostic prostate cancer samples

Author: Liesel M. FitzGerald, Chol-hee Jung, Ee Ming Wong, JiHoon E. Joo, Julie K. Bassett, James G. Dowty, Xiaoyu Wang, James Y. Dai, Janet L. Stanford, Neil O’Callaghan, Tim Nottle, John Pedersen, Graham G. Giles, and Melissa C. Southey
Subjects: Medicine, Science
Abstract: Abstract Differentially methylated CpG sites (dmCpGs) that distinguish prostate tumour from adjacent benign tissue could aid in the diagnosis and prognosis of prostate cancer. Previously, the identification of such dmCpGs has only been undertaken in radical prostatectomy (RP) samples and not primary diagnostic tumour samples (needle biopsy or transurethral resection of the prostate). We interrogated an Australian dataset comprising 125 tumour and 43 adjacent histologically benign diagnostic tissue samples, including 41 paired samples, using the Infinium Human Methylation450 BeadChip. Regression analyses of paired tumour and adjacent benign samples identified 2,386 significant dmCpGs (Bonferroni p
Published: 2024
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3. Cluster effect for SNP–SNP interaction pairs for predicting complex traits

Author: Hui-Yi Lin, Harun Mazumder, Indrani Sarkar, Po-Yu Huang, Rosalind A. Eeles, Zsofia Kote-Jarai, Kenneth R. Muir, UKGPCS collaborators, Johanna Schleutker, Nora Pashayan, Jyotsna Batra, APCB (Australian Prostate Cancer BioResource), David E. Neal, Sune F. Nielsen, Børge G. Nordestgaard, Henrik Grönberg, Fredrik Wiklund, Robert J. MacInnis, Christopher A. Haiman, Ruth C. Travis, Janet L. Stanford, Adam S. Kibel, Cezary Cybulski, Kay-Tee Khaw, Christiane Maier, Stephen N. Thibodeau, Manuel R. Teixeira, Lisa Cannon-Albright, Hermann Brenner, Radka Kaneva, Hardev Pandha, The PRACTICAL consortium, and Jong Y. Park
Subjects: SNP interaction, Cluster, False positivity, Simulation, Medicine, Science
Abstract: Abstract Single nucleotide polymorphism (SNP) interactions are the key to improving polygenic risk scores. Previous studies reported several significant SNP–SNP interaction pairs that shared a common SNP to form a cluster, but some identified pairs might be false positives. This study aims to identify factors associated with the cluster effect of false positivity and develop strategies to enhance the accuracy of SNP–SNP interactions. The results showed the cluster effect is a major cause of false-positive findings of SNP–SNP interactions. This cluster effect is due to high correlations between a causal pair and null pairs in a cluster. The clusters with a hub SNP with a significant main effect and a large minor allele frequency (MAF) tended to have a higher false-positive rate. In addition, peripheral null SNPs in a cluster with a small MAF tended to enhance false positivity. We also demonstrated that using the modified significance criterion based on the 3 p-value rules and the bootstrap approach (3pRule + bootstrap) can reduce false positivity and maintain high true positivity. In addition, our results also showed that a pair without a significant main effect tends to have weak or no interaction. This study identified the cluster effect and suggested using the 3pRule + bootstrap approach to enhance SNP–SNP interaction detection accuracy.
Published: 2024
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4. KLK3 SNP–SNP interactions for prediction of prostate cancer aggressiveness

Author: Hui-Yi Lin, Po-Yu Huang, Chia-Ho Cheng, Heng-Yuan Tung, Zhide Fang, Anders E. Berglund, Ann Chen, Jennifer French-Kwawu, Darian Harris, Julio Pow-Sang, Kosj Yamoah, John L. Cleveland, Shivanshu Awasthi, Robert J. Rounbehler, Travis Gerke, Jasreman Dhillon, Rosalind Eeles, Zsofia Kote-Jarai, Kenneth Muir, UKGPCS collaborators, Johanna Schleutker, Nora Pashayan, APCB (Australian Prostate Cancer BioResource), David E. Neal, Sune F. Nielsen, Børge G. Nordestgaard, Henrik Gronberg, Fredrik Wiklund, Graham G. Giles, Christopher A. Haiman, Ruth C. Travis, Janet L. Stanford, Adam S. Kibel, Cezary Cybulski, Kay-Tee Khaw, Christiane Maier, Stephen N. Thibodeau, Manuel R. Teixeira, Lisa Cannon-Albright, Hermann Brenner, Radka Kaneva, Hardev Pandha, The PRACTICAL consortium, Srilakshmi Srinivasan, Judith Clements, Jyotsna Batra, and Jong Y. Park
Subjects: Medicine, Science
Abstract: Abstract Risk classification for prostate cancer (PCa) aggressiveness and underlying mechanisms remain inadequate. Interactions between single nucleotide polymorphisms (SNPs) may provide a solution to fill these gaps. To identify SNP–SNP interactions in the four pathways (the angiogenesis-, mitochondria-, miRNA-, and androgen metabolism-related pathways) associated with PCa aggressiveness, we tested 8587 SNPs for 20,729 cases from the PCa consortium. We identified 3 KLK3 SNPs, and 1083 (P
Published: 2021
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5. Polygenic hazard score is associated with prostate cancer in multi-ethnic populations

Author: Minh-Phuong Huynh-Le, Chun Chieh Fan, Roshan Karunamuni, Wesley K. Thompson, Maria Elena Martinez, Rosalind A. Eeles, Zsofia Kote-Jarai, Kenneth Muir, Johanna Schleutker, Nora Pashayan, Jyotsna Batra, Henrik Grönberg, David E. Neal, Jenny L. Donovan, Freddie C. Hamdy, Richard M. Martin, Sune F. Nielsen, Børge G. Nordestgaard, Fredrik Wiklund, Catherine M. Tangen, Graham G. Giles, Alicja Wolk, Demetrius Albanes, Ruth C. Travis, William J. Blot, Wei Zheng, Maureen Sanderson, Janet L. Stanford, Lorelei A. Mucci, Catharine M. L. West, Adam S. Kibel, Olivier Cussenot, Sonja I. Berndt, Stella Koutros, Karina Dalsgaard Sørensen, Cezary Cybulski, Eli Marie Grindedal, Florence Menegaux, Kay-Tee Khaw, Jong Y. Park, Sue A. Ingles, Christiane Maier, Robert J. Hamilton, Stephen N. Thibodeau, Barry S. Rosenstein, Yong-Jie Lu, Stephen Watya, Ana Vega, Manolis Kogevinas, Kathryn L. Penney, Chad Huff, Manuel R. Teixeira, Luc Multigner, Robin J. Leach, Lisa Cannon-Albright, Hermann Brenner, Esther M. John, Radka Kaneva, Christopher J. Logothetis, Susan L. Neuhausen, Kim De Ruyck, Hardev Pandha, Azad Razack, Lisa F. Newcomb, Jay H. Fowke, Marija Gamulin, Nawaid Usmani, Frank Claessens, Manuela Gago-Dominguez, Paul A. Townsend, William S. Bush, Monique J. Roobol, Marie-Élise Parent, Jennifer J. Hu, Ian G. Mills, Ole A. Andreassen, Anders M. Dale, Tyler M. Seibert, UKGPCS collaborators, APCB (Australian Prostate Cancer BioResource), NC-LA PCaP Investigators, The IMPACT Study Steering Committee and Collaborators, Canary PASS Investigators, The Profile Study Steering Committee, and The PRACTICAL Consortium
Subjects: Science
Abstract: A polygenic hazard score (PHS1) improves prostate cancer screening accuracy in European patients. Here, the authors test the performance of a version compatible with OncoArray genotypes (PHS2) in a multi-ethnic dataset and find that it risk-stratifies men for any, aggressive, and fatal prostate cancer.
Published: 2021
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6. An integrative multi-omics analysis to identify candidate DNA methylation biomarkers related to prostate cancer risk

Author: Lang Wu, Yaohua Yang, Xingyi Guo, Xiao-Ou Shu, Qiuyin Cai, Xiang Shu, Bingshan Li, Ran Tao, Chong Wu, Jason B. Nikas, Yanfa Sun, Jingjing Zhu, Monique J. Roobol, Graham G. Giles, Hermann Brenner, Esther M. John, Judith Clements, Eli Marie Grindedal, Jong Y. Park, Janet L. Stanford, Zsofia Kote-Jarai, Christopher A. Haiman, Rosalind A. Eeles, Wei Zheng, Jirong Long, The PRACTICAL consortium, CRUK Consortium, BPC3 Consortium, CAPS Consortium, and PEGASUS Consortium
Subjects: Science
Abstract: Genome wide association studies have identified multiple loci associated with risk of developing prostate cancer but the functional significance of many of these are unknown. Here, after generating models to predict methylation, the authors identify CpG methylation sites associated with prostate cancer.
Published: 2020
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7. Genetic factors associated with prostate cancer conversion from active surveillance to treatment

Author: Yu Jiang, Travis J. Meyers, Adaeze A. Emeka, Lauren Folgosa Cooley, Phillip R. Cooper, Nicola Lancki, Irene Helenowski, Linda Kachuri, Daniel W. Lin, Janet L. Stanford, Lisa F. Newcomb, Suzanne Kolb, Antonio Finelli, Neil E. Fleshner, Maria Komisarenko, James A. Eastham, Behfar Ehdaie, Nicole Benfante, Christopher J. Logothetis, Justin R. Gregg, Cherie A. Perez, Sergio Garza, Jeri Kim, Leonard S. Marks, Merdie Delfin, Danielle Barsa, Danny Vesprini, Laurence H. Klotz, Andrew Loblaw, Alexandre Mamedov, S. Larry Goldenberg, Celestia S. Higano, Maria Spillane, Eugenia Wu, H. Ballentine Carter, Christian P. Pavlovich, Mufaddal Mamawala, Tricia Landis, Peter R. Carroll, June M. Chan, Matthew R. Cooperberg, Janet E. Cowan, Todd M. Morgan, Javed Siddiqui, Rabia Martin, Eric A. Klein, Karen Brittain, Paige Gotwald, Daniel A. Barocas, Jeremiah R. Dallmer, Jennifer B. Gordetsky, Pam Steele, Shilajit D. Kundu, Jazmine Stockdale, Monique J. Roobol, Lionne D.F. Venderbos, Martin G. Sanda, Rebecca Arnold, Dattatraya Patil, Christopher P. Evans, Marc A. Dall’Era, Anjali Vij, Anthony J. Costello, Ken Chow, Niall M. Corcoran, Soroush Rais-Bahrami, Courtney Phares, Douglas S. Scherr, Thomas Flynn, R. Jeffrey Karnes, Michael Koch, Courtney Rose Dhondt, Joel B. Nelson, Dawn McBride, Michael S. Cookson, Kelly L. Stratton, Stephen Farriester, Erin Hemken, Walter M. Stadler, Tuula Pera, Deimante Banionyte, Fernando J. Bianco, Jr., Isabel H. Lopez, Stacy Loeb, Samir S. Taneja, Nataliya Byrne, Christopher L. Amling, Ann Martinez, Luc Boileau, Franklin D. Gaylis, Jacqueline Petkewicz, Nicholas Kirwen, Brian T. Helfand, Jianfeng Xu, Denise M. Scholtens, William J. Catalona, and John S. Witte
Subjects: prostatic neoplasms, prostate, genome-wide association study, genetics, Genetics, QH426-470
Abstract: Summary: Men diagnosed with low-risk prostate cancer (PC) are increasingly electing active surveillance (AS) as their initial management strategy. While this may reduce the side effects of treatment for PC, many men on AS eventually convert to active treatment. PC is one of the most heritable cancers, and genetic factors that predispose to aggressive tumors may help distinguish men who are more likely to discontinue AS. To investigate this, we undertook a multi-institutional genome-wide association study (GWAS) of 5,222 PC patients and 1,139 other patients from replication cohorts, all of whom initially elected AS and were followed over time for the potential outcome of conversion from AS to active treatment. In the GWAS we detected 18 variants associated with conversion, 15 of which were not previously associated with PC risk. With a transcriptome-wide association study (TWAS), we found two genes associated with conversion (MAST3, p = 6.9 × 10−7 and GAB2, p = 2.0 × 10−6). Moreover, increasing values of a previously validated 269-variant genetic risk score (GRS) for PC was positively associated with conversion (e.g., comparing the highest to the two middle deciles gave a hazard ratio [HR] = 1.13; 95% confidence interval [CI] = 0.94–1.36); whereas decreasing values of a 36-variant GRS for prostate-specific antigen (PSA) levels were positively associated with conversion (e.g., comparing the lowest to the two middle deciles gave a HR = 1.25; 95% CI, 1.04–1.50). These results suggest that germline genetics may help inform and individualize the decision of AS—or the intensity of monitoring on AS—versus treatment for the initial management of patients with low-risk PC.
Published: 2022
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8. A meta-analysis of genome-wide association studies of multiple myeloma among men and women of African ancestry

Author: Zhaohui Du, Niels Weinhold, Gregory Chi Song, Kristin A. Rand, David J. Van Den Berg, Amie E. Hwang, Xin Sheng, Victor Hom, Sikander Ailawadhi, Ajay K. Nooka, Seema Singhal, Karen Pawlish, Edward S. Peters, Cathryn Bock, Ann Mohrbacher, Alexander Stram, Sonja I. Berndt, William J. Blot, Graham Casey, Victoria L. Stevens, Rick Kittles, Phyllis J. Goodman, W. Ryan Diver, Anselm Hennis, Barbara Nemesure, Eric A. Klein, Benjamin A. Rybicki, Janet L. Stanford, John S. Witte, Lisa Signorello, Esther M. John, Leslie Bernstein, Antoinette M. Stroup, Owen W. Stephens, Maurizio Zangari, Frits Van Rhee, Andrew Olshan, Wei Zheng, Jennifer J. Hu, Regina Ziegler, Sarah J. Nyante, Sue Ann Ingles, Michael F. Press, John David Carpten, Stephen J. Chanock, Jayesh Mehta, Graham A. Colditz, Jeffrey Wolf, Thomas G. Martin, Michael Tomasson, Mark A. Fiala, Howard Terebelo, Nalini Janakiraman, Laurence Kolonel, Kenneth C. Anderson, Loic Le Marchand, Daniel Auclair, Brian C.-H. Chiu, Elad Ziv, Daniel Stram, Ravi Vij, Leon Bernal-Mizrachi, Gareth J. Morgan, Jeffrey A. Zonder, Carol Ann Huff, Sagar Lonial, Robert Z. Orlowski, David V. Conti, Christopher A. Haiman, and Wendy Cozen
Subjects: Specialties of internal medicine, RC581-951
Abstract: Abstract: Persons of African ancestry (AA) have a twofold higher risk for multiple myeloma (MM) compared with persons of European ancestry (EA). Genome-wide association studies (GWASs) support a genetic contribution to MM etiology in individuals of EA. Little is known about genetic risk factors for MM in individuals of AA. We performed a meta-analysis of 2 GWASs of MM in 1813 cases and 8871 controls and conducted an admixture mapping scan to identify risk alleles. We fine-mapped the 23 known susceptibility loci to find markers that could better capture MM risk in individuals of AA and constructed a polygenic risk score (PRS) to assess the aggregated effect of known MM risk alleles. In GWAS meta-analysis, we identified 2 suggestive novel loci located at 9p24.3 and 9p13.1 at P < 1 × 10−6; however, no genome-wide significant association was noted. In admixture mapping, we observed a genome-wide significant inverse association between local AA at 2p24.1-23.1 and MM risk in AA individuals. Of the 23 known EA risk variants, 20 showed directional consistency, and 9 replicated at P < .05 in AA individuals. In 8 regions, we identified markers that better capture MM risk in persons with AA. AA individuals with a PRS in the top 10% had a 1.82-fold (95% confidence interval, 1.56-2.11) increased MM risk compared with those with average risk (25%-75%). The strongest functional association was between the risk allele for variant rs56219066 at 5q15 and lower ELL2 expression (P = 5.1 × 10−12). Our study shows that common genetic variation contributes to MM risk in individuals with AA.
Published: 2020
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9. Publisher Correction: Shared heritability and functional enrichment across six solid cancers

Author: Xia Jiang, Hilary K. Finucane, Fredrick R. Schumacher, Stephanie L. Schmit, Jonathan P. Tyrer, Younghun Han, Kyriaki Michailidou, Corina Lesseur, Karoline B. Kuchenbaecker, Joe Dennis, David V. Conti, Graham Casey, Mia M. Gaudet, Jeroen R. Huyghe, Demetrius Albanes, Melinda C. Aldrich, Angeline S. Andrew, Irene L. Andrulis, Hoda Anton-Culver, Antonis C. Antoniou, Natalia N. Antonenkova, Susanne M. Arnold, Kristan J. Aronson, Banu K. Arun, Elisa V. Bandera, Rosa B. Barkardottir, Daniel R. Barnes, Jyotsna Batra, Matthias W. Beckmann, Javier Benitez, Sara Benlloch, Andrew Berchuck, Sonja I. Berndt, Heike Bickeböller, Stephanie A. Bien, Carl Blomqvist, Stefania Boccia, Natalia V. Bogdanova, Stig E. Bojesen, Manjeet K. Bolla, Hiltrud Brauch, Hermann Brenner, James D. Brenton, Mark N. Brook, Joan Brunet, Hans Brunnström, Daniel D. Buchanan, Barbara Burwinkel, Ralf Butzow, Gabriella Cadoni, Trinidad Caldés, Maria A. Caligo, Ian Campbell, Peter T. Campbell, Géraldine Cancel-Tassin, Lisa Cannon-Albright, Daniele Campa, Neil Caporaso, André L. Carvalho, Andrew T. Chan, Jenny Chang-Claude, Stephen J. Chanock, Chu Chen, David C. Christiani, Kathleen B. M. Claes, Frank Claessens, Judith Clements, J. Margriet Collée, Marcia Cruz Correa, Fergus J. Couch, Angela Cox, Julie M. Cunningham, Cezary Cybulski, Kamila Czene, Mary B. Daly, Anna deFazio, Peter Devilee, Orland Diez, Manuela Gago-Dominguez, Jenny L. Donovan, Thilo Dörk, Eric J. Duell, Alison M. Dunning, Miriam Dwek, Diana M. Eccles, Christopher K. Edlund, Digna R. Velez Edwards, Carolina Ellberg, D. Gareth Evans, Peter A. Fasching, Robert L. Ferris, Triantafillos Liloglou, Jane C. Figueiredo, Olivia Fletcher, Renée T. Fortner, Florentia Fostira, Silvia Franceschi, Eitan Friedman, Steven J. Gallinger, Patricia A. Ganz, Judy Garber, José A. García-Sáenz, Simon A. Gayther, Graham G. Giles, Andrew K. Godwin, Mark S. Goldberg, David E. Goldgar, Ellen L. Goode, Marc T. Goodman, Gary Goodman, Kjell Grankvist, Mark H. Greene, Henrik Gronberg, Jacek Gronwald, Pascal Guénel, Niclas Håkansson, Per Hall, Ute Hamann, Freddie C. Hamdy, Robert J. Hamilton, Jochen Hampe, Aage Haugen, Florian Heitz, Rolando Herrero, Peter Hillemanns, Michael Hoffmeister, Estrid Høgdall, Yun-Chul Hong, John L. Hopper, Richard Houlston, Peter J. Hulick, David J. Hunter, David G. Huntsman, Gregory Idos, Evgeny N. Imyanitov, Sue Ann Ingles, Claudine Isaacs, Anna Jakubowska, Paul James, Mark A. Jenkins, Mattias Johansson, Mikael Johansson, Esther M. John, Amit D. Joshi, Radka Kaneva, Beth Y. Karlan, Linda E. Kelemen, Tabea Kühl, Kay-Tee Khaw, Elza Khusnutdinova, Adam S. Kibel, Lambertus A. Kiemeney, Jeri Kim, Susanne K. Kjaer, Julia A. Knight, Manolis Kogevinas, Zsofia Kote-Jarai, Stella Koutros, Vessela N. Kristensen, Jolanta Kupryjanczyk, Martin Lacko, Stephan Lam, Diether Lambrechts, Maria Teresa Landi, Philip Lazarus, Nhu D. Le, Eunjung Lee, Flavio Lejbkowicz, Heinz-Josef Lenz, Goska Leslie, Davor Lessel, Jenny Lester, Douglas A. Levine, Li Li, Christopher I. Li, Annika Lindblom, Noralane M. Lindor, Geoffrey Liu, Fotios Loupakis, Jan Lubiński, Lovise Maehle, Christiane Maier, Arto Mannermaa, Loic Le Marchand, Sara Margolin, Taymaa May, Lesley McGuffog, Alfons Meindl, Pooja Middha, Austin Miller, Roger L. Milne, Robert J. MacInnis, Francesmary Modugno, Marco Montagna, Victor Moreno, Kirsten B. Moysich, Lorelei Mucci, Kenneth Muir, Anna Marie Mulligan, Katherine L. Nathanson, David E. Neal, Andrew R. Ness, Susan L. Neuhausen, Heli Nevanlinna, Polly A. Newcomb, Lisa F. Newcomb, Finn Cilius Nielsen, Liene Nikitina-Zake, Børge G. Nordestgaard, Robert L. Nussbaum, Kenneth Offit, Edith Olah, Ali Amin Al Olama, Olufunmilayo I. Olopade, Andrew F. Olshan, Håkan Olsson, Ana Osorio, Hardev Pandha, Jong Y. Park, Nora Pashayan, Michael T. Parsons, Tanja Pejovic, Kathryn L. Penney, Wilbert H. M. Peters, Catherine M. Phelan, Amanda I. Phipps, Dijana Plaseska-Karanfilska, Miranda Pring, Darya Prokofyeva, Paolo Radice, Kari Stefansson, Susan J. Ramus, Leon Raskin, Gad Rennert, Hedy S. Rennert, Elizabeth J. van Rensburg, Marjorie J. Riggan, Harvey A. Risch, Angela Risch, Monique J. Roobol, Barry S. Rosenstein, Mary Anne Rossing, Kim De Ruyck, Emmanouil Saloustros, Dale P. Sandler, Elinor J. Sawyer, Matthew B. Schabath, Johanna Schleutker, Marjanka K. Schmidt, V. Wendy Setiawan, Hongbing Shen, Erin M. Siegel, Weiva Sieh, Christian F. Singer, Martha L. Slattery, Karina Dalsgaard Sorensen, Melissa C. Southey, Amanda B. Spurdle, Janet L. Stanford, Victoria L. Stevens, Sebastian Stintzing, Jennifer Stone, Karin Sundfeldt, Rebecca Sutphen, Anthony J. Swerdlow, Eloiza H. Tajara, Catherine M. Tangen, Adonina Tardon, Jack A. Taylor, M. Dawn Teare, Manuel R. Teixeira, Mary Beth Terry, Kathryn L. Terry, Stephen N. Thibodeau, Mads Thomassen, Line Bjørge, Marc Tischkowitz, Amanda E. Toland, Diana Torres, Paul A. Townsend, Ruth C. Travis, Nadine Tung, Shelley S. Tworoger, Cornelia M. Ulrich, Nawaid Usmani, Celine M. Vachon, Els Van Nieuwenhuysen, Ana Vega, Miguel Elías Aguado-Barrera, Qin Wang, Penelope M. Webb, Clarice R. Weinberg, Stephanie Weinstein, Mark C. Weissler, Jeffrey N. Weitzel, Catharine M. L. West, Emily White, Alice S. Whittemore, H-Erich Wichmann, Fredrik Wiklund, Robert Winqvist, Alicja Wolk, Penella Woll, Michael Woods, Anna H. Wu, Xifeng Wu, Drakoulis Yannoukakos, Wei Zheng, Shanbeh Zienolddiny, Argyrios Ziogas, Kristin K. Zorn, Jacqueline M. Lane, Richa Saxena, Duncan Thomas, Rayjean J. Hung, Brenda Diergaarde, James McKay, Ulrike Peters, Li Hsu, Montserrat García-Closas, Rosalind A. Eeles, Georgia Chenevix-Trench, Paul J. Brennan, Christopher A. Haiman, Jacques Simard, Douglas F. Easton, Stephen B. Gruber, Paul D. P. Pharoah, Alkes L. Price, Bogdan Pasaniuc, Christopher I. Amos, Peter Kraft, and Sara Lindström
Subjects: Science
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Published: 2019
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10. Author Correction: Germline variation at 8q24 and prostate cancer risk in men of European ancestry

Author: Marco Matejcic, Edward J. Saunders, Tokhir Dadaev, Mark N. Brook, Kan Wang, Xin Sheng, Ali Amin Al Olama, Fredrick R. Schumacher, Sue A. Ingles, Koveela Govindasami, Sara Benlloch, Sonja I. Berndt, Demetrius Albanes, Stella Koutros, Kenneth Muir, Victoria L. Stevens, Susan M. Gapstur, Catherine M. Tangen, Jyotsna Batra, Judith Clements, Henrik Gronberg, Nora Pashayan, Johanna Schleutker, Alicja Wolk, Catharine West, Lorelei Mucci, Peter Kraft, Géraldine Cancel-Tassin, Karina D. Sorensen, Lovise Maehle, Eli M. Grindedal, Sara S. Strom, David E. Neal, Freddie C. Hamdy, Jenny L. Donovan, Ruth C. Travis, Robert J. Hamilton, Barry Rosenstein, Yong-Jie Lu, Graham G. Giles, Adam S. Kibel, Ana Vega, Jeanette T. Bensen, Manolis Kogevinas, Kathryn L. Penney, Jong Y. Park, Janet L. Stanford, Cezary Cybulski, Børge G. Nordestgaard, Hermann Brenner, Christiane Maier, Jeri Kim, Manuel R. Teixeira, Susan L. Neuhausen, Kim De Ruyck, Azad Razack, Lisa F. Newcomb, Davor Lessel, Radka Kaneva, Nawaid Usmani, Frank Claessens, Paul A. Townsend, Manuela Gago-Dominguez, Monique J. Roobol, Florence Menegaux, Kay-Tee Khaw, Lisa A. Cannon-Albright, Hardev Pandha, Stephen N. Thibodeau, Daniel J. Schaid, The PRACTICAL Consortium, Fredrik Wiklund, Stephen J. Chanock, Douglas F. Easton, Rosalind A. Eeles, Zsofia Kote-Jarai, David V. Conti, and Christopher A. Haiman
Subjects: Science
Abstract: The original version of this Article contained an error in the spelling of the author Manuela Gago-Dominguez, which was incorrectly given as Manuela G. Dominguez. This has now been corrected in both the PDF and HTML versions of the Article.
Published: 2019
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11. Shared heritability and functional enrichment across six solid cancers

Author: Xia Jiang, Hilary K. Finucane, Fredrick R. Schumacher, Stephanie L. Schmit, Jonathan P. Tyrer, Younghun Han, Kyriaki Michailidou, Corina Lesseur, Karoline B. Kuchenbaecker, Joe Dennis, David V. Conti, Graham Casey, Mia M. Gaudet, Jeroen R. Huyghe, Demetrius Albanes, Melinda C. Aldrich, Angeline S. Andrew, Irene L. Andrulis, Hoda Anton-Culver, Antonis C. Antoniou, Natalia N. Antonenkova, Susanne M. Arnold, Kristan J. Aronson, Banu K. Arun, Elisa V. Bandera, Rosa B. Barkardottir, Daniel R. Barnes, Jyotsna Batra, Matthias W. Beckmann, Javier Benitez, Sara Benlloch, Andrew Berchuck, Sonja I. Berndt, Heike Bickeböller, Stephanie A. Bien, Carl Blomqvist, Stefania Boccia, Natalia V. Bogdanova, Stig E. Bojesen, Manjeet K. Bolla, Hiltrud Brauch, Hermann Brenner, James D. Brenton, Mark N. Brook, Joan Brunet, Hans Brunnström, Daniel D. Buchanan, Barbara Burwinkel, Ralf Butzow, Gabriella Cadoni, Trinidad Caldés, Maria A. Caligo, Ian Campbell, Peter T. Campbell, Géraldine Cancel-Tassin, Lisa Cannon-Albright, Daniele Campa, Neil Caporaso, André L. Carvalho, Andrew T. Chan, Jenny Chang-Claude, Stephen J. Chanock, Chu Chen, David C. Christiani, Kathleen B. M. Claes, Frank Claessens, Judith Clements, J. Margriet Collée, Marcia Cruz Correa, Fergus J. Couch, Angela Cox, Julie M. Cunningham, Cezary Cybulski, Kamila Czene, Mary B. Daly, Anna deFazio, Peter Devilee, Orland Diez, Manuela Gago-Dominguez, Jenny L. Donovan, Thilo Dörk, Eric J. Duell, Alison M. Dunning, Miriam Dwek, Diana M. Eccles, Christopher K. Edlund, Digna R Velez Edwards, Carolina Ellberg, D. Gareth Evans, Peter A. Fasching, Robert L. Ferris, Triantafillos Liloglou, Jane C. Figueiredo, Olivia Fletcher, Renée T. Fortner, Florentia Fostira, Silvia Franceschi, Eitan Friedman, Steven J. Gallinger, Patricia A. Ganz, Judy Garber, José A. García-Sáenz, Simon A. Gayther, Graham G. Giles, Andrew K. Godwin, Mark S. Goldberg, David E. Goldgar, Ellen L. Goode, Marc T. Goodman, Gary Goodman, Kjell Grankvist, Mark H. Greene, Henrik Gronberg, Jacek Gronwald, Pascal Guénel, Niclas Håkansson, Per Hall, Ute Hamann, Freddie C. Hamdy, Robert J. Hamilton, Jochen Hampe, Aage Haugen, Florian Heitz, Rolando Herrero, Peter Hillemanns, Michael Hoffmeister, Estrid Høgdall, Yun-Chul Hong, John L. Hopper, Richard Houlston, Peter J. Hulick, David J. Hunter, David G. Huntsman, Gregory Idos, Evgeny N. Imyanitov, Sue Ann Ingles, Claudine Isaacs, Anna Jakubowska, Paul James, Mark A. Jenkins, Mattias Johansson, Mikael Johansson, Esther M. John, Amit D. Joshi, Radka Kaneva, Beth Y. Karlan, Linda E. Kelemen, Tabea Kühl, Kay-Tee Khaw, Elza Khusnutdinova, Adam S. Kibel, Lambertus A. Kiemeney, Jeri Kim, Susanne K. Kjaer, Julia A. Knight, Manolis Kogevinas, Zsofia Kote-Jarai, Stella Koutros, Vessela N. Kristensen, Jolanta Kupryjanczyk, Martin Lacko, Stephan Lam, Diether Lambrechts, Maria Teresa Landi, Philip Lazarus, Nhu D. Le, Eunjung Lee, Flavio Lejbkowicz, Heinz-Josef Lenz, Goska Leslie, Davor Lessel, Jenny Lester, Douglas A. Levine, Li Li, Christopher I. Li, Annika Lindblom, Noralane M. Lindor, Geoffrey Liu, Fotios Loupakis, Jan Lubiński, Lovise Maehle, Christiane Maier, Arto Mannermaa, Loic Le Marchand, Sara Margolin, Taymaa May, Lesley McGuffog, Alfons Meindl, Pooja Middha, Austin Miller, Roger L. Milne, Robert J. MacInnis, Francesmary Modugno, Marco Montagna, Victor Moreno, Kirsten B. Moysich, Lorelei Mucci, Kenneth Muir, Anna Marie Mulligan, Katherine L. Nathanson, David E. Neal, Andrew R. Ness, Susan L. Neuhausen, Heli Nevanlinna, Polly A. Newcomb, Lisa F. Newcomb, Finn Cilius Nielsen, Liene Nikitina-Zake, Børge G. Nordestgaard, Robert L. Nussbaum, Kenneth Offit, Edith Olah, Ali Amin Al Olama, Olufunmilayo I. Olopade, Andrew F. Olshan, Håkan Olsson, Ana Osorio, Hardev Pandha, Jong Y. Park, Nora Pashayan, Michael T. Parsons, Tanja Pejovic, Kathryn L. Penney, Wilbert H M. Peters, Catherine M. Phelan, Amanda I. Phipps, Dijana Plaseska-Karanfilska, Miranda Pring, Darya Prokofyeva, Paolo Radice, Kari Stefansson, Susan J. Ramus, Leon Raskin, Gad Rennert, Hedy S. Rennert, Elizabeth J. van Rensburg, Marjorie J. Riggan, Harvey A. Risch, Angela Risch, Monique J. Roobol, Barry S. Rosenstein, Mary Anne Rossing, Kim De Ruyck, Emmanouil Saloustros, Dale P. Sandler, Elinor J. Sawyer, Matthew B. Schabath, Johanna Schleutker, Marjanka K. Schmidt, V. Wendy Setiawan, Hongbing Shen, Erin M. Siegel, Weiva Sieh, Christian F. Singer, Martha L. Slattery, Karina Dalsgaard Sorensen, Melissa C. Southey, Amanda B. Spurdle, Janet L. Stanford, Victoria L. Stevens, Sebastian Stintzing, Jennifer Stone, Karin Sundfeldt, Rebecca Sutphen, Anthony J. Swerdlow, Eloiza H. Tajara, Catherine M. Tangen, Adonina Tardon, Jack A. Taylor, M. Dawn Teare, Manuel R. Teixeira, Mary Beth Terry, Kathryn L. Terry, Stephen N. Thibodeau, Mads Thomassen, Line Bjørge, Marc Tischkowitz, Amanda E. Toland, Diana Torres, Paul A. Townsend, Ruth C. Travis, Nadine Tung, Shelley S. Tworoger, Cornelia M. Ulrich, Nawaid Usmani, Celine M. Vachon, Els Van Nieuwenhuysen, Ana Vega, Miguel Elías Aguado-Barrera, Qin Wang, Penelope M. Webb, Clarice R. Weinberg, Stephanie Weinstein, Mark C. Weissler, Jeffrey N. Weitzel, Catharine M. L. West, Emily White, Alice S. Whittemore, H-Erich Wichmann, Fredrik Wiklund, Robert Winqvist, Alicja Wolk, Penella Woll, Michael Woods, Anna H. Wu, Xifeng Wu, Drakoulis Yannoukakos, Wei Zheng, Shanbeh Zienolddiny, Argyrios Ziogas, Kristin K. Zorn, Jacqueline M. Lane, Richa Saxena, Duncan Thomas, Rayjean J. Hung, Brenda Diergaarde, James McKay, Ulrike Peters, Li Hsu, Montserrat García-Closas, Rosalind A. Eeles, Georgia Chenevix-Trench, Paul J. Brennan, Christopher A. Haiman, Jacques Simard, Douglas F. Easton, Stephen B. Gruber, Paul D. P. Pharoah, Alkes L. Price, Bogdan Pasaniuc, Christopher I. Amos, Peter Kraft, and Sara Lindström
Subjects: Science
Abstract: Similarities in cancers can be studied to interrogate their etiology. Here, the authors use genome-wide association study summary statistics from six cancer types based on 296,215 cases and 301,319 controls of European ancestry, showing that solid tumours arising from different tissues share a degree of common germline genetic basis.
Published: 2019
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12. DNA methylation and cis-regulation of gene expression by prostate cancer risk SNPs.

Author: James Y Dai, Xiaoyu Wang, Bo Wang, Wei Sun, Kristina M Jordahl, Suzanne Kolb, Yaw A Nyame, Jonathan L Wright, Elaine A Ostrander, Ziding Feng, and Janet L Stanford
Subjects: Genetics, QH426-470
Abstract: Genome-wide association studies have identified more than 100 SNPs that increase the risk of prostate cancer (PrCa). We identify and compare expression quantitative trait loci (eQTLs) and CpG methylation quantitative trait loci (meQTLs) among 147 established PrCa risk SNPs in primary prostate tumors (n = 355 from a Seattle-based study and n = 495 from The Cancer Genome Atlas, TCGA) and tumor-adjacent, histologically benign samples (n = 471 from a Mayo Clinic study). The role of DNA methylation in eQTL regulation of gene expression was investigated by data triangulation using several causal inference approaches, including a proposed adaptation of the Causal Inference Test (CIT) for causal direction. Comparing eQTLs between tumors and benign samples, we show that 98 of the 147 risk SNPs were identified as eQTLs in the tumor-adjacent benign samples, and almost all 34 eQTL identified in tumor sets were also eQTLs in the benign samples. Three lines of results support the causal role of DNA methylation. First, nearly 100 of the 147 risk SNPs were identified as meQTLs in one tumor set, and almost all eQTLs in tumors were meQTLs. Second, the loss of eQTLs in tumors relative to benign samples was associated with altered DNA methylation. Third, among risk SNPs identified as both eQTLs and meQTLs, mediation analyses suggest that over two-thirds have evidence of a causal role for DNA methylation, mostly mediating genetic influence on gene expression. In summary, we provide a comprehensive catalog of eQTLs, meQTLs and putative cancer genes for known PrCa risk SNPs. We observe that a substantial portion of germline eQTL regulatory mechanisms are maintained in the tumor development, despite somatic alterations in tumor genome. Finally, our mediation analyses illuminate the likely intermediary role of CpG methylation in eQTL regulation of gene expression.
Published: 2020
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13. Germline variation at 8q24 and prostate cancer risk in men of European ancestry

Author: Marco Matejcic, Edward J. Saunders, Tokhir Dadaev, Mark N. Brook, Kan Wang, Xin Sheng, Ali Amin Al Olama, Fredrick R. Schumacher, Sue A. Ingles, Koveela Govindasami, Sara Benlloch, Sonja I. Berndt, Demetrius Albanes, Stella Koutros, Kenneth Muir, Victoria L. Stevens, Susan M. Gapstur, Catherine M. Tangen, Jyotsna Batra, Judith Clements, Henrik Gronberg, Nora Pashayan, Johanna Schleutker, Alicja Wolk, Catharine West, Lorelei Mucci, Peter Kraft, Géraldine Cancel-Tassin, Karina D. Sorensen, Lovise Maehle, Eli M. Grindedal, Sara S. Strom, David E. Neal, Freddie C. Hamdy, Jenny L. Donovan, Ruth C. Travis, Robert J. Hamilton, Barry Rosenstein, Yong-Jie Lu, Graham G. Giles, Adam S. Kibel, Ana Vega, Jeanette T. Bensen, Manolis Kogevinas, Kathryn L. Penney, Jong Y. Park, Janet L. Stanford, Cezary Cybulski, Børge G. Nordestgaard, Hermann Brenner, Christiane Maier, Jeri Kim, Manuel R. Teixeira, Susan L. Neuhausen, Kim De Ruyck, Azad Razack, Lisa F. Newcomb, Davor Lessel, Radka Kaneva, Nawaid Usmani, Frank Claessens, Paul A. Townsend, Manuela Gago-Dominguez, Monique J. Roobol, Florence Menegaux, Kay-Tee Khaw, Lisa A. Cannon-Albright, Hardev Pandha, Stephen N. Thibodeau, Daniel J. Schaid, The PRACTICAL (Prostate Cancer Association Group to Investigate Cancer-Associated Alterations in the Genome) Consortium, Fredrik Wiklund, Stephen J. Chanock, Douglas F. Easton, Rosalind A. Eeles, Zsofia Kote-Jarai, David V. Conti, and Christopher A. Haiman
Subjects: Science
Abstract: Chromosome 8q24 is known to be a major susceptibility region for prostate cancer risk. Here the authors analyze genetic data across the 8q24 region from 71,535 prostate cancer patients identifying 12 risk loci, three previously unreported, highlighting the contribution of germline variation at this locus.
Published: 2018
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14. Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants

Author: Tokhir Dadaev, Edward J. Saunders, Paul J. Newcombe, Ezequiel Anokian, Daniel A. Leongamornlert, Mark N. Brook, Clara Cieza-Borrella, Martina Mijuskovic, Sarah Wakerell, Ali Amin Al Olama, Fredrick R. Schumacher, Sonja I. Berndt, Sara Benlloch, Mahbubl Ahmed, Chee Goh, Xin Sheng, Zhuo Zhang, Kenneth Muir, Koveela Govindasami, Artitaya Lophatananon, Victoria L. Stevens, Susan M. Gapstur, Brian D. Carter, Catherine M. Tangen, Phyllis Goodman, Ian M. Thompson, Jyotsna Batra, Suzanne Chambers, Leire Moya, Judith Clements, Lisa Horvath, Wayne Tilley, Gail Risbridger, Henrik Gronberg, Markus Aly, Tobias Nordström, Paul Pharoah, Nora Pashayan, Johanna Schleutker, Teuvo L. J. Tammela, Csilla Sipeky, Anssi Auvinen, Demetrius Albanes, Stephanie Weinstein, Alicja Wolk, Niclas Hakansson, Catharine West, Alison M. Dunning, Neil Burnet, Lorelei Mucci, Edward Giovannucci, Gerald Andriole, Olivier Cussenot, Géraldine Cancel-Tassin, Stella Koutros, Laura E. Beane Freeman, Karina Dalsgaard Sorensen, Torben Falck Orntoft, Michael Borre, Lovise Maehle, Eli Marie Grindedal, David E. Neal, Jenny L. Donovan, Freddie C. Hamdy, Richard M. Martin, Ruth C. Travis, Tim J. Key, Robert J. Hamilton, Neil E. Fleshner, Antonio Finelli, Sue Ann Ingles, Mariana C. Stern, Barry Rosenstein, Sarah Kerns, Harry Ostrer, Yong-Jie Lu, Hong-Wei Zhang, Ninghan Feng, Xueying Mao, Xin Guo, Guomin Wang, Zan Sun, Graham G. Giles, Melissa C. Southey, Robert J. MacInnis, Liesel M. FitzGerald, Adam S. Kibel, Bettina F. Drake, Ana Vega, Antonio Gómez-Caamaño, Laura Fachal, Robert Szulkin, Martin Eklund, Manolis Kogevinas, Javier Llorca, Gemma Castaño-Vinyals, Kathryn L. Penney, Meir Stampfer, Jong Y. Park, Thomas A. Sellers, Hui-Yi Lin, Janet L. Stanford, Cezary Cybulski, Dominika Wokolorczyk, Jan Lubinski, Elaine A. Ostrander, Milan S. Geybels, Børge G. Nordestgaard, Sune F. Nielsen, Maren Weisher, Rasmus Bisbjerg, Martin Andreas Røder, Peter Iversen, Hermann Brenner, Katarina Cuk, Bernd Holleczek, Christiane Maier, Manuel Luedeke, Thomas Schnoeller, Jeri Kim, Christopher J. Logothetis, Esther M. John, Manuel R. Teixeira, Paula Paulo, Marta Cardoso, Susan L. Neuhausen, Linda Steele, Yuan Chun Ding, Kim De Ruyck, Gert De Meerleer, Piet Ost, Azad Razack, Jasmine Lim, Soo-Hwang Teo, Daniel W. Lin, Lisa F. Newcomb, Davor Lessel, Marija Gamulin, Tomislav Kulis, Radka Kaneva, Nawaid Usmani, Chavdar Slavov, Vanio Mitev, Matthew Parliament, Sandeep Singhal, Frank Claessens, Steven Joniau, Thomas Van den Broeck, Samantha Larkin, Paul A. Townsend, Claire Aukim-Hastie, Manuela Gago-Dominguez, Jose Esteban Castelao, Maria Elena Martinez, Monique J. Roobol, Guido Jenster, Ron H. N. van Schaik, Florence Menegaux, Thérèse Truong, Yves Akoli Koudou, Jianfeng Xu, Kay-Tee Khaw, Lisa Cannon-Albright, Hardev Pandha, Agnieszka Michael, Andrzej Kierzek, Stephen N. Thibodeau, Shannon K. McDonnell, Daniel J. Schaid, Sara Lindstrom, Constance Turman, Jing Ma, David J. Hunter, Elio Riboli, Afshan Siddiq, Federico Canzian, Laurence N. Kolonel, Loic Le Marchand, Robert N. Hoover, Mitchell J. Machiela, Peter Kraft, The PRACTICAL (Prostate Cancer Association Group to Investigate Cancer-Associated Alterations in the Genome) Consortium, Matthew Freedman, Fredrik Wiklund, Stephen Chanock, Brian E. Henderson, Douglas F. Easton, Christopher A. Haiman, Rosalind A. Eeles, David V. Conti, and Zsofia Kote-Jarai
Subjects: Science
Abstract: Prostate cancer (PrCa) involves a large heritable genetic component. Here, the authors perform multivariate fine-mapping of known PrCa GWAS loci, identifying variants enriched for biological function, explaining more familial relative risk, and with potential application in clinical risk profiling.
Published: 2018
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15. AA9int: SNP interaction pattern search using non-hierarchical additive model set.

Author: Hui-Yi Lin, Po-Yu Huang, Dung-Tsa Chen, Heng-Yuan Tung, Thomas A. Sellers, Julio M. Pow-Sang, Rosalind A. Eeles, Doug Easton, Zsofia Kote-Jarai, Ali Amin Al Olama, Sara Benlloch, Kenneth Muir, Graham G. Giles, Fredrik Wiklund, Henrik Gronberg, Christopher A. Haiman, Johanna Schleutker, Børge G. Nordestgaard, Ruth C. Travis, Freddie Hamdy, David E. Neal, Nora Pashayan, Kay-Tee Khaw, Janet L. Stanford, William J. Blot, Stephen N. Thibodeau, Christiane Maier, Adam S. Kibel, Cezary Cybulski, Lisa A. Cannon-Albright, Hermann Brenner, Radka Kaneva, Jyotsna Batra, Manuel R. Teixeira, Hardev Pandha, Yong-Jie Lu, The PRACTICAL Consortium, and Jong Y. Park
Published: 2018
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16. SNP interaction pattern identifier (SIPI): an intensive search for SNP-SNP interaction patterns.

Author: Hui-Yi Lin, Dung-Tsa Chen, Po-Yu Huang, Yung-Hsin Liu, Augusto Ochoa, Jovanny Zabaleta, Donald Mercante, Zhide Fang, Thomas A. Sellers, Julio M. Pow-Sang, Chia-Ho Cheng, Rosalind A. Eeles, Doug Easton, Zsofia Kote-Jarai, Ali Amin Al Olama, Sara Benlloch, Kenneth Muir, Graham G. Giles, Fredrik Wiklund, Henrik Gronberg, Christopher A. Haiman, Johanna Schleutker, Børge G. Nordestgaard, Ruth C. Travis, Freddie Hamdy, Nora Pashayan, Kay-Tee Khaw, Janet L. Stanford, William J. Blot, Stephen N. Thibodeau, Christiane Maier, Adam S. Kibel, Cezary Cybulski, Lisa A. Cannon-Albright, Hermann Brenner, Radka Kaneva, Jyotsna Batra, Manuel R. Teixeira, Hardev Pandha, Yong-Jie Lu, The PRACTICAL Consortium, and Jong Y. Park
Published: 2017
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17. Association of a novel BRCA2 mutation with prostate cancer risk further supports germline genetic testing

Author: Georgea R. Foley, James R. Marthick, Elaine A. Ostrander, Janet L. Stanford, Joanne L. Dickinson, and Liesel M. FitzGerald
Subjects: Cancer Research, Oncology
Published: 2023
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18. Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation

Author: Alexander Gusev, Huwenbo Shi, Gleb Kichaev, Mark Pomerantz, Fugen Li, Henry W. Long, Sue A. Ingles, Rick A. Kittles, Sara S. Strom, Benjamin A. Rybicki, Barbara Nemesure, William B. Isaacs, Wei Zheng, Curtis A. Pettaway, Edward D. Yeboah, Yao Tettey, Richard B. Biritwum, Andrew A. Adjei, Evelyn Tay, Ann Truelove, Shelley Niwa, Anand P. Chokkalingam, Esther M. John, Adam B. Murphy, Lisa B. Signorello, John Carpten, M. Cristina Leske, Suh-Yuh Wu, Anslem J. M. Hennis, Christine Neslund-Dudas, Ann W. Hsing, Lisa Chu, Phyllis J. Goodman, Eric A. Klein, John S. Witte, Graham Casey, Sam Kaggwa, Michael B. Cook, Daniel O. Stram, William J. Blot, Rosalind A. Eeles, Douglas Easton, ZSofia Kote-Jarai, Ali Amin Al Olama, Sara Benlloch, Kenneth Muir, Graham G. Giles, Melissa C. Southey, Liesel M. Fitzgerald, Henrik Gronberg, Fredrik Wiklund, Markus Aly, Brian E. Henderson, Johanna Schleutker, Tiina Wahlfors, Teuvo L. J. Tammela, Børge G. Nordestgaard, Tim J. Key, Ruth C. Travis, David E. Neal, Jenny L. Donovan, Freddie C. Hamdy, Paul Pharoah, Nora Pashayan, Kay-Tee Khaw, Janet L. Stanford, Stephen N. Thibodeau, Shannon K. McDonnell, Daniel J. Schaid, Christiane Maier, Walther Vogel, Manuel Luedeke, Kathleen Herkommer, Adam S. Kibel, Cezary Cybulski, Dominika Wokolorczyk, Wojciech Kluzniak, Lisa Cannon-Albright, Craig Teerlink, Hermann Brenner, Aida K. Dieffenbach, Volker Arndt, Jong Y. Park, Thomas A. Sellers, Hui-Yi Lin, Chavdar Slavov, Radka Kaneva, Vanio Mitev, Jyotsna Batra, Amanda Spurdle, Judith A. Clements, Manuel R. Teixeira, Hardev Pandha, Agnieszka Michael, Paula Paulo, Sofia Maia, Andrzej Kierzek, The PRACTICAL consortium, David V. Conti, Demetrius Albanes, Christine Berg, Sonja I. Berndt, Daniele Campa, E. David Crawford, W. Ryan Diver, Susan M. Gapstur, J. Michael Gaziano, Edward Giovannucci, Robert Hoover, David J. Hunter, Mattias Johansson, Peter Kraft, Loic Le Marchand, Sara Lindström, Carmen Navarro, Kim Overvad, Elio Riboli, Afshan Siddiq, Victoria L. Stevens, Dimitrios Trichopoulos, Paolo Vineis, Meredith Yeager, Gosia Trynka, Soumya Raychaudhuri, Frederick R. Schumacher, Alkes L. Price, Matthew L. Freedman, Christopher A. Haiman, and Bogdan Pasaniuc
Subjects: Science
Abstract: Over one hundred loci have been identified to be associated with the familial risk of prostate cancer but the functional effects are poorly understood. Here the authors use single-nucleotide variant and epigentic data to show an underlying genetic architecture marked by histone modification.
Published: 2016
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19. Supplementary Grant Support from Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types

Author: Diether Lambrechts, Paul D.P. Pharoah, Rosalind Eeles, Georgia Chenevix-Trench, Douglas F. Easton, Simon A. Gayther, Per Hall, Fergus J. Couch, Stephen J. Chanock, Peter Kraft, Brian E. Henderson, David J. Hunter, Thomas A. Sellers, Amanda Spurdle, Christopher A. Haiman, Jacques Simard, Alison M. Dunning, Andrew Berchuck, Matthew L. Freedman, Fredrick Schumacher, Yu-Tang Gao, Xiao-Ou Shu, Wojciech Kluzniak, William J. Blot, Weiva Sieh, Wei Zheng, Walther Vogel, Volker Arndt, Vessela Kristensen, Veronica Wendy Setiawan, Veli-Matti Kosma, Vanio Mitev, Ute Hamann, Usha Menon, Todd L. Edwards, Tim J. Key, Tiina Wahlfors, Thomas Brüning, Thilo Dörk, Teuvo L.J. Tammela, Tanja Pejovic, Susanne Krüger Kjær, Susan M. Gapstur, Stig E. Bojesen, Stephen N. Thibodeau, Soo-Hwang Teo, Soo Chin Lee, Sonja Berndt, Sofia Maia, Shelley S. Tworoger, Shannon K. McDonnell, Sara H. Olson, Sara Benlloch, Ruth C. Travis, Roger L. Milne, Roberta Ness, Robert Winqvist, Robert N. Hoover, Robert J. MacInnis, Robert A. Stephenson, Rita K. Schmutzler, Reidun Kristin Kopperud, Ralf Butzow, Radka Kaneva, Qiyuan Li, Qiuyin Cai, Qin Wang, Peter Devilee, Peter A. Fasching, Per Broberg, Penelope M. Webb, Paula Paulo, Paul Brennan, Pascal Guénel, Paolo Peterlongo, Nora Pashayan, Nicolas Wentzensen, Nick Orr, Nhu D. Le, Nazneen Rahman, Natalia Bogdanova, Montserrat Garcia-Closas, Minouk J. Schoemaker, Ming-Feng Hou, Michelle A.T. Hildebrandt, Michael Lush, Michael Jones, Melissa C. Southey, Maureen Sanderson, Matthieu Moisse, Matthias W. Beckmann, Mary Anne Rossing, Markus Aly, Marjorie Riggan, Marjanka K. Schmidt, Marc T. Goodman, Manuel R. Teixeira, Manuel Luedeke, Manjeet K. Bolla, Malcolm C. Pike, Maartje J. Hooning, Lisa Cannon-Albright, Linda S. Cook, Liesel M. Fitzgerald, Leon F.A.G. Massuger, Lambertus A. Kiemeney, Kunle Odunsi, Kristiina Aittomäki, Kirsten B. Moysich, Kexin Chen, Kenneth Offitt, Kenneth Muir, Keitaro Matsuo, Kay-Tee Khaw, Kathleen Herkommer, Karen H. Lu, Kamila Czene, Jyotsna Batra, Julio Pow-Sang, Julie M. Cunningham, Julian Peto, Julia A. Knight, Judith A. Clements, Jonine Figueroa, Jong Y. Park, Jolanta Kupryjanczyk, John L. Hopper, Johanna Schleutker, Joellen M. Schildkraut, Joe Dennis, Jenny L. Donovan, Jenny Chang-Claude, Jennifer B. Permuth, Jennifer A. Doherty, Javier Benítez, Janet L. Stanford, Jan Lubiński, Jacek Gronwald, Ignace Vergote, Ian Campbell, Iain McNeish, Hui-Yi Lim, Honglin Song, Hoda Anton-Culver, Hiltrud Brauch, Hermann Brenner, Henrik Gronberg, Heli Nevanlinna, Helga B. Salvesen, Hatef Darabi, Harvey A. Risch, Hardev Pandha, Hans-Ulrich Ulmer, Hans Wildiers, Håkan Olsson, Graham G. Giles, Fredrik Wiklund, Freddie C. Hamdy, Francesmary Modugno, Florian Heitz, Fiona Bruinsma, Fengju Song, Estrid Høgdall, Elza Khusnutdinova, Ellen L. Goode, Elizabeth M. Poole, Elisa V. Bandera, Elinor J. Sawyer, Drakoulis Yannoukakos, Douglas A. Levine, Dominika Wokozorczyk, Digna R. Velez Edwards, Dieter Flesch-Janys, Diana Eccles, David E. Neal, Daniel W. Cramer, Daniel O. Stram, Daniel J. Schaid, Daniel C. Tessier, Daehee Kang, Craig C. Teerlink, Claus K. Høgdall, Christine B. Ambrosone, Christiane Maier, Christa Stegmaier, Chavdar Slavov, Cezary Cybulski, Celine Vachon, Celeste Leigh Pearce, Catriona McLean, Catherine Phelan, Carl Blomqvist, Børge G. Nordestgaard, Beth Y. Karlan, Barbara Burwinkel, Arif B. Ekici, Argyrios Ziogas, Anthony Swerdlow, Annika Lindblom, Anna H. Wu, Anna Gonzalez-Neira, Anja Rudolph, Angela Cox, Andrzej Kierzek, Ana Peixoto, Alvaro Monteiro, Alicja Wolk, Alice S. Whittemore, Aleksandra Gentry-Maharaj, Aida K. Dieffenbach, Agnieszka Michael, Agnieszka Dansonka-Mieszkowska, Adam S. Kibel, Deborah J. Thompson, Susan J. Ramus, Sara Lindstrom, Kate Lawrenson, ZSofia Kote-Jarai, Jonathan Tyrer, Kyriaki Michailidou, Ali Amin Al Olama, Jonathan Beesley, and Siddhartha P. Kar
Abstract: Supplementary Grant Support
Published: 2023
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20. Supp. Table S22 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer

Author: Ulrike Peters, Shuji Ogino, Antoni Ribas, Charles S. Fuchs, Thomas J. Hudson, Levi A. Garraway, Eric S. Lander, Stacey B. Gabriel, Jesse M. Zaretsky, Syed H. Zaidi, Ming Yu, Catherine J. Wu, David A. Wheeler, Alexander Upfill-Brown, Jennifer Tsoi, Wei Sun, Janet L. Stanford, Sachet Shukla, Brian Shirts, Eve Shinbrot, Daniel Sanghoon Shin, Stephen J. Salipante, Ben J. Raphael, Elleanor H. Quist, Cristina Puig-Saus, Colin C. Pritchard, Matteo Pellegrini, Brian B. Nadel, Dennis J. Montoya, Mark D.M. Leiserson, Paige Krystofinski, Yeon Joo Kim, Jeroen R. Huyghe, Siwen Hu-Lieskovan, Li Hsu, William M. Grady, Milan S. Geybels, Helena Escuin-Ordinas, Charles Connolly, Gabriel Abril-Rodriguez, Katsuhiko Nosho, Teppei Morikawa, Kentaro Inamura, Zhi Rong Qian, Reiko Nishihara, Jonathan A. Nowak, Michael Quist, Xinmeng Jasmine Mu, Tsuyoshi Hamada, Daniel K. Wells, Marios Giannakis, and Catherine S. Grasso
Abstract: Supplementary Table S22: Segmented b-allele deficits
Published: 2023
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21. Supp. Tables S16-S19 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer

Author: Ulrike Peters, Shuji Ogino, Antoni Ribas, Charles S. Fuchs, Thomas J. Hudson, Levi A. Garraway, Eric S. Lander, Stacey B. Gabriel, Jesse M. Zaretsky, Syed H. Zaidi, Ming Yu, Catherine J. Wu, David A. Wheeler, Alexander Upfill-Brown, Jennifer Tsoi, Wei Sun, Janet L. Stanford, Sachet Shukla, Brian Shirts, Eve Shinbrot, Daniel Sanghoon Shin, Stephen J. Salipante, Ben J. Raphael, Elleanor H. Quist, Cristina Puig-Saus, Colin C. Pritchard, Matteo Pellegrini, Brian B. Nadel, Dennis J. Montoya, Mark D.M. Leiserson, Paige Krystofinski, Yeon Joo Kim, Jeroen R. Huyghe, Siwen Hu-Lieskovan, Li Hsu, William M. Grady, Milan S. Geybels, Helena Escuin-Ordinas, Charles Connolly, Gabriel Abril-Rodriguez, Katsuhiko Nosho, Teppei Morikawa, Kentaro Inamura, Zhi Rong Qian, Reiko Nishihara, Jonathan A. Nowak, Michael Quist, Xinmeng Jasmine Mu, Tsuyoshi Hamada, Daniel K. Wells, Marios Giannakis, and Catherine S. Grasso
Abstract: Supplementary Tables S16-S19, describing IHC results on NHS/HPFS data
Published: 2023
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22. Supplementary Methods, Figures S1 - S3 from Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types

Author: Diether Lambrechts, Paul D.P. Pharoah, Rosalind Eeles, Georgia Chenevix-Trench, Douglas F. Easton, Simon A. Gayther, Per Hall, Fergus J. Couch, Stephen J. Chanock, Peter Kraft, Brian E. Henderson, David J. Hunter, Thomas A. Sellers, Amanda Spurdle, Christopher A. Haiman, Jacques Simard, Alison M. Dunning, Andrew Berchuck, Matthew L. Freedman, Fredrick Schumacher, Yu-Tang Gao, Xiao-Ou Shu, Wojciech Kluzniak, William J. Blot, Weiva Sieh, Wei Zheng, Walther Vogel, Volker Arndt, Vessela Kristensen, Veronica Wendy Setiawan, Veli-Matti Kosma, Vanio Mitev, Ute Hamann, Usha Menon, Todd L. Edwards, Tim J. Key, Tiina Wahlfors, Thomas Brüning, Thilo Dörk, Teuvo L.J. Tammela, Tanja Pejovic, Susanne Krüger Kjær, Susan M. Gapstur, Stig E. Bojesen, Stephen N. Thibodeau, Soo-Hwang Teo, Soo Chin Lee, Sonja Berndt, Sofia Maia, Shelley S. Tworoger, Shannon K. McDonnell, Sara H. Olson, Sara Benlloch, Ruth C. Travis, Roger L. Milne, Roberta Ness, Robert Winqvist, Robert N. Hoover, Robert J. MacInnis, Robert A. Stephenson, Rita K. Schmutzler, Reidun Kristin Kopperud, Ralf Butzow, Radka Kaneva, Qiyuan Li, Qiuyin Cai, Qin Wang, Peter Devilee, Peter A. Fasching, Per Broberg, Penelope M. Webb, Paula Paulo, Paul Brennan, Pascal Guénel, Paolo Peterlongo, Nora Pashayan, Nicolas Wentzensen, Nick Orr, Nhu D. Le, Nazneen Rahman, Natalia Bogdanova, Montserrat Garcia-Closas, Minouk J. Schoemaker, Ming-Feng Hou, Michelle A.T. Hildebrandt, Michael Lush, Michael Jones, Melissa C. Southey, Maureen Sanderson, Matthieu Moisse, Matthias W. Beckmann, Mary Anne Rossing, Markus Aly, Marjorie Riggan, Marjanka K. Schmidt, Marc T. Goodman, Manuel R. Teixeira, Manuel Luedeke, Manjeet K. Bolla, Malcolm C. Pike, Maartje J. Hooning, Lisa Cannon-Albright, Linda S. Cook, Liesel M. Fitzgerald, Leon F.A.G. Massuger, Lambertus A. Kiemeney, Kunle Odunsi, Kristiina Aittomäki, Kirsten B. Moysich, Kexin Chen, Kenneth Offitt, Kenneth Muir, Keitaro Matsuo, Kay-Tee Khaw, Kathleen Herkommer, Karen H. Lu, Kamila Czene, Jyotsna Batra, Julio Pow-Sang, Julie M. Cunningham, Julian Peto, Julia A. Knight, Judith A. Clements, Jonine Figueroa, Jong Y. Park, Jolanta Kupryjanczyk, John L. Hopper, Johanna Schleutker, Joellen M. Schildkraut, Joe Dennis, Jenny L. Donovan, Jenny Chang-Claude, Jennifer B. Permuth, Jennifer A. Doherty, Javier Benítez, Janet L. Stanford, Jan Lubiński, Jacek Gronwald, Ignace Vergote, Ian Campbell, Iain McNeish, Hui-Yi Lim, Honglin Song, Hoda Anton-Culver, Hiltrud Brauch, Hermann Brenner, Henrik Gronberg, Heli Nevanlinna, Helga B. Salvesen, Hatef Darabi, Harvey A. Risch, Hardev Pandha, Hans-Ulrich Ulmer, Hans Wildiers, Håkan Olsson, Graham G. Giles, Fredrik Wiklund, Freddie C. Hamdy, Francesmary Modugno, Florian Heitz, Fiona Bruinsma, Fengju Song, Estrid Høgdall, Elza Khusnutdinova, Ellen L. Goode, Elizabeth M. Poole, Elisa V. Bandera, Elinor J. Sawyer, Drakoulis Yannoukakos, Douglas A. Levine, Dominika Wokozorczyk, Digna R. Velez Edwards, Dieter Flesch-Janys, Diana Eccles, David E. Neal, Daniel W. Cramer, Daniel O. Stram, Daniel J. Schaid, Daniel C. Tessier, Daehee Kang, Craig C. Teerlink, Claus K. Høgdall, Christine B. Ambrosone, Christiane Maier, Christa Stegmaier, Chavdar Slavov, Cezary Cybulski, Celine Vachon, Celeste Leigh Pearce, Catriona McLean, Catherine Phelan, Carl Blomqvist, Børge G. Nordestgaard, Beth Y. Karlan, Barbara Burwinkel, Arif B. Ekici, Argyrios Ziogas, Anthony Swerdlow, Annika Lindblom, Anna H. Wu, Anna Gonzalez-Neira, Anja Rudolph, Angela Cox, Andrzej Kierzek, Ana Peixoto, Alvaro Monteiro, Alicja Wolk, Alice S. Whittemore, Aleksandra Gentry-Maharaj, Aida K. Dieffenbach, Agnieszka Michael, Agnieszka Dansonka-Mieszkowska, Adam S. Kibel, Deborah J. Thompson, Susan J. Ramus, Sara Lindstrom, Kate Lawrenson, ZSofia Kote-Jarai, Jonathan Tyrer, Kyriaki Michailidou, Ali Amin Al Olama, Jonathan Beesley, and Siddhartha P. Kar
Abstract: Supplementary Figure S1. LocusZoom regional association plots for the seven new cross-cancer loci that were > 1 Mb from known index SNPs. Supplementary Figure S2A-B. Box plots showing eQTL associations between (A) rs9375701 and L3MBTL3 in normal breast and prostate tissues and (B) rs8037137 and RCCD1 in normal breast and ovarian tissues. Supplementary Figure S3. Interactions between BCL2L11 and the 32 Biocarta "Death Pathway" genes. Interactions were identified using the GeneMania server. Circles contain gene names, lines represent interactions, and the color of the line indicates a specific type of interaction as listed in the legend.
Published: 2023
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23. Supplementary Tables S1 - S10 from Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types

Author: Diether Lambrechts, Paul D.P. Pharoah, Rosalind Eeles, Georgia Chenevix-Trench, Douglas F. Easton, Simon A. Gayther, Per Hall, Fergus J. Couch, Stephen J. Chanock, Peter Kraft, Brian E. Henderson, David J. Hunter, Thomas A. Sellers, Amanda Spurdle, Christopher A. Haiman, Jacques Simard, Alison M. Dunning, Andrew Berchuck, Matthew L. Freedman, Fredrick Schumacher, Yu-Tang Gao, Xiao-Ou Shu, Wojciech Kluzniak, William J. Blot, Weiva Sieh, Wei Zheng, Walther Vogel, Volker Arndt, Vessela Kristensen, Veronica Wendy Setiawan, Veli-Matti Kosma, Vanio Mitev, Ute Hamann, Usha Menon, Todd L. Edwards, Tim J. Key, Tiina Wahlfors, Thomas Brüning, Thilo Dörk, Teuvo L.J. Tammela, Tanja Pejovic, Susanne Krüger Kjær, Susan M. Gapstur, Stig E. Bojesen, Stephen N. Thibodeau, Soo-Hwang Teo, Soo Chin Lee, Sonja Berndt, Sofia Maia, Shelley S. Tworoger, Shannon K. McDonnell, Sara H. Olson, Sara Benlloch, Ruth C. Travis, Roger L. Milne, Roberta Ness, Robert Winqvist, Robert N. Hoover, Robert J. MacInnis, Robert A. Stephenson, Rita K. Schmutzler, Reidun Kristin Kopperud, Ralf Butzow, Radka Kaneva, Qiyuan Li, Qiuyin Cai, Qin Wang, Peter Devilee, Peter A. Fasching, Per Broberg, Penelope M. Webb, Paula Paulo, Paul Brennan, Pascal Guénel, Paolo Peterlongo, Nora Pashayan, Nicolas Wentzensen, Nick Orr, Nhu D. Le, Nazneen Rahman, Natalia Bogdanova, Montserrat Garcia-Closas, Minouk J. Schoemaker, Ming-Feng Hou, Michelle A.T. Hildebrandt, Michael Lush, Michael Jones, Melissa C. Southey, Maureen Sanderson, Matthieu Moisse, Matthias W. Beckmann, Mary Anne Rossing, Markus Aly, Marjorie Riggan, Marjanka K. Schmidt, Marc T. Goodman, Manuel R. Teixeira, Manuel Luedeke, Manjeet K. Bolla, Malcolm C. Pike, Maartje J. Hooning, Lisa Cannon-Albright, Linda S. Cook, Liesel M. Fitzgerald, Leon F.A.G. Massuger, Lambertus A. Kiemeney, Kunle Odunsi, Kristiina Aittomäki, Kirsten B. Moysich, Kexin Chen, Kenneth Offitt, Kenneth Muir, Keitaro Matsuo, Kay-Tee Khaw, Kathleen Herkommer, Karen H. Lu, Kamila Czene, Jyotsna Batra, Julio Pow-Sang, Julie M. Cunningham, Julian Peto, Julia A. Knight, Judith A. Clements, Jonine Figueroa, Jong Y. Park, Jolanta Kupryjanczyk, John L. Hopper, Johanna Schleutker, Joellen M. Schildkraut, Joe Dennis, Jenny L. Donovan, Jenny Chang-Claude, Jennifer B. Permuth, Jennifer A. Doherty, Javier Benítez, Janet L. Stanford, Jan Lubiński, Jacek Gronwald, Ignace Vergote, Ian Campbell, Iain McNeish, Hui-Yi Lim, Honglin Song, Hoda Anton-Culver, Hiltrud Brauch, Hermann Brenner, Henrik Gronberg, Heli Nevanlinna, Helga B. Salvesen, Hatef Darabi, Harvey A. Risch, Hardev Pandha, Hans-Ulrich Ulmer, Hans Wildiers, Håkan Olsson, Graham G. Giles, Fredrik Wiklund, Freddie C. Hamdy, Francesmary Modugno, Florian Heitz, Fiona Bruinsma, Fengju Song, Estrid Høgdall, Elza Khusnutdinova, Ellen L. Goode, Elizabeth M. Poole, Elisa V. Bandera, Elinor J. Sawyer, Drakoulis Yannoukakos, Douglas A. Levine, Dominika Wokozorczyk, Digna R. Velez Edwards, Dieter Flesch-Janys, Diana Eccles, David E. Neal, Daniel W. Cramer, Daniel O. Stram, Daniel J. Schaid, Daniel C. Tessier, Daehee Kang, Craig C. Teerlink, Claus K. Høgdall, Christine B. Ambrosone, Christiane Maier, Christa Stegmaier, Chavdar Slavov, Cezary Cybulski, Celine Vachon, Celeste Leigh Pearce, Catriona McLean, Catherine Phelan, Carl Blomqvist, Børge G. Nordestgaard, Beth Y. Karlan, Barbara Burwinkel, Arif B. Ekici, Argyrios Ziogas, Anthony Swerdlow, Annika Lindblom, Anna H. Wu, Anna Gonzalez-Neira, Anja Rudolph, Angela Cox, Andrzej Kierzek, Ana Peixoto, Alvaro Monteiro, Alicja Wolk, Alice S. Whittemore, Aleksandra Gentry-Maharaj, Aida K. Dieffenbach, Agnieszka Michael, Agnieszka Dansonka-Mieszkowska, Adam S. Kibel, Deborah J. Thompson, Susan J. Ramus, Sara Lindstrom, Kate Lawrenson, ZSofia Kote-Jarai, Jonathan Tyrer, Kyriaki Michailidou, Ali Amin Al Olama, Jonathan Beesley, and Siddhartha P. Kar
Abstract: Supplementary Table S1. Known risk loci for each cancer. Supplementary Table S2. Regions where known index SNPs for at least two of the three cancers lie within 1 Mb of each other. Supplementary Table S3. Full results from the meta-analysis of breast, ovarian, and prostate cancer showing the 18 independent loci associated at P < 10-8 with the same direction of effect across all three cancers. Supplementary Table S4. Conditional analysis of the rs1469713 (breast-ovarian-prostate cancer) signal, conditioning on the rs4808801 (breast cancer-specific) signal that was < 1 Mb away using GCTA software. Supplementary Table S5. Most significantly-associated genotyped SNP at new loci where index SNPs were imputed. Supplementary Table S6. Expression QTL analysis results from the GTEx Portal for the new cross-cancer risk loci listed in main Table 2. Supplementary Table S7. SNPs with P < 10-8 at the new cross-cancer risk loci listed in main Table 2 that overlap predicted enhancers in at least two cell types. Supplementary Table S8. HaploReg and non-coding RNA annotation of variants with P < 10-8 at the new cross-cancer risk loci listed in main Table 2. Supplementary Table S9. Eight of the 32 genes involved in induction of apoptosis through DR3 and DR4/5 Death Receptors (MSigDB: Biocarta "Death Pathway") a that were < 1 Mb away from an independent P < 10-5 index SNP in the 3-cancer meta-analysis. Supplementary Table S10. INRICH pathway analysis results for pathways with empirical P < 0.05. Apoptosis-related pathways containing BCL2L11 are shaded.
Published: 2023
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24. Supp. Tables S1, S3-S15, S20, and S23 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer

Author: Ulrike Peters, Shuji Ogino, Antoni Ribas, Charles S. Fuchs, Thomas J. Hudson, Levi A. Garraway, Eric S. Lander, Stacey B. Gabriel, Jesse M. Zaretsky, Syed H. Zaidi, Ming Yu, Catherine J. Wu, David A. Wheeler, Alexander Upfill-Brown, Jennifer Tsoi, Wei Sun, Janet L. Stanford, Sachet Shukla, Brian Shirts, Eve Shinbrot, Daniel Sanghoon Shin, Stephen J. Salipante, Ben J. Raphael, Elleanor H. Quist, Cristina Puig-Saus, Colin C. Pritchard, Matteo Pellegrini, Brian B. Nadel, Dennis J. Montoya, Mark D.M. Leiserson, Paige Krystofinski, Yeon Joo Kim, Jeroen R. Huyghe, Siwen Hu-Lieskovan, Li Hsu, William M. Grady, Milan S. Geybels, Helena Escuin-Ordinas, Charles Connolly, Gabriel Abril-Rodriguez, Katsuhiko Nosho, Teppei Morikawa, Kentaro Inamura, Zhi Rong Qian, Reiko Nishihara, Jonathan A. Nowak, Michael Quist, Xinmeng Jasmine Mu, Tsuyoshi Hamada, Daniel K. Wells, Marios Giannakis, and Catherine S. Grasso
Abstract: Supplementary Tables S1, S3 through S15, S20, and S23
Published: 2023
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25. Supplementary Tables 2 - 5, Figures 2 - 3 from A Large-Scale Analysis of Genetic Variants within Putative miRNA Binding Sites in Prostate Cancer

Author: Jyotsna Batra, Jong Y. Park, Judith A. Clements, Amanda B. Spurdle, Manuel R. Teixeira, Radka Kaneva, Hermann Brenner, Lisa Cannon-Albright, Cezary Cybulski, Adam S. Kibel, Christiane Maier, Stephen Thibodeau, William J. Blot, Janet L. Stanford, Kay-Tee Khaw, Paul Pharoah, David Neal, Ruth C. Travis, Børge G. Nordestgaard, Johanna Schleutker, Christopher A. Haiman, Henrik Gronberg, Fredrik Wiklund, Graham G. Giles, Kenneth Muir, Sara Benlloch, Ali Amin Al Olama, Zsofia Kote-Jarai, Doug Easton, Rosalind Eeles, Srilakshmi Srinivasan, Thomas A. Sellers, Jennifer Permuth-Wey, Hui-Yi Lin, Donghwa Kim, Tracy A. O'Mara, Kerenaftali Klein, Ernest Amankwah, and Shane Stegeman
Abstract: Supplementary Table 2. Indolent versus aggressive disease analysis. Supplementary Table 3. Geometric mean PSA levels by genotype in cases and controls. Supplementary Table 4. Association of miRSNPs with prostate cancer risk in different age categories. Supplementary Table 5. Association of miRSNPs with expression of genes located in cis using TCGA SNP array and RNASeq data. Supplementary Figure 2. miRNA target reporter vector assays. Supplementary Figure 3. miR-3162-5p is expressed in prostate and prostate cancer-derived cell lines as well as in prostate cancer patient tissue samples.
Published: 2023
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26. Supplementary Table 1 from A Large-Scale Analysis of Genetic Variants within Putative miRNA Binding Sites in Prostate Cancer

Author: Jyotsna Batra, Jong Y. Park, Judith A. Clements, Amanda B. Spurdle, Manuel R. Teixeira, Radka Kaneva, Hermann Brenner, Lisa Cannon-Albright, Cezary Cybulski, Adam S. Kibel, Christiane Maier, Stephen Thibodeau, William J. Blot, Janet L. Stanford, Kay-Tee Khaw, Paul Pharoah, David Neal, Ruth C. Travis, Børge G. Nordestgaard, Johanna Schleutker, Christopher A. Haiman, Henrik Gronberg, Fredrik Wiklund, Graham G. Giles, Kenneth Muir, Sara Benlloch, Ali Amin Al Olama, Zsofia Kote-Jarai, Doug Easton, Rosalind Eeles, Srilakshmi Srinivasan, Thomas A. Sellers, Jennifer Permuth-Wey, Hui-Yi Lin, Donghwa Kim, Tracy A. O'Mara, Kerenaftali Klein, Ernest Amankwah, and Shane Stegeman
Abstract: Supplementary Table 1. Prostate cancer risk estimates for 2169 putative miRSNPs.
Published: 2023
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27. Supplementary Figure 1 from A Large-Scale Analysis of Genetic Variants within Putative miRNA Binding Sites in Prostate Cancer

Author: Jyotsna Batra, Jong Y. Park, Judith A. Clements, Amanda B. Spurdle, Manuel R. Teixeira, Radka Kaneva, Hermann Brenner, Lisa Cannon-Albright, Cezary Cybulski, Adam S. Kibel, Christiane Maier, Stephen Thibodeau, William J. Blot, Janet L. Stanford, Kay-Tee Khaw, Paul Pharoah, David Neal, Ruth C. Travis, Børge G. Nordestgaard, Johanna Schleutker, Christopher A. Haiman, Henrik Gronberg, Fredrik Wiklund, Graham G. Giles, Kenneth Muir, Sara Benlloch, Ali Amin Al Olama, Zsofia Kote-Jarai, Doug Easton, Rosalind Eeles, Srilakshmi Srinivasan, Thomas A. Sellers, Jennifer Permuth-Wey, Hui-Yi Lin, Donghwa Kim, Tracy A. O'Mara, Kerenaftali Klein, Ernest Amankwah, and Shane Stegeman
Abstract: Supplementary Figure 1. Forest Plot (Fixed effects model) of the 22 prostate cancer risk associated miRSNPs.
Published: 2023
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28. Data from Genetic Mechanisms of Immune Evasion in Colorectal Cancer

Author: Ulrike Peters, Shuji Ogino, Antoni Ribas, Charles S. Fuchs, Thomas J. Hudson, Levi A. Garraway, Eric S. Lander, Stacey B. Gabriel, Jesse M. Zaretsky, Syed H. Zaidi, Ming Yu, Catherine J. Wu, David A. Wheeler, Alexander Upfill-Brown, Jennifer Tsoi, Wei Sun, Janet L. Stanford, Sachet Shukla, Brian Shirts, Eve Shinbrot, Daniel Sanghoon Shin, Stephen J. Salipante, Ben J. Raphael, Elleanor H. Quist, Cristina Puig-Saus, Colin C. Pritchard, Matteo Pellegrini, Brian B. Nadel, Dennis J. Montoya, Mark D.M. Leiserson, Paige Krystofinski, Yeon Joo Kim, Jeroen R. Huyghe, Siwen Hu-Lieskovan, Li Hsu, William M. Grady, Milan S. Geybels, Helena Escuin-Ordinas, Charles Connolly, Gabriel Abril-Rodriguez, Katsuhiko Nosho, Teppei Morikawa, Kentaro Inamura, Zhi Rong Qian, Reiko Nishihara, Jonathan A. Nowak, Michael Quist, Xinmeng Jasmine Mu, Tsuyoshi Hamada, Daniel K. Wells, Marios Giannakis, and Catherine S. Grasso
Abstract: To understand the genetic drivers of immune recognition and evasion in colorectal cancer, we analyzed 1,211 colorectal cancer primary tumor samples, including 179 classified as microsatellite instability–high (MSI-high). This set includes The Cancer Genome Atlas colorectal cancer cohort of 592 samples, completed and analyzed here. MSI-high, a hypermutated, immunogenic subtype of colorectal cancer, had a high rate of significantly mutated genes in important immune-modulating pathways and in the antigen presentation machinery, including biallelic losses of B2M and HLA genes due to copy-number alterations and copy-neutral loss of heterozygosity. WNT/β-catenin signaling genes were significantly mutated in all colorectal cancer subtypes, and activated WNT/β-catenin signaling was correlated with the absence of T-cell infiltration. This large-scale genomic analysis of colorectal cancer demonstrates that MSI-high cases frequently undergo an immunoediting process that provides them with genetic events allowing immune escape despite high mutational load and frequent lymphocytic infiltration and, furthermore, that colorectal cancer tumors have genetic and methylation events associated with activated WNT signaling and T-cell exclusion.Significance: This multi-omic analysis of 1,211 colorectal cancer primary tumors reveals that it should be possible to better monitor resistance in the 15% of cases that respond to immune blockade therapy and also to use WNT signaling inhibitors to reverse immune exclusion in the 85% of cases that currently do not. Cancer Discov; 8(6); 730–49. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 663
Published: 2023
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29. Data from Risk Analysis of Prostate Cancer in PRACTICAL, a Multinational Consortium, Using 25 Known Prostate Cancer Susceptibility Loci

Author: Douglas F. Easton, Rosalind A. Eeles, Zsofia Kote-Jarai, Antje E. Rinckleb, Aritaya Lophatonanon, John L. Hopper, Kathleen Herkommer, Rosemary Wilkinson, Emma Sawyer, Koveela Govindasami, Sarah J. Little, Tokhir Dadaev, Michelle Guy, Malgorzata Tymrakiewicz, Edward Saunders, Daniel Leongamornlert, Liesel FitzGerald, Amanda B. Spurdle, Melissa C. Southey, Angela Cox, Robert Stephenson, Hong-Wei Zhang, Yong-Jie Lu, Maurice P. Zeegers, William D. Foulkes, Radka P. Kaneva, Pierre Hutter, Pierre O. Chappuis, Kathleen A. Cooney, Stephen N. Thibodeau, Tomonori Habuchi, Charnita Zeigler-Johnson, Timothy R. Rebbeck, Hermann Brenner, Lisa Cannon-Albright, Joanne L. Dickinson, Thilo Doerk, Christiane Maier, Cezary Cybulski, Jong Y. Park, Torben F. Orntoft, Karina D. Sorensen, Sue A. Ingles, Børge G. Nordestgaard, Maren Weischer, Suzanne K. Chambers, Judith A. Clements, Jyotsna Batra, Janet L. Stanford, Elaine A. Ostrander, Paul D.P. Pharoah, Nora Pashayan, Fredrick R. Schumacher, Christopher A. Haiman, Brian E. Henderson, Johanna Schleutker, Kenneth Muir, Jenny L. Donovan, Freddie C. Hamdy, David E. Neal, Gianluca Severi, Graham G. Giles, Antonis C. Antoniou, Sara Benlloch, and Ali Amin Al Olama
Abstract: Background: Genome-wide association studies have identified multiple genetic variants associated with prostate cancer risk which explain a substantial proportion of familial relative risk. These variants can be used to stratify individuals by their risk of prostate cancer.Methods: We genotyped 25 prostate cancer susceptibility loci in 40,414 individuals and derived a polygenic risk score (PRS). We estimated empirical odds ratios (OR) for prostate cancer associated with different risk strata defined by PRS and derived age-specific absolute risks of developing prostate cancer by PRS stratum and family history.Results: The prostate cancer risk for men in the top 1% of the PRS distribution was 30.6 (95% CI, 16.4–57.3) fold compared with men in the bottom 1%, and 4.2 (95% CI, 3.2–5.5) fold compared with the median risk. The absolute risk of prostate cancer by age of 85 years was 65.8% for a man with family history in the top 1% of the PRS distribution, compared with 3.7% for a man in the bottom 1%. The PRS was only weakly correlated with serum PSA level (correlation = 0.09).Conclusions: Risk profiling can identify men at substantially increased or reduced risk of prostate cancer. The effect size, measured by OR per unit PRS, was higher in men at younger ages and in men with family history of prostate cancer. Incorporating additional newly identified loci into a PRS should improve the predictive value of risk profiles.Impact: We demonstrate that the risk profiling based on SNPs can identify men at substantially increased or reduced risk that could have useful implications for targeted prevention and screening programs. Cancer Epidemiol Biomarkers Prev; 24(7); 1121–9. ©2015 AACR.
Published: 2023
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30. Supplementary Figure 1 from Risk Analysis of Prostate Cancer in PRACTICAL, a Multinational Consortium, Using 25 Known Prostate Cancer Susceptibility Loci

Author: Douglas F. Easton, Rosalind A. Eeles, Zsofia Kote-Jarai, Antje E. Rinckleb, Aritaya Lophatonanon, John L. Hopper, Kathleen Herkommer, Rosemary Wilkinson, Emma Sawyer, Koveela Govindasami, Sarah J. Little, Tokhir Dadaev, Michelle Guy, Malgorzata Tymrakiewicz, Edward Saunders, Daniel Leongamornlert, Liesel FitzGerald, Amanda B. Spurdle, Melissa C. Southey, Angela Cox, Robert Stephenson, Hong-Wei Zhang, Yong-Jie Lu, Maurice P. Zeegers, William D. Foulkes, Radka P. Kaneva, Pierre Hutter, Pierre O. Chappuis, Kathleen A. Cooney, Stephen N. Thibodeau, Tomonori Habuchi, Charnita Zeigler-Johnson, Timothy R. Rebbeck, Hermann Brenner, Lisa Cannon-Albright, Joanne L. Dickinson, Thilo Doerk, Christiane Maier, Cezary Cybulski, Jong Y. Park, Torben F. Orntoft, Karina D. Sorensen, Sue A. Ingles, Børge G. Nordestgaard, Maren Weischer, Suzanne K. Chambers, Judith A. Clements, Jyotsna Batra, Janet L. Stanford, Elaine A. Ostrander, Paul D.P. Pharoah, Nora Pashayan, Fredrick R. Schumacher, Christopher A. Haiman, Brian E. Henderson, Johanna Schleutker, Kenneth Muir, Jenny L. Donovan, Freddie C. Hamdy, David E. Neal, Gianluca Severi, Graham G. Giles, Antonis C. Antoniou, Sara Benlloch, and Ali Amin Al Olama
Abstract: Supplementary Figure 1. Absolute Risk (With family history of prostate cancer)
Published: 2023
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31. Data from Validation Study of Genes with Hypermethylated Promoter Regions Associated with Prostate Cancer Recurrence

Author: Janet L. Stanford, Ziding Feng, Jian-Bing Fan, Elaine A. Ostrander, Brandy Klotzle, Marina Bibikova, Suzanne Kolb, Jonathan L. Wright, Shanshan Zhao, and Marni Stott-Miller
Abstract: Background: One challenge in prostate cancer is distinguishing indolent from aggressive disease at diagnosis. DNA promoter hypermethylation is a frequent epigenetic event in prostate cancer, but few studies of DNA methylation in relation to features of more aggressive tumors or prostate cancer recurrence have been completed.Methods: We used the Infinium HumanMethylation450 BeadChip to assess DNA methylation in tumor tissue from 407 patients with clinically localized prostate cancer who underwent radical prostatectomy. Recurrence status was determined by follow-up patient surveys, medical record review, and linkage with the Surveillance, Epidemiology, and End Results (SEER) registry. The methylation status of 14 genes for which promoter hypermethylation was previously correlated with advanced disease or biochemical recurrence was evaluated. Average methylation level for promoter region CpGs in patients who recurred compared with those with no evidence of recurrence was analyzed. For two genes with differential methylation, time to recurrence was examined.Results: During an average follow-up of 11.7 years, 104 (26%) patients recurred. Significant promoter hypermethylation in at least 50% of CpG sites in two genes, ABHD9 and HOXD3, was found in tumors from patients who recurred compared with those without recurrence. Evidence was strongest for HOXD3 (lowest P = 9.46 × 10−6), with higher average methylation across promoter region CpGs associated with reduced recurrence-free survival (P = 2 × 10−4). DNA methylation profiles did not differ by recurrence status for the other genes.Conclusions: These results validate the association between promoter hypermethylation of ADHB9 and HOXD3 and prostate cancer recurrence.Impact: Tumor DNA methylation profiling may help to distinguish patients with prostate cancer at higher risk for disease recurrence. Cancer Epidemiol Biomarkers Prev; 23(7); 1331–9. ©2014 AACR.
Published: 2023
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32. Data from Evaluation of 8q24 and 17q Risk Loci and Prostate Cancer Mortality

Author: Matthew L. Freedman, Meir J. Stampfer, David J. Hunter, Philip W. Kantoff, Janet L. Stanford, Lorelei Mucci, Jing Ma, Tobias Kurth, Elaine A. Ostrander, Oliver Sartor, William K. Oh, Gwo-Shu Lee, Christine A. Beckwith, Fredrick R. Schumacher, Mark Pomerantz, Claudia A. Salinas, and Kathryn L. Penney
Abstract: Purpose: Variants at chromosomal loci 8q24 and 17q are established risk factors for prostate cancer. Many studies have confirmed the findings for risk, but few have examined aggressiveness and other clinical variables in detail. Additionally, Gleason score is typically used as a surrogate for the primary end point of prostate cancer mortality. We investigated whether the 8q24 and 17q risk variants are associated with clinical variables as well as prostate cancer mortality.Experimental Design: In the Physicians' Health Study (1,347 cases and 1,462 controls), the Dana-Farber Harvard Cancer Center Specialized Program of Research Excellence (Gelb Center; 3,714 cases), and the Fred Hutchinson Cancer Research Center King County Case-Control Studies (1,308 cases and 1,266 controls), we examined eight previously identified 8q24 and 17q risk variants for association with prostate cancer mortality in men of European ancestry. We considered associations with other surrogate markers of prostate cancer aggressiveness, such as Gleason score, pathologic stage, prostate-specific antigen at diagnosis, and age at diagnosis.Results: Six of the eight variants were confirmed as prostate cancer risk factors. Several variants were nominally associated with age at diagnosis; when totaling all alleles for single nucleotide polymorphisms significantly associated with risk, each additional allele decreased age at diagnosis by an average of 6 months in the Physicians' Health Study (P = 0.0005) and 4 months in the Dana-Farber Harvard Cancer Center Specialized Program of Research Excellence (Gelb Center) cohort (P = 0.0016). However, there were no statistically significant associations with prostate cancer mortality.Conclusions: Our results suggest that the 8q24 and 17q prostate cancer risk variants may influence age at diagnosis but not disease aggressiveness.
Published: 2023
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33. Data from Validation of Genome-Wide Prostate Cancer Associations in Men of African Descent

Author: Timothy R. Rebbeck, Charnita Zeigler-Johnson, Klara Stefflova, Jong Park, Esther M. John, Jennifer J. Hu, Stephen Chanock, Ann W. Hsing, Rosalind Eeles, Graham Casey, John Witte, Janet L. Stanford, Elaine A. Ostrander, Robin J. Leach, Ian M. Thompson, Adam S. Kibel, Christine Neslund-Dudas, Benjamin Rybicki, Veda N. Giri, Jianfeng Xu, Amit D. Joshi, Roman Corral, Mariana C. Stern, Sue Ann Ingles, Sara Strom, Kathleen Cooney, LaCreis R. Kidd, Marnita L. Benford, William Isaacs, Brian Henderson, Christopher A. Haiman, Stephen Gallagher, Elaine Spangler, and Bao-Li Chang
Abstract: Background: Genome-wide association studies (GWAS) have identified numerous prostate cancer susceptibility alleles, but these loci have been identified primarily in men of European descent. There is limited information about the role of these loci in men of African descent.Methods: We identified 7,788 prostate cancer cases and controls with genotype data for 47 GWAS-identified loci.Results: We identified significant associations for SNP rs10486567 at JAZF1, rs10993994 at MSMB, rs12418451 and rs7931342 at 11q13, and rs5945572 and rs5945619 at NUDT10/11. These associations were in the same direction and of similar magnitude as those reported in men of European descent. Significance was attained at all reported prostate cancer susceptibility regions at chromosome 8q24, including associations reaching genome-wide significance in region 2.Conclusion: We have validated in men of African descent the associations at some, but not all, prostate cancer susceptibility loci originally identified in European descent populations. This may be due to the heterogeneity in genetic etiology or in the pattern of genetic variation across populations.Impact: The genetic etiology of prostate cancer in men of African descent differs from that of men of European descent. Cancer Epidemiol Biomarkers Prev; 20(1); 23–32. ©2011 AACR.
Published: 2023
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34. Data from Epigenome-Wide Tumor DNA Methylation Profiling Identifies Novel Prognostic Biomarkers of Metastatic-Lethal Progression in Men Diagnosed with Clinically Localized Prostate Cancer

Author: Janet L. Stanford, Ziding Feng, Jian-Bing Fan, Elaine A. Ostrander, Jonathan L. Wright, Daniel W. Lin, Raymond Lance, Dean Troyer, Antonio Hurtado-Coll, Marina Bibikova, Brandy Klotzle, Qingxiang Yan, Suzanne Kolb, Rohina Rubicz, Amy Leonardson, Milan S. Geybels, and Shanshan Zhao
Abstract: Purpose: Aside from Gleason sum, few factors accurately identify the subset of prostate cancer patients at high risk for metastatic progression. We hypothesized that epigenetic alterations could distinguish prostate tumors with life-threatening potential.Experimental Design: Epigenome-wide DNA methylation profiling was performed in surgically resected primary tumor tissues from a population-based (n = 430) and a replication (n = 80) cohort of prostate cancer patients followed prospectively for at least 5 years. Metastasis was confirmed by positive bone scan, MRI, CT, or biopsy, and death certificates confirmed cause of death. AUC, partial AUC (pAUC, 95% specificity), and P value criteria were used to select differentially methylated CpG sites that robustly stratify patients with metastatic-lethal from nonrecurrent tumors, and which were complementary to Gleason sum.Results: Forty-two CpG biomarkers stratified patients with metastatic-lethal versus nonrecurrent prostate cancer in the discovery cohort, and eight of these CpGs replicated in the validation cohort based on a significant (P < 0.05) AUC (range, 0.66–0.75) or pAUC (range, 0.007–0.009). The biomarkers that improved discrimination of patients with metastatic-lethal prostate cancer include CpGs in five genes (ALKBH5, ATP11A, FHAD1, KLHL8, and PI15) and three intergenic regions. In the validation dataset, the AUC for Gleason sum alone (0.82) significantly increased with the addition of four individual CpGs (range, 0.86–0.89; all P Conclusions: Eight differentially methylated CpGs that distinguish patients with metastatic-lethal from nonrecurrent tumors were validated. These novel epigenetic biomarkers warrant further investigation as they may improve prognostic classification of patients with clinically localized prostate cancer and provide new insights on tumor aggressiveness. Clin Cancer Res; 23(1); 311–9. ©2016 AACR.
Published: 2023
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35. Supplementary Table 1 from Validation Study of Genes with Hypermethylated Promoter Regions Associated with Prostate Cancer Recurrence

Author: Janet L. Stanford, Ziding Feng, Jian-Bing Fan, Elaine A. Ostrander, Brandy Klotzle, Marina Bibikova, Suzanne Kolb, Jonathan L. Wright, Shanshan Zhao, and Marni Stott-Miller
Abstract: PDF file - 57K, Genes with over 50% of the 5' region CpG sites having higher methylation in tumor tissue from prostate cancer patients with recurrence versus no recurrence.
Published: 2023
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36. Supplementary Figure 3 from Risk Analysis of Prostate Cancer in PRACTICAL, a Multinational Consortium, Using 25 Known Prostate Cancer Susceptibility Loci

Author: Douglas F. Easton, Rosalind A. Eeles, Zsofia Kote-Jarai, Antje E. Rinckleb, Aritaya Lophatonanon, John L. Hopper, Kathleen Herkommer, Rosemary Wilkinson, Emma Sawyer, Koveela Govindasami, Sarah J. Little, Tokhir Dadaev, Michelle Guy, Malgorzata Tymrakiewicz, Edward Saunders, Daniel Leongamornlert, Liesel FitzGerald, Amanda B. Spurdle, Melissa C. Southey, Angela Cox, Robert Stephenson, Hong-Wei Zhang, Yong-Jie Lu, Maurice P. Zeegers, William D. Foulkes, Radka P. Kaneva, Pierre Hutter, Pierre O. Chappuis, Kathleen A. Cooney, Stephen N. Thibodeau, Tomonori Habuchi, Charnita Zeigler-Johnson, Timothy R. Rebbeck, Hermann Brenner, Lisa Cannon-Albright, Joanne L. Dickinson, Thilo Doerk, Christiane Maier, Cezary Cybulski, Jong Y. Park, Torben F. Orntoft, Karina D. Sorensen, Sue A. Ingles, Børge G. Nordestgaard, Maren Weischer, Suzanne K. Chambers, Judith A. Clements, Jyotsna Batra, Janet L. Stanford, Elaine A. Ostrander, Paul D.P. Pharoah, Nora Pashayan, Fredrick R. Schumacher, Christopher A. Haiman, Brian E. Henderson, Johanna Schleutker, Kenneth Muir, Jenny L. Donovan, Freddie C. Hamdy, David E. Neal, Gianluca Severi, Graham G. Giles, Antonis C. Antoniou, Sara Benlloch, and Ali Amin Al Olama
Abstract: Supplementary Figure 3. Absolute Risk (A model with only family history of prostate cancer)
Published: 2023
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37. Supplementary Materials from Validation of Genome-Wide Prostate Cancer Associations in Men of African Descent

Author: Timothy R. Rebbeck, Charnita Zeigler-Johnson, Klara Stefflova, Jong Park, Esther M. John, Jennifer J. Hu, Stephen Chanock, Ann W. Hsing, Rosalind Eeles, Graham Casey, John Witte, Janet L. Stanford, Elaine A. Ostrander, Robin J. Leach, Ian M. Thompson, Adam S. Kibel, Christine Neslund-Dudas, Benjamin Rybicki, Veda N. Giri, Jianfeng Xu, Amit D. Joshi, Roman Corral, Mariana C. Stern, Sue Ann Ingles, Sara Strom, Kathleen Cooney, LaCreis R. Kidd, Marnita L. Benford, William Isaacs, Brian Henderson, Christopher A. Haiman, Stephen Gallagher, Elaine Spangler, and Bao-Li Chang
Abstract: Supplementary Materials from Validation of Genome-Wide Prostate Cancer Associations in Men of African Descent
Published: 2023
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38. Supplemental Table 1 from Epigenome-Wide Tumor DNA Methylation Profiling Identifies Novel Prognostic Biomarkers of Metastatic-Lethal Progression in Men Diagnosed with Clinically Localized Prostate Cancer

Author: Janet L. Stanford, Ziding Feng, Jian-Bing Fan, Elaine A. Ostrander, Jonathan L. Wright, Daniel W. Lin, Raymond Lance, Dean Troyer, Antonio Hurtado-Coll, Marina Bibikova, Brandy Klotzle, Qingxiang Yan, Suzanne Kolb, Rohina Rubicz, Amy Leonardson, Milan S. Geybels, and Shanshan Zhao
Abstract: Number of time the 42 DNA methylation biomarkers were selected in the bootstrap samples
Published: 2023
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39. Supplementary Table 1 from Expression of SLCO Transport Genes in Castration-Resistant Prostate Cancer and Impact of Genetic Variation in SLCO1B3 and SLCO2B1 on Prostate Cancer Outcomes

Author: Elahe A. Mostaghel, Janet L. Stanford, Robert Vessella, Daniel W. Lin, R. Bruce Montgomery, Elaine A. Ostrander, Erika M. Kwon, and Jonathan L. Wright
Abstract: Supplementary Table 1 from Expression of SLCO Transport Genes in Castration-Resistant Prostate Cancer and Impact of Genetic Variation in SLCO1B3 and SLCO2B1 on Prostate Cancer Outcomes
Published: 2023
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40. Supplementary notes from Genome-Wide Association Study of Prostate Cancer–Specific Survival

Author: Fredrik Wiklund, Sara Lindström, Johanna Schleutker, Lovise Maehle, David G. Cox, Anne Tjønneland, Bas H. Bueno-de-Mesquita, Antonia Trichopoulou, Stephanie J. Weinstein, Victoria L. Stevens, Meir J. Stampfer, Kathryn L. Penney, Alison M. Mondul, Jing Ma, Loic Le Marchand, Peter Kraft, David J. Hunter, Edward L. Giovannucci, Susan M. Gapstur, Stephen Chanock, Sonja I. Berndt, Gerald L. Andriole, Demetrius Albanes, Judith A. Clements, Jyotsna Batra, Andrzej Kierzek, Agnieszka Michael, Hardev Pandha, Sofia Maia, Paula Paulo, Manuel R. Teixeira, Amanda Spurdle, Vanio I. Mitev, Radka P. Kaneva, Chavdar Slavov, Hui-Yi Lim, Thomas A. Sellers, Jong Y. Park, Bernd Holleczek, Volker Herrmann, Hermann Brenner, Lisa Cannon-Albright, Wojciech Kluźniak, Jan Lubiński, Cezary Cybulski, Adam S. Kibel, Kathleen Herkommer, Manuel Luedeke, Walther Vogel, Christiane Maier, Daniel J. Schaid, Shannon K. McDonnell, Stephen N. Thibodeau, Janet L. Stanford, Kay-Tee Khaw, Nora Pashayan, Paul D.P. Pharoah, Freddie C. Hamdy, Jenny L. Donovan, David E. Neal, Ruth C. Travis, Timothy J. Key, Børge G. Nordestgaard, Teuvo L.J. Tammela, Csilla Sipeky, Christopher A. Haiman, Fredrick R. Schumacher, Brian E. Henderson, Liesel M. FitzGerald, Melissa C. Southey, Graham G. Giles, Kenneth Muir, Sara Benlloch, Ali Amin Al Olama, Zsofia Kote-Jarai, Douglas F. Easton, Rosalind A. Eeles, Henrik Gronberg, Markus Aly, Thomas Whitington, Robert Karlsson, and Robert Szulkin
Abstract: Supplementary acknowledgments.
Published: 2023
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41. Data from Population-Based Study of the Association of Variants in Mismatch Repair Genes with Prostate Cancer Risk and Outcomes

Author: Janet L. Stanford, Elaine A. Ostrander, Joseph S. Koopmeiners, Erika M. Kwon, and Wendy J. Langeberg
Abstract: Background: Mismatch repair (MMR) gene activity may be associated with prostate cancer risk and outcomes. This study evaluated whether single nucleotide polymorphisms (SNP) in key MMR genes are related to prostate cancer outcomes.Methods: Data from two population-based case-control studies of prostate cancer among Caucasian and African-American men residing in King County, Washington were combined for this analysis. Cases (n = 1,458) were diagnosed with prostate cancer in 1993 to 1996 or 2002 to 2005 and were identified through the Seattle-Puget Sound Surveillance Epidemiology and End Results cancer registry. Controls (n = 1,351) were age-matched to cases and were identified through random digit dialing. Logistic regression was used to assess the relationship between haplotype-tagging SNPs and prostate cancer risk and disease aggressiveness. Cox proportional hazards regression was used to assess the relationship between SNPs and prostate cancer recurrence and prostate cancer–specific death.Results: Nineteen SNPs were evaluated in the key MMR genes: five in MLH1, 10 in MSH2, and 4 in PMS2. Among Caucasian men, one SNP in MLH1 (rs9852810) was associated with overall prostate cancer risk [odds ratio, 1.21; 95% confidence interval (95% CI), 1.02, 1.44; P = 0.03], more aggressive prostate cancer (odds ratio, 1.49; 95% CI, 1.15, 1.91; P < 0.01), and prostate cancer recurrence (hazard ratio, 1.83; 95% CI, 1.18, 2.86; P < 0.01), but not prostate cancer–specific mortality. A nonsynonymous coding SNP in MLH1, rs1799977 (I219V), was also found to be associated with more aggressive disease. These results did not remain significant after adjusting for multiple comparisons.Conclusion: This population-based case-control study provides evidence for a possible association with a gene variant in MLH1 in relation to the risk of overall prostate cancer, more aggressive disease, and prostate cancer recurrence, which warrants replication. Cancer Epidemiol Biomarkers Prev;19(1); OF1–7
Published: 2023
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42. Data from Genetic Polymorphisms in Inflammation Pathway Genes and Prostate Cancer Risk

Author: Elaine A. Ostrander, Janet L. Stanford, Ziding Feng, Rong Fu, Suzanne Kolb, Claudia A. Salinas, and Erika M. Kwon
Abstract: Background: Chronic inflammation is an important mechanism for the development and progression of prostate cancer (PC). To better understand the potential relationship between genes in the inflammation pathway and PC risk, we evaluated variants in 16 candidate genes.Methods: A total of 143 tagging and amino acid altering single nucleotide polymorphisms (SNPs) were genotyped in Caucasian and African American men participating in one of two population-based, case–control studies (n = 1,458 cases and 1,351 controls). The relative risk of PC was estimated using logistic and polytomous regression models.Results: Ten SNPs in seven genes (CXCL12, IL4, IL6, IL6ST, PTGS2, STAT3, and TNF) were nominally associated (P < 0.05) with risk of PC in Caucasians. The most significant effect on risk was seen with rs11574783 in the interleukin 6 signal transducer (IL6ST) gene (OR = 0.08, 95% CI: 0.01–0.63). Cumulatively, four SNPs in genes interleukin 4 (IL4), IL6ST, PTGS2, and signal transducer and activator of transcription 3 (STAT3) conferred a three-fold elevation in PC risk among men carrying the maximum number of high-risk alleles (OR = 2.97, 95% CI: 1.41–6.25, Ptrend = 0.0003). Risk estimates for seven SNPs varied significantly according to disease aggressiveness (Phomogeneity < 0.05), with SNPs in AKT1, PIK3R1, and STAT3 independently associated with more aggressive PC; OR = 5.1 (95% CI: 2.29–11.40, Ptrend = 3.8 × 10−5) for carriers of all high-risk genotypes.Conclusions: These results suggest that variants in genes within the inflammation pathway may play a role in the development of PC, however, further studies are needed to replicate our findings.Impact: These results underline the potential importance of the inflammation pathway in PC development and progression. Cancer Epidemiol Biomarkers Prev; 20(5); 923–33. ©2011 AACR.
Published: 2023
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43. Supplementary Data from Evaluation of 8q24 and 17q Risk Loci and Prostate Cancer Mortality

Author: Matthew L. Freedman, Meir J. Stampfer, David J. Hunter, Philip W. Kantoff, Janet L. Stanford, Lorelei Mucci, Jing Ma, Tobias Kurth, Elaine A. Ostrander, Oliver Sartor, William K. Oh, Gwo-Shu Lee, Christine A. Beckwith, Fredrick R. Schumacher, Mark Pomerantz, Claudia A. Salinas, and Kathryn L. Penney
Abstract: Supplementary Data from Evaluation of 8q24 and 17q Risk Loci and Prostate Cancer Mortality
Published: 2023
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44. Supplementary Notes from Risk Analysis of Prostate Cancer in PRACTICAL, a Multinational Consortium, Using 25 Known Prostate Cancer Susceptibility Loci

Author: Douglas F. Easton, Rosalind A. Eeles, Zsofia Kote-Jarai, Antje E. Rinckleb, Aritaya Lophatonanon, John L. Hopper, Kathleen Herkommer, Rosemary Wilkinson, Emma Sawyer, Koveela Govindasami, Sarah J. Little, Tokhir Dadaev, Michelle Guy, Malgorzata Tymrakiewicz, Edward Saunders, Daniel Leongamornlert, Liesel FitzGerald, Amanda B. Spurdle, Melissa C. Southey, Angela Cox, Robert Stephenson, Hong-Wei Zhang, Yong-Jie Lu, Maurice P. Zeegers, William D. Foulkes, Radka P. Kaneva, Pierre Hutter, Pierre O. Chappuis, Kathleen A. Cooney, Stephen N. Thibodeau, Tomonori Habuchi, Charnita Zeigler-Johnson, Timothy R. Rebbeck, Hermann Brenner, Lisa Cannon-Albright, Joanne L. Dickinson, Thilo Doerk, Christiane Maier, Cezary Cybulski, Jong Y. Park, Torben F. Orntoft, Karina D. Sorensen, Sue A. Ingles, Børge G. Nordestgaard, Maren Weischer, Suzanne K. Chambers, Judith A. Clements, Jyotsna Batra, Janet L. Stanford, Elaine A. Ostrander, Paul D.P. Pharoah, Nora Pashayan, Fredrick R. Schumacher, Christopher A. Haiman, Brian E. Henderson, Johanna Schleutker, Kenneth Muir, Jenny L. Donovan, Freddie C. Hamdy, David E. Neal, Gianluca Severi, Graham G. Giles, Antonis C. Antoniou, Sara Benlloch, and Ali Amin Al Olama
Abstract: Supplementary Notes. This document includes description of studies that they have been used for the analysis.
Published: 2023
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45. Data from Expression of SLCO Transport Genes in Castration-Resistant Prostate Cancer and Impact of Genetic Variation in SLCO1B3 and SLCO2B1 on Prostate Cancer Outcomes

Author: Elahe A. Mostaghel, Janet L. Stanford, Robert Vessella, Daniel W. Lin, R. Bruce Montgomery, Elaine A. Ostrander, Erika M. Kwon, and Jonathan L. Wright
Abstract: Background: Metastases from men with castration-resistant prostate cancer (CRPC) harbor increased tumoral androgens versus untreated prostate cancers. This may reflect steroid uptake by OATP (organic anion transporting polypeptide)/SLCO transporters. We evaluated SLCO gene expression in CRPC metastases and determined whether prostate cancer outcomes are associated with single nucleotide polymorphisms (SNP) in SLCO2B1 and SLCO1B3, transporters previously shown to mediate androgen uptake.Methods: Transcripts encoding eleven SLCO genes were analyzed in untreated prostate cancer and in metastatic CRPC tumors obtained by rapid autopsy. SNPs in SLCO2B1 and SLCO1B3 were genotyped in a population-based cohort of 1,309 Caucasian prostate cancer patients. Median survival follow-up was 7.0 years (0.77–16.4). The risk of prostate cancer recurrence/progression and prostate cancer–specific mortality (PCSM) was estimated with Cox proportional hazards analysis.Results: Six SLCO genes were highly expressed in CRPC metastases versus untreated prostate cancer, including SLCO1B3 (3.6-fold; P = 0.0517) and SLCO2B1 (5.5-fold; P = 0.0034). Carriers of the variant alleles SLCO2B1 SNP rs12422149 (HR: 1.99; 95% CI: 1.11–3.55) or SLCO1B3 SNP rs4149117 (HR: 1.76; 95% CI: 1.00–3.08) had an increased risk of PCSM.Conclusions: CRPC metastases show increased expression of SLCO genes versus primary prostate cancer. Genetic variants of SLCO1B3 and SLCO2B1 are associated with PCSM. Expression and genetic variation of SLCO genes which alter androgen uptake may be important in prostate cancer outcomes.Impact: OATP/SLCO genes may be potential biomarkers for assessing risk of PCSM. Expression and genetic variation in these genes may allow stratification of patients to more aggressive hormonal therapy or earlier incorporation of nonhormonal-based treatment strategies. Cancer Epidemiol Biomarkers Prev; 20(4); 619–27. ©2011 AACR.
Published: 2023
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46. Supplementary Table 1 from Genetic Polymorphisms in Inflammation Pathway Genes and Prostate Cancer Risk

Author: Elaine A. Ostrander, Janet L. Stanford, Ziding Feng, Rong Fu, Suzanne Kolb, Claudia A. Salinas, and Erika M. Kwon
Abstract: Supplementary Table 1 from Genetic Polymorphisms in Inflammation Pathway Genes and Prostate Cancer Risk
Published: 2023
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47. Data from Germline Missense Variants in the BTNL2 Gene Are Associated with Prostate Cancer Susceptibility

Author: Janet L. Stanford, Jay Shendure, Li Hsu, Elaine A. Ostrander, Danielle M. Karyadi, Tiffany Smith, Marni Stott-Miller, Suzanne Kolb, Laura M. McIntosh, Yuzheng Zhang, Evan A. Boyle, Akash Kumar, and Liesel M. FitzGerald
Abstract: Background: Rare, inherited mutations account for 5% to 10% of all prostate cancer cases. However, to date, few causative mutations have been identified.Methods: To identify rare mutations for prostate cancer, we conducted whole-exome sequencing (WES) in multiple kindreds (n = 91) from 19 hereditary prostate cancer (HPC) families characterized by aggressive or early-onset phenotypes. Candidate variants (n = 130) identified through family- and bioinformatics-based filtering of WES data were then genotyped in an independent set of 270 HPC families (n = 819 prostate cancer cases; n = 496 unaffected relatives) for replication. Two variants with supportive evidence were subsequently genotyped in a population-based case–control study (n = 1,155 incident prostate cancer cases; n = 1,060 age-matched controls) for further confirmation. All participants were men of European ancestry.Results: The strongest evidence was for two germline missense variants in the butyrophilin-like 2 (BTNL2) gene (rs41441651, p.Asp336Asn and rs28362675, p.Gly454Cys) that segregated with affection status in two of the WES families. In the independent set of 270 HPC families, 1.5% (rs41441651; P = 0.0032) and 1.2% (rs28362675; P = 0.0070) of affected men, but no unaffected men, carried a variant. Both variants were associated with elevated prostate cancer risk in the population-based study (rs41441651: OR, 2.7; 95% CI, 1.27–5.87; P = 0.010; rs28362675: OR, 2.5; 95% CI, 1.16–5.46; P = 0.019).Conclusions: Results indicate that rare BTNL2 variants play a role in susceptibility to both familial and sporadic prostate cancer.Impact: Results implicate BTNL2 as a novel prostate cancer susceptibility gene. Cancer Epidemiol Biomarkers Prev; 22(9); 1520–8. ©2013 AACR.
Published: 2023
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48. Supplementary Figure Legend from Germline Missense Variants in the BTNL2 Gene Are Associated with Prostate Cancer Susceptibility

Author: Janet L. Stanford, Jay Shendure, Li Hsu, Elaine A. Ostrander, Danielle M. Karyadi, Tiffany Smith, Marni Stott-Miller, Suzanne Kolb, Laura M. McIntosh, Yuzheng Zhang, Evan A. Boyle, Akash Kumar, and Liesel M. FitzGerald
Abstract: PDF - 59K, Legend for Supplementary Figure 1.
Published: 2023
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49. Supplementary Table 3 from Germline Missense Variants in the BTNL2 Gene Are Associated with Prostate Cancer Susceptibility

Author: Janet L. Stanford, Jay Shendure, Li Hsu, Elaine A. Ostrander, Danielle M. Karyadi, Tiffany Smith, Marni Stott-Miller, Suzanne Kolb, Laura M. McIntosh, Yuzheng Zhang, Evan A. Boyle, Akash Kumar, and Liesel M. FitzGerald
Abstract: PDF - 51K, Summary of the whole-exome sequencing statistics for the 91 members of 19 hereditary prostate cancer families.
Published: 2023
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50. Supplementary Table 1 from Genetic Variants in the LEPR, CRY1, RNASEL, IL4, and ARVCF Genes Are Prognostic Markers of Prostate Cancer-Specific Mortality

Author: Janet L. Stanford, Henrik Grönberg, Ziding Feng, Elaine A. Ostrander, Jianfeng Xu, William B. Isaacs, Pär Stattin, Fredrik Wiklund, Suzanne Kolb, Siqun Lilly Zheng, Erika M. Kwon, Rong Fu, Liesel M. FitzGerald, and Daniel W. Lin
Abstract: XLS file - 88K
Published: 2023
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