Improving on polygenic scores across complex traits using select and shrink with summary statistics (S4) and LDpred2

Autor: Jonathan P. Tyrer, Pei-Chen Peng, Amber A. DeVries, Simon A. Gayther, Michelle R. Jones, Paul D. Pharoah

Publikováno v: BMC Genomics, Vol 25, Iss 1, Pp 1-12 (2024)

Abstract Background As precision medicine advances, polygenic scores (PGS) have become increasingly important for clinical risk assessment. Many methods have been developed to create polygenic models with increased accuracy for risk prediction. Our s

Externí odkaz: https://doaj.org/article/17d3eb6aa9614ebbb8e169af80d269e8

Opium use and subsequent incidence of cancer: results from the Golestan Cohort Study

Autor: Mahdi Sheikh, MD, Ramin Shakeri, PhD, Hossein Poustchi, PhD, Akram Pourshams, ProfMD, Arash Etemadi, PhD, Farhad Islami, PhD, Masoud Khoshnia, MD, Abdolsamad Gharavi, MD, Gholamreza Roshandel, PhD, Hooman Khademi, MD, Sadaf G Sepanlou, PhD, Maryam Hashemian, PhD, Abdolreza Fazel, MD, Mahdi Zahedi, MD, Behnoush Abedi-Ardekani, MD, Paolo Boffetta, ProfPhD, Sanford M Dawsey, MD, Paul D Pharoah, ProfPhD, Masoud Sotoudeh, ProfMD, Neal D Freedman, PhD, Christian C Abnet, PhD, Nicholas E Day, ProfPhD, Paul Brennan, PhD, Farin Kamangar, ProfPhD, Reza Malekzadeh, ProfMD

Publikováno v: The Lancet Global Health, Vol 8, Iss 5, Pp e649-e660 (2020)

Summary: Background: Evidence is emerging for a role of opiates in various cancers. In this study, we aimed to investigate the association between regular opium use and cancer incidence. Methods: This study was done in a population-based cohort of 50

Externí odkaz: https://doaj.org/article/1b760c4cfe8349c6925f3b1a06b6f67f

Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast–ovarian cancer susceptibility locus

Autor: Kate Lawrenson, Siddhartha Kar, Karen McCue, Karoline Kuchenbaeker, Kyriaki Michailidou, Jonathan Tyrer, Jonathan Beesley, Susan J. Ramus, Qiyuan Li, Melissa K. Delgado, Janet M. Lee, Kristiina Aittomäki, Irene L. Andrulis, Hoda Anton-Culver, Volker Arndt, Banu K. Arun, Brita Arver, Elisa V. Bandera, Monica Barile, Rosa B. Barkardottir, Daniel Barrowdale, Matthias W. Beckmann, Javier Benitez, Andrew Berchuck, Maria Bisogna, Line Bjorge, Carl Blomqvist, William Blot, Natalia Bogdanova, Anders Bojesen, Stig E. Bojesen, Manjeet K. Bolla, Bernardo Bonanni, Anne-Lise Børresen-Dale, Hiltrud Brauch, Paul Brennan, Hermann Brenner, Fiona Bruinsma, Joan Brunet, Shaik Ahmad Buhari, Barbara Burwinkel, Ralf Butzow, Saundra S. Buys, Qiuyin Cai, Trinidad Caldes, Ian Campbell, Rikki Canniotto, Jenny Chang-Claude, Jocelyne Chiquette, Ji-Yeob Choi, Kathleen B. M. Claes, GEMO Study Collaborators, Linda S. Cook, Angela Cox, Daniel W. Cramer, Simon S. Cross, Cezary Cybulski, Kamila Czene, Mary B. Daly, Francesca Damiola, Agnieszka Dansonka-Mieszkowska, Hatef Darabi, Joe Dennis, Peter Devilee, Orland Diez, Jennifer A. Doherty, Susan M. Domchek, Cecilia M. Dorfling, Thilo Dörk, Martine Dumont, Hans Ehrencrona, Bent Ejlertsen, Steve Ellis, EMBRACE, Christoph Engel, Eunjung Lee, D. Gareth Evans, Peter A. Fasching, Lidia Feliubadalo, Jonine Figueroa, Dieter Flesch-Janys, Olivia Fletcher, Henrik Flyger, Lenka Foretova, Florentia Fostira, William D. Foulkes, Brooke L. Fridley, Eitan Friedman, Debra Frost, Gaetana Gambino, Patricia A. Ganz, Judy Garber, Montserrat García-Closas, Aleksandra Gentry-Maharaj, Maya Ghoussaini, Graham G. Giles, Rosalind Glasspool, Andrew K. Godwin, Mark S. Goldberg, David E. Goldgar, Anna González-Neira, Ellen L. Goode, Marc T. Goodman, Mark H. Greene, Jacek Gronwald, Pascal Guénel, Christopher A. Haiman, Per Hall, Emily Hallberg, Ute Hamann, Thomas V. O. Hansen, Patricia A. Harrington, Mikael Hartman, Norhashimah Hassan, Sue Healey, The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON), Florian Heitz, Josef Herzog, Estrid Høgdall, Claus K. Høgdall, Frans B. L. Hogervorst, Antoinette Hollestelle, John L. Hopper, Peter J. Hulick, Tomasz Huzarski, Evgeny N. Imyanitov, KConFab Investigators, Australian Ovarian Cancer Study Group, Claudine Isaacs, Hidemi Ito, Anna Jakubowska, Ramunas Janavicius, Allan Jensen, Esther M. John, Nichola Johnson, Maria Kabisch, Daehee Kang, Miroslav Kapuscinski, Beth Y. Karlan, Sofia Khan, Lambertus A. Kiemeney, Susanne Kruger Kjaer, Julia A. Knight, Irene Konstantopoulou, Veli-Matti Kosma, Vessela Kristensen, Jolanta Kupryjanczyk, Ava Kwong, Miguel de la Hoya, Yael Laitman, Diether Lambrechts, Nhu Le, Kim De Leeneer, Jenny Lester, Douglas A. Levine, Jingmei Li, Annika Lindblom, Jirong Long, Artitaya Lophatananon, Jennifer T. Loud, Karen Lu, Jan Lubinski, Arto Mannermaa, Siranoush Manoukian, Loic Le Marchand, Sara Margolin, Frederik Marme, Leon F. A. G. Massuger, Keitaro Matsuo, Sylvie Mazoyer, Lesley McGuffog, Catriona McLean, Iain McNeish, Alfons Meindl, Usha Menon, Arjen R. Mensenkamp, Roger L. Milne, Marco Montagna, Kirsten B. Moysich, Kenneth Muir, Anna Marie Mulligan, Katherine L. Nathanson, Roberta B. Ness, Susan L. Neuhausen, Heli Nevanlinna, Silje Nord, Robert L. Nussbaum, Kunle Odunsi, Kenneth Offit, Edith Olah, Olufunmilayo I. Olopade, Janet E. Olson, Curtis Olswold, David O’Malley, Irene Orlow, Nick Orr, Ana Osorio, Sue Kyung Park, Celeste L. Pearce, Tanja Pejovic, Paolo Peterlongo, Georg Pfeiler, Catherine M. Phelan, Elizabeth M. Poole, Katri Pylkäs, Paolo Radice, Johanna Rantala, Muhammad Usman Rashid, Gad Rennert, Valerie Rhenius, Kerstin Rhiem, Harvey A. Risch, Gus Rodriguez, Mary Anne Rossing, Anja Rudolph, Helga B. Salvesen, Suleeporn Sangrajrang, Elinor J. Sawyer, Joellen M. Schildkraut, Marjanka K. Schmidt, Rita K. Schmutzler, Thomas A. Sellers, Caroline Seynaeve, Mitul Shah, Chen-Yang Shen, Xiao-Ou Shu, Weiva Sieh, Christian F. Singer, Olga M. Sinilnikova, Susan Slager, Honglin Song, Penny Soucy, Melissa C. Southey, Marie Stenmark-Askmalm, Dominique Stoppa-Lyonnet, Christian Sutter, Anthony Swerdlow, Sandrine Tchatchou, Manuel R. Teixeira, Soo H. Teo, Kathryn L. Terry, Mary Beth Terry, Mads Thomassen, Maria Grazia Tibiletti, Laima Tihomirova, Silvia Tognazzo, Amanda Ewart Toland, Ian Tomlinson, Diana Torres, Thérèse Truong, Chiu-chen Tseng, Nadine Tung, Shelley S. Tworoger, Celine Vachon, Ans M. W. van den Ouweland, Helena C. van Doorn, Elizabeth J. van Rensburg, Laura J. Van't Veer, Adriaan Vanderstichele, Ignace Vergote, Joseph Vijai, Qin Wang, Shan Wang-Gohrke, Jeffrey N. Weitzel, Nicolas Wentzensen, Alice S. Whittemore, Hans Wildiers, Robert Winqvist, Anna H. Wu, Drakoulis Yannoukakos, Sook-Yee Yoon, Jyh-Cherng Yu, Wei Zheng, Ying Zheng, Kum Kum Khanna, Jacques Simard, Alvaro N. Monteiro, Juliet D. French, Fergus J. Couch, Matthew L. Freedman, Douglas F. Easton, Alison M. Dunning, Paul D. Pharoah, Stacey L. Edwards, Georgia Chenevix-Trench, Antonis C. Antoniou, Simon A. Gayther

Publikováno v: Nature Communications, Vol 7, Iss 1, Pp 1-22 (2016)

A region on chromosome 19p13 is associated with the risk of developing ovarian and breast cancer. Here, the authors genotyped SNPs in this region in thousands of breast and ovarian cancer patients and identified SNPs associated with three genes, whic

Externí odkaz: https://doaj.org/article/7f7ca2a3e022413db18aa0dafbffc2d4

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

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

eQTL Associations from GTEx (Release V7 (dbGaP Accession phs000424.v7.p2). Contains single gene eQTLs for BNC2, CNTLN, c9orf92 and SH3GL2 in all tissues and single SNP eQTL for all 40 SNPs in the credible candidate set.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::32c81250434a2db83e4437c4b6315b74
https://doi.org/10.1158/0008-5472.22423766.v1

Supplementary Data from Germline and Somatic Genetic Variants in the p53 Pathway Interact to Affect Cancer Risk, Progression, and Drug Response

Autor: Gareth L. Bond, Hannah Carter, Clare Turnbull, Ian Tomlinson, Enric Domingo, Timothy S. Maughan, Sarah P. Blagden, Meghana Pagadala, Daniel V. Ebner, Val Millar, Andrew Protheroe, Claire Palles, Lukasz F. Grochola, Rick Jansen, Chey Loveday, Paul D. Pharoah, Siddhartha Kar, Janet Shipley, Joanna L. Selfe, Anderson J. Ryan, Yanyan Jiang, Jorge Zeron-Medina, Douglas A. Bell, Xuting Wang, David Sims, Mirvat Surakhy, Sarah De Val, Svanhild Nornes, Samantha Moore, Natasha Sahgal, Elisabeth Bond, Marsha D. Wallace, Philipp H. Richter, Katherine Brown, Giovanni Stracquadanio, Lingyun Xiong, Isaac Kitchen-Smith, Ping Zhang

Supplementary Methods; Supplementary Figures S1-S5

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::43c5eb435e059e37b7df5dbe2572af66
https://doi.org/10.1158/0008-5472.22429038.v1