BACKGROUND: Genome-wide association studies of prostate cancer have identified single nucleotide polymorphism (SNP) markers in a region of chromosome 11q13.3 in men of European decent. A fine-mapping analysis with tag SNPs in the cancer genetic markers of susceptibility study identified three independent loci, marked by rs10896438, rs12793759, and rs10896449. This study further annotates common and uncommon variation across this region. METHODS: A next generation resequence analysis of a 122.9-kb region of 11q13.3(68,642,755-68,765,690) was conducted in 78 unrelated individuals of European background,1 CEPH trio, and 1 YRI trio. RESULTS: In total, 644 polymorphic loci were identified by our sequence analysis. Of these,166 variants—118 SNPs and 48 insertion-deletion polymorphisms (indels)—were novel,namely not present in the 1000 Genomes or International HapMap Projects. We identified 22,25, 6, and 4 variants strongly correlated (r2 ≥ 0.8) with rs10896438, rs10896449, rs12793759,and rs11228565, respectively. HapMap SNPs were in linkage disequilibrium (r2 ≥ 0.8) with 48%, 69%, 14%, and 60% of SNPs marking bins by rs10896438, rs10896449, rs12793759, and rs11228565, respectively. CONCLUSIONS: Our next generation resequence analysis compliments publicly available datasets of European descent (HapMap, build 28 and 1000 Genome, Pilot 1, October 2010),underscoring the value of targeted resequence analysis prior to initiating functional studies based on public databases alone. Increasing the number of common variants enables investigators to better prioritize variants for functional studies designed to uncover the biological basis of the direct association(s) in the region.
BACKGROUND: Genome-wide association studies of prostate cancer have identified single nucleotide polymorphism (SNP) markers in a region of chromosome 11q13.3 in men of European decent. A fine-mapping analysis with tag SNPs in the cancer genetic markers of susceptibility study identified three independent loci, marked by rs10896438, rs12793759, and rs10896449. This study further annotates common and uncommon variation across this region. METHODS: A next generation resequence analysis of a 122.9-kb region of 11q13.3(68,642,755-68,765,690) was conducted in 78 unrelated individuals of European background,1 CEPH trio, and 1 YRI trio. RESULTS: In total, 644 polymorphic loci were identified by our sequence analysis. Of these,166 variants—118 SNPs and 48 insertion-deletion polymorphisms (indels)—were novel,namely not present in the 1000 Genomes or International HapMap Projects. We identified 22,25, 6, and 4 variants strongly correlated (r2 ≥ 0.8) with rs10896438, rs10896449, rs12793759,and rs11228565, respectively. HapMap SNPs were in linkage disequilibrium (r2 ≥ 0.8) with 48%, 69%, 14%, and 60% of SNPs marking bins by rs10896438, rs10896449, rs12793759, and rs11228565, respectively. CONCLUSIONS: Our next generation resequence analysis compliments publicly available datasets of European descent (HapMap, build 28 and 1000 Genome, Pilot 1, October 2010),underscoring the value of targeted resequence analysis prior to initiating functional studies based on public databases alone. Increasing the number of common variants enables investigators to better prioritize variants for functional studies designed to uncover the biological basis of the direct association(s) in the region.
Authors: Ali Amin Al Olama; Zsofia Kote-Jarai; Graham G Giles; Michelle Guy; Jonathan Morrison; Gianluca Severi; Daniel A Leongamornlert; Malgorzata Tymrakiewicz; Sameer Jhavar; Ed Saunders; John L Hopper; Melissa C Southey; Kenneth R Muir; Dallas R English; David P Dearnaley; Audrey T Ardern-Jones; Amanda L Hall; Lynne T O'Brien; Rosemary A Wilkinson; Emma Sawyer; Artitaya Lophatananon; Alan Horwich; Robert A Huddart; Vincent S Khoo; Christopher C Parker; Christopher J Woodhouse; Alan Thompson; Tim Christmas; Chris Ogden; Colin Cooper; Jenny L Donovan; Freddie C Hamdy; David E Neal; Rosalind A Eeles; Douglas F Easton Journal: Nat Genet Date: 2009-09-20 Impact factor: 38.330
Authors: Meredith Yeager; Nick Orr; Richard B Hayes; Kevin B Jacobs; Peter Kraft; Sholom Wacholder; Mark J Minichiello; Paul Fearnhead; Kai Yu; Nilanjan Chatterjee; Zhaoming Wang; Robert Welch; Brian J Staats; Eugenia E Calle; Heather Spencer Feigelson; Michael J Thun; Carmen Rodriguez; Demetrius Albanes; Jarmo Virtamo; Stephanie Weinstein; Fredrick R Schumacher; Edward Giovannucci; Walter C Willett; Geraldine Cancel-Tassin; Olivier Cussenot; Antoine Valeri; Gerald L Andriole; Edward P Gelmann; Margaret Tucker; Daniela S Gerhard; Joseph F Fraumeni; Robert Hoover; David J Hunter; Stephen J Chanock; Gilles Thomas Journal: Nat Genet Date: 2007-04-01 Impact factor: 38.330
Authors: Seong-Tae Kim; Yu Cheng; Fang-Chi Hsu; Tao Jin; A Karim Kader; S Lilly Zheng; William B Isaacs; Jianfeng Xu; Jielin Sun Journal: Prostate Date: 2010-12-01 Impact factor: 4.104
Authors: Julius Gudmundsson; Patrick Sulem; Daniel F Gudbjartsson; Thorarinn Blondal; Arnaldur Gylfason; Bjarni A Agnarsson; Kristrun R Benediktsdottir; Droplaug N Magnusdottir; Gudbjorg Orlygsdottir; Margret Jakobsdottir; Simon N Stacey; Asgeir Sigurdsson; Tiina Wahlfors; Teuvo Tammela; Joan P Breyer; Kate M McReynolds; Kevin M Bradley; Berta Saez; Javier Godino; Sebastian Navarrete; Fernando Fuertes; Laura Murillo; Eduardo Polo; Katja K Aben; Inge M van Oort; Brian K Suarez; Brian T Helfand; Donghui Kan; Carlo Zanon; Michael L Frigge; Kristleifur Kristjansson; Jeffrey R Gulcher; Gudmundur V Einarsson; Eirikur Jonsson; William J Catalona; Jose I Mayordomo; Lambertus A Kiemeney; Jeffrey R Smith; Johanna Schleutker; Rosa B Barkardottir; Augustine Kong; Unnur Thorsteinsdottir; Thorunn Rafnar; Kari Stefansson Journal: Nat Genet Date: 2009-09-20 Impact factor: 38.330
Authors: Mark P Purdue; Mattias Johansson; Diana Zelenika; Jorge R Toro; Ghislaine Scelo; Lee E Moore; Egor Prokhortchouk; Xifeng Wu; Lambertus A Kiemeney; Valerie Gaborieau; Kevin B Jacobs; Wong-Ho Chow; David Zaridze; Vsevolod Matveev; Jan Lubinski; Joanna Trubicka; Neonila Szeszenia-Dabrowska; Jolanta Lissowska; Péter Rudnai; Eleonora Fabianova; Alexandru Bucur; Vladimir Bencko; Lenka Foretova; Vladimir Janout; Paolo Boffetta; Joanne S Colt; Faith G Davis; Kendra L Schwartz; Rosamonde E Banks; Peter J Selby; Patricia Harnden; Christine D Berg; Ann W Hsing; Robert L Grubb; Heiner Boeing; Paolo Vineis; Françoise Clavel-Chapelon; Domenico Palli; Rosario Tumino; Vittorio Krogh; Salvatore Panico; Eric J Duell; José Ramón Quirós; Maria-José Sanchez; Carmen Navarro; Eva Ardanaz; Miren Dorronsoro; Kay-Tee Khaw; Naomi E Allen; H Bas Bueno-de-Mesquita; Petra H M Peeters; Dimitrios Trichopoulos; Jakob Linseisen; Börje Ljungberg; Kim Overvad; Anne Tjønneland; Isabelle Romieu; Elio Riboli; Anush Mukeria; Oxana Shangina; Victoria L Stevens; Michael J Thun; W Ryan Diver; Susan M Gapstur; Paul D Pharoah; Douglas F Easton; Demetrius Albanes; Stephanie J Weinstein; Jarmo Virtamo; Lars Vatten; Kristian Hveem; Inger Njølstad; Grethe S Tell; Camilla Stoltenberg; Rajiv Kumar; Kvetoslava Koppova; Olivier Cussenot; Simone Benhamou; Egbert Oosterwijk; Sita H Vermeulen; Katja K H Aben; Saskia L van der Marel; Yuanqing Ye; Christopher G Wood; Xia Pu; Alexander M Mazur; Eugenia S Boulygina; Nikolai N Chekanov; Mario Foglio; Doris Lechner; Ivo Gut; Simon Heath; Hélène Blanche; Amy Hutchinson; Gilles Thomas; Zhaoming Wang; Meredith Yeager; Joseph F Fraumeni; Konstantin G Skryabin; James D McKay; Nathaniel Rothman; Stephen J Chanock; Mark Lathrop; Paul Brennan Journal: Nat Genet Date: 2010-12-05 Impact factor: 38.330
Authors: Meredith Yeager; Nilanjan Chatterjee; Julia Ciampa; Kevin B Jacobs; Jesus Gonzalez-Bosquet; Richard B Hayes; Peter Kraft; Sholom Wacholder; Nick Orr; Sonja Berndt; Kai Yu; Amy Hutchinson; Zhaoming Wang; Laufey Amundadottir; Heather Spencer Feigelson; Michael J Thun; W Ryan Diver; Demetrius Albanes; Jarmo Virtamo; Stephanie Weinstein; Fredrick R Schumacher; Geraldine Cancel-Tassin; Olivier Cussenot; Antoine Valeri; Gerald L Andriole; E David Crawford; Christopher A Haiman; Brian Henderson; Laurence Kolonel; Loic Le Marchand; Afshan Siddiq; Elio Riboli; Timothy J Key; Rudolf Kaaks; William Isaacs; Sarah Isaacs; Kathleen E Wiley; Henrik Gronberg; Fredrik Wiklund; Pär Stattin; Jianfeng Xu; S Lilly Zheng; Jielin Sun; Lars J Vatten; Kristian Hveem; Merethe Kumle; Margaret Tucker; Daniela S Gerhard; Robert N Hoover; Joseph F Fraumeni; David J Hunter; Gilles Thomas; Stephen J Chanock Journal: Nat Genet Date: 2009-09-20 Impact factor: 38.330
Authors: Ying Han; Dennis J Hazelett; Fredrik Wiklund; Fredrick R Schumacher; Daniel O Stram; Sonja I Berndt; Zhaoming Wang; Kristin A Rand; Robert N Hoover; Mitchell J Machiela; Merideth Yeager; Laurie Burdette; Charles C Chung; Amy Hutchinson; Kai Yu; Jianfeng Xu; Ruth C Travis; Timothy J Key; Afshan Siddiq; Federico Canzian; Atsushi Takahashi; Michiaki Kubo; Janet L Stanford; Suzanne Kolb; Susan M Gapstur; W Ryan Diver; Victoria L Stevens; Sara S Strom; Curtis A Pettaway; Ali Amin Al Olama; Zsofia Kote-Jarai; Rosalind A Eeles; Edward D Yeboah; Yao Tettey; Richard B Biritwum; Andrew A Adjei; Evelyn Tay; Ann Truelove; Shelley Niwa; Anand P Chokkalingam; William B Isaacs; Constance Chen; Sara Lindstrom; Loic Le Marchand; Edward L Giovannucci; Mark Pomerantz; Henry Long; Fugen Li; Jing Ma; Meir Stampfer; Esther M John; Sue A Ingles; Rick A Kittles; Adam B Murphy; William J Blot; Lisa B Signorello; Wei Zheng; Demetrius Albanes; Jarmo Virtamo; Stephanie Weinstein; Barbara Nemesure; John Carpten; M Cristina Leske; Suh-Yuh Wu; Anselm J M Hennis; Benjamin A Rybicki; Christine Neslund-Dudas; Ann W Hsing; Lisa Chu; Phyllis J Goodman; Eric A Klein; S Lilly Zheng; John S Witte; Graham Casey; Elio Riboli; Qiyuan Li; Matthew L Freedman; David J Hunter; Henrik Gronberg; Michael B Cook; Hidewaki Nakagawa; Peter Kraft; Stephen J Chanock; Douglas F Easton; Brian E Henderson; Gerhard A Coetzee; David V Conti; Christopher A Haiman Journal: Hum Mol Genet Date: 2015-07-10 Impact factor: 6.150
Authors: Maria Azrad; Kui Zhang; Robin T Vollmer; John Madden; Thomas J Polascik; Denise C Snyder; Mack T Ruffin; Judd W Moul; Dean Brenner; Robert W Hardy; Wendy Demark-Wahnefried Journal: PLoS One Date: 2012-12-28 Impact factor: 3.240