Literature DB >> 28115406

Genetic Variants in Epigenetic Pathways and Risks of Multiple Cancers in the GAME-ON Consortium.

Reka Toth1,2, Dominique Scherer1,3, Linda E Kelemen4, Angela Risch2,5,6,7, Aditi Hazra8,9, Yesilda Balavarca1, Jean-Pierre J Issa10, Victor Moreno11, Rosalind A Eeles12, Shuji Ogino13,14,15, Xifeng Wu16, Yuanqing Ye16, Rayjean J Hung17,18, Ellen L Goode19, Cornelia M Ulrich20,21,22.   

Abstract

Background: Epigenetic disturbances are crucial in cancer initiation, potentially with pleiotropic effects, and may be influenced by the genetic background.
Methods: In a subsets (ASSET) meta-analytic approach, we investigated associations of genetic variants related to epigenetic mechanisms with risks of breast, lung, colorectal, ovarian and prostate carcinomas using 51,724 cases and 52,001 controls. False discovery rate-corrected P values (q values < 0.05) were considered statistically significant.
Results: Among 162,887 imputed or genotyped variants in 555 candidate genes, SNPs in eight genes were associated with risk of more than one cancer type. For example, variants in BABAM1 were confirmed as a susceptibility locus for squamous cell lung, overall breast, estrogen receptor (ER)-negative breast, and overall prostate, and overall serous ovarian cancer; the most significant variant was rs4808076 [OR = 1.14; 95% confidence interval (CI) = 1.10-1.19; q = 6.87 × 10-5]. DPF1 rs12611084 was inversely associated with ER-negative breast, endometrioid ovarian, and overall and aggressive prostate cancer risk (OR = 0.93; 95% CI = 0.91-0.96; q = 0.005). Variants in L3MBTL3 were associated with colorectal, overall breast, ER-negative breast, clear cell ovarian, and overall and aggressive prostate cancer risk (e.g., rs9388766: OR = 1.06; 95% CI = 1.03-1.08; q = 0.02). Variants in TET2 were significantly associated with overall breast, overall prostate, overall ovarian, and endometrioid ovarian cancer risk, with rs62331150 showing bidirectional effects. Analyses of subpathways did not reveal gene subsets that contributed disproportionately to susceptibility.Conclusions: Functional and correlative studies are now needed to elucidate the potential links between germline genotype, epigenetic function, and cancer etiology.Impact: This approach provides novel insight into possible pleiotropic effects of genes involved in epigenetic processes. Cancer Epidemiol Biomarkers Prev; 26(6); 816-25. ©2017 AACR. ©2017 American Association for Cancer Research.

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Year:  2017        PMID： 28115406      PMCID： PMC6054308          DOI： 10.1158/1055-9965.EPI-16-0728

Source DB:  PubMed          Journal:  Cancer Epidemiol Biomarkers Prev        ISSN： 1055-9965            Impact factor:   4.254


  45 in total

1.  A subset-based approach improves power and interpretation for the combined analysis of genetic association studies of heterogeneous traits.

Authors:  Samsiddhi Bhattacharjee; Preetha Rajaraman; Kevin B Jacobs; William A Wheeler; Beatrice S Melin; Patricia Hartge; Meredith Yeager; Charles C Chung; Stephen J Chanock; Nilanjan Chatterjee
Journal:  Am J Hum Genet       Date:  2012-05-04       Impact factor: 11.025

2.  Genome-scale analysis of aberrant DNA methylation in colorectal cancer.

Authors:  Toshinori Hinoue; Daniel J Weisenberger; Christopher P E Lange; Hui Shen; Hyang-Min Byun; David Van Den Berg; Simeen Malik; Fei Pan; Houtan Noushmehr; Cornelis M van Dijk; Rob A E M Tollenaar; Peter W Laird
Journal:  Genome Res       Date:  2011-06-09       Impact factor: 9.043

3.  A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24.

Authors:  Ellen L Goode; Georgia Chenevix-Trench; Honglin Song; Susan J Ramus; Maria Notaridou; Kate Lawrenson; Martin Widschwendter; Robert A Vierkant; Melissa C Larson; Susanne K Kjaer; Michael J Birrer; Andrew Berchuck; Joellen Schildkraut; Ian Tomlinson; Lambertus A Kiemeney; Linda S Cook; Jacek Gronwald; Montserrat Garcia-Closas; Martin E Gore; Ian Campbell; Alice S Whittemore; Rebecca Sutphen; Catherine Phelan; Hoda Anton-Culver; Celeste Leigh Pearce; Diether Lambrechts; Mary Anne Rossing; Jenny Chang-Claude; Kirsten B Moysich; Marc T Goodman; Thilo Dörk; Heli Nevanlinna; Roberta B Ness; Thorunn Rafnar; Claus Hogdall; Estrid Hogdall; Brooke L Fridley; Julie M Cunningham; Weiva Sieh; Valerie McGuire; Andrew K Godwin; Daniel W Cramer; Dena Hernandez; Douglas Levine; Karen Lu; Edwin S Iversen; Rachel T Palmieri; Richard Houlston; Anne M van Altena; Katja K H Aben; Leon F A G Massuger; Angela Brooks-Wilson; Linda E Kelemen; Nhu D Le; Anna Jakubowska; Jan Lubinski; Krzysztof Medrek; Anne Stafford; Douglas F Easton; Jonathan Tyrer; Kelly L Bolton; Patricia Harrington; Diana Eccles; Ann Chen; Ashley N Molina; Barbara N Davila; Hector Arango; Ya-Yu Tsai; Zhihua Chen; Harvey A Risch; John McLaughlin; Steven A Narod; Argyrios Ziogas; Wendy Brewster; Aleksandra Gentry-Maharaj; Usha Menon; Anna H Wu; Daniel O Stram; Malcolm C Pike; Jonathan Beesley; Penelope M Webb; Xiaoqing Chen; Arif B Ekici; Falk C Thiel; Matthias W Beckmann; Hannah Yang; Nicolas Wentzensen; Jolanta Lissowska; Peter A Fasching; Evelyn Despierre; Frederic Amant; Ignace Vergote; Jennifer Doherty; Rebecca Hein; Shan Wang-Gohrke; Galina Lurie; Michael E Carney; Pamela J Thompson; Ingo Runnebaum; Peter Hillemanns; Matthias Dürst; Natalia Antonenkova; Natalia Bogdanova; Arto Leminen; Ralf Butzow; Tuomas Heikkinen; Kari Stefansson; Patrick Sulem; Sören Besenbacher; Thomas A Sellers; Simon A Gayther; Paul D P Pharoah
Journal:  Nat Genet       Date:  2010-09-19       Impact factor: 38.330

Review 4.  Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer.

Authors:  Christoph Plass; Stefan M Pfister; Anders M Lindroth; Olga Bogatyrova; Rainer Claus; Peter Lichter
Journal:  Nat Rev Genet       Date:  2013-10-09       Impact factor: 53.242

5.  Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy.

Authors:  Cigall Kadoch; Diana C Hargreaves; Courtney Hodges; Laura Elias; Lena Ho; Jeff Ranish; Gerald R Crabtree
Journal:  Nat Genet       Date:  2013-05-05       Impact factor: 38.330

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

Authors:  Afshan Siddiq; Fergus J Couch; Gary K Chen; Sara Lindström; Diana Eccles; Robert C Millikan; Kyriaki Michailidou; Daniel O Stram; Lars Beckmann; Suhn Kyong Rhie; Christine B Ambrosone; Kristiina Aittomäki; Pilar Amiano; Carmel Apicella; Laura Baglietto; Elisa V Bandera; Matthias W Beckmann; Christine D Berg; Leslie Bernstein; Carl Blomqvist; Hiltrud Brauch; Louise Brinton; Quang M Bui; Julie E Buring; Saundra S Buys; Daniele Campa; Jane E Carpenter; Daniel I Chasman; Jenny Chang-Claude; Constance Chen; Françoise Clavel-Chapelon; Angela Cox; Simon S Cross; Kamila Czene; Sandra L Deming; Robert B Diasio; W Ryan Diver; Alison M Dunning; Lorraine Durcan; Arif B Ekici; Peter A Fasching; Heather Spencer Feigelson; Laura Fejerman; Jonine D Figueroa; Olivia Fletcher; Dieter Flesch-Janys; Mia M Gaudet; Susan M Gerty; Jorge L Rodriguez-Gil; Graham G Giles; Carla H van Gils; Andrew K Godwin; Nikki Graham; Dario Greco; Per Hall; Susan E Hankinson; Arndt Hartmann; Rebecca Hein; Judith Heinz; Robert N Hoover; John L Hopper; Jennifer J Hu; Scott Huntsman; Sue A Ingles; Astrid Irwanto; Claudine Isaacs; Kevin B Jacobs; Esther M John; Christina Justenhoven; Rudolf Kaaks; Laurence N Kolonel; Gerhard A Coetzee; Mark Lathrop; Loic Le Marchand; Adam M Lee; I-Min Lee; Timothy Lesnick; Peter Lichtner; Jianjun Liu; Eiliv Lund; Enes Makalic; Nicholas G Martin; Catriona A McLean; Hanne Meijers-Heijboer; Alfons Meindl; Penelope Miron; Kristine R Monroe; Grant W Montgomery; Bertram Müller-Myhsok; Stefan Nickels; Sarah J Nyante; Curtis Olswold; Kim Overvad; Domenico Palli; Daniel J Park; Julie R Palmer; Harsh Pathak; Julian Peto; Paul Pharoah; Nazneen Rahman; Fernando Rivadeneira; Daniel F Schmidt; Rita K Schmutzler; Susan Slager; Melissa C Southey; Kristen N Stevens; Hans-Peter Sinn; Michael F Press; Eric Ross; Elio Riboli; Paul M Ridker; Fredrick R Schumacher; Gianluca Severi; Isabel Dos Santos Silva; Jennifer Stone; Malin Sund; William J Tapper; Michael J Thun; Ruth C Travis; Clare Turnbull; Andre G Uitterlinden; Quinten Waisfisz; Xianshu Wang; Zhaoming Wang; Joellen Weaver; Rüdiger Schulz-Wendtland; Lynne R Wilkens; David Van Den Berg; Wei Zheng; Regina G Ziegler; Elad Ziv; Heli Nevanlinna; Douglas F Easton; David J Hunter; Brian E Henderson; Stephen J Chanock; Montserrat Garcia-Closas; Peter Kraft; Christopher A Haiman; Celine M Vachon
Journal:  Hum Mol Genet       Date:  2012-09-13       Impact factor: 6.150

7.  Fine-scale mapping of the 4q24 locus identifies two independent loci associated with breast cancer risk.

Authors:  Xingyi Guo; Jirong Long; Chenjie Zeng; Kyriaki Michailidou; Maya Ghoussaini; Manjeet K Bolla; Qin Wang; Roger L Milne; Xiao-Ou Shu; Qiuyin Cai; Jonathan Beesley; Siddhartha P Kar; Irene L Andrulis; Hoda Anton-Culver; Volker Arndt; Matthias W Beckmann; Alicia Beeghly-Fadiel; Javier Benitez; William Blot; Natalia Bogdanova; Stig E Bojesen; Hiltrud Brauch; Hermann Brenner; Louise Brinton; Annegien Broeks; Thomas Brüning; Barbara Burwinkel; Hui Cai; Sander Canisius; Jenny Chang-Claude; Ji-Yeob Choi; Fergus J Couch; Angela Cox; Simon S Cross; Kamila Czene; Hatef Darabi; Peter Devilee; Arnaud Droit; Thilo Dörk; Peter A Fasching; Olivia Fletcher; Henrik Flyger; Florentia Fostira; Valerie Gaborieau; Montserrat García-Closas; Graham G Giles; Mervi Grip; Pascal Guénel; Christopher A Haiman; Ute Hamann; Mikael Hartman; Antoinette Hollestelle; John L Hopper; Chia-Ni Hsiung; Hidemi Ito; Anna Jakubowska; Nichola Johnson; Maria Kabisch; Daehee Kang; Sofia Khan; Julia A Knight; Veli-Matti Kosma; Diether Lambrechts; Loic Le Marchand; Jingmei Li; Annika Lindblom; Artitaya Lophatananon; Jan Lubinski; Arto Mannermaa; Siranoush Manoukian; Sara Margolin; Frederik Marme; Keitaro Matsuo; Catriona A McLean; Alfons Meindl; Kenneth Muir; Susan L Neuhausen; Heli Nevanlinna; Silje Nord; Janet E Olson; Nick Orr; Paolo Peterlongo; Thomas Choudary Putti; Anja Rudolph; Suleeporn Sangrajrang; Elinor J Sawyer; Marjanka K Schmidt; Rita K Schmutzler; Chen-Yang Shen; Jiajun Shi; Martha J Shrubsole; Melissa C Southey; Anthony Swerdlow; Soo Hwang Teo; Bernard Thienpont; Amanda Ewart Toland; Robert A E M Tollenaar; Ian P M Tomlinson; Thérèse Truong; Chiu-Chen Tseng; Ans van den Ouweland; Wanqing Wen; Robert Winqvist; Anna Wu; Cheng Har Yip; M Pilar Zamora; Ying Zheng; Per Hall; Paul D P Pharoah; Jacques Simard; Georgia Chenevix-Trench; Alison M Dunning; Douglas F Easton; Wei Zheng
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2015-09-09       Impact factor: 4.254

8.  A meta-analysis of genome-wide association studies to identify prostate cancer susceptibility loci associated with aggressive and non-aggressive disease.

Authors:  Ali Amin Al Olama; Zsofia Kote-Jarai; Fredrick R Schumacher; Fredrik Wiklund; Sonja I Berndt; Sara Benlloch; Graham G Giles; Gianluca Severi; David E Neal; Freddie C Hamdy; Jenny L Donovan; David J Hunter; Brian E Henderson; Michael J Thun; Michael Gaziano; Edward L Giovannucci; Afshan Siddiq; Ruth C Travis; David G Cox; Federico Canzian; Elio Riboli; Timothy J Key; Gerald Andriole; Demetrius Albanes; Richard B Hayes; Johanna Schleutker; Anssi Auvinen; Teuvo L J Tammela; Maren Weischer; Janet L Stanford; Elaine A Ostrander; Cezary Cybulski; Jan Lubinski; Stephen N Thibodeau; Daniel J Schaid; Karina D Sorensen; Jyotsna Batra; Judith A Clements; Suzanne Chambers; Joanne Aitken; Robert A Gardiner; Christiane Maier; Walther Vogel; Thilo Dörk; Hermann Brenner; Tomonori Habuchi; Sue Ingles; Esther M John; Joanne L Dickinson; Lisa Cannon-Albright; Manuel R Teixeira; Radka Kaneva; Hong-Wei Zhang; Yong-Jie Lu; Jong Y Park; Kathleen A Cooney; Kenneth R Muir; Daniel A Leongamornlert; Edward Saunders; Malgorzata Tymrakiewicz; Nadiya Mahmud; Michelle Guy; Koveela Govindasami; Lynne T O'Brien; Rosemary A Wilkinson; Amanda L Hall; Emma J Sawyer; Tokhir Dadaev; Jonathan Morrison; David P Dearnaley; Alan Horwich; Robert A Huddart; Vincent S Khoo; Christopher C Parker; Nicholas Van As; Christopher J Woodhouse; Alan Thompson; Tim Dudderidge; Chris Ogden; Colin S Cooper; Artitaya Lophatonanon; Melissa C Southey; John L Hopper; Dallas English; Jarmo Virtamo; Loic Le Marchand; Daniele Campa; Rudolf Kaaks; Sara Lindstrom; W Ryan Diver; Susan Gapstur; Meredith Yeager; Angela Cox; Mariana C Stern; Roman Corral; Markus Aly; William Isaacs; Jan Adolfsson; Jianfeng Xu; S Lilly Zheng; Tiina Wahlfors; Kimmo Taari; Paula Kujala; Peter Klarskov; Børge G Nordestgaard; M Andreas Røder; Ruth Frikke-Schmidt; Stig E Bojesen; Liesel M FitzGerald; Suzanne Kolb; Erika M Kwon; Danielle M Karyadi; Torben Falck Orntoft; Michael Borre; Antje Rinckleb; Manuel Luedeke; Kathleen Herkommer; Andreas Meyer; Jürgen Serth; James R Marthick; Briony Patterson; Dominika Wokolorczyk; Amanda Spurdle; Felicity Lose; Shannon K McDonnell; Amit D Joshi; Ahva Shahabi; Pedro Pinto; Joana Santos; Ana Ray; Thomas A Sellers; Hui-Yi Lin; Robert A Stephenson; Craig Teerlink; Heiko Muller; Dietrich Rothenbacher; Norihiko Tsuchiya; Shintaro Narita; Guang-Wen Cao; Chavdar Slavov; Vanio Mitev; Stephen Chanock; Henrik Gronberg; Christopher A Haiman; Peter Kraft; Douglas F Easton; Rosalind A Eeles
Journal:  Hum Mol Genet       Date:  2012-10-12       Impact factor: 6.150

9.  FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs.

Authors:  Simon G Coetzee; Suhn K Rhie; Benjamin P Berman; Gerhard A Coetzee; Houtan Noushmehr
Journal:  Nucleic Acids Res       Date:  2012-06-08       Impact factor: 16.971

10.  Integrative annotation of chromatin elements from ENCODE data.

Authors:  Michael M Hoffman; Jason Ernst; Steven P Wilder; Anshul Kundaje; Robert S Harris; Max Libbrecht; Belinda Giardine; Paul M Ellenbogen; Jeffrey A Bilmes; Ewan Birney; Ross C Hardison; Ian Dunham; Manolis Kellis; William Stafford Noble
Journal:  Nucleic Acids Res       Date:  2012-12-05       Impact factor: 16.971
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  4 in total

1.  Cadmium-induced genome-wide DNA methylation changes in growth and oxidative metabolism in Drosophila melanogaster.

Authors:  De-Long Guan; Rui-Rui Ding; Xiao-Yu Hu; Xing-Ran Yang; Sheng-Quan Xu; Wei Gu; Min Zhang
Journal:  BMC Genomics       Date:  2019-05-09       Impact factor: 3.969

Review 2.  The Epigenomics of Embryonic Pathway Signaling in Colorectal Cancer.

Authors:  Curt Balch; Jayaram B Ramapuram; Amit K Tiwari
Journal:  Front Pharmacol       Date:  2017-05-19       Impact factor: 5.810

3.  Elucidation of the Genomic-Epigenomic Interaction Landscape of Aggressive Prostate Cancer.

Authors:  Tarun Karthik Kumar Mamidi; Jiande Wu; Chindo Hicks
Journal:  Biomed Res Int       Date:  2021-01-13       Impact factor: 3.411

4.  Cross-cancer evaluation of polygenic risk scores for 16 cancer types in two large cohorts.

Authors:  Rebecca E Graff; Taylor B Cavazos; Khanh K Thai; Linda Kachuri; Sara R Rashkin; Joshua D Hoffman; Stacey E Alexeeff; Maruta Blatchins; Travis J Meyers; Lancelote Leong; Caroline G Tai; Nima C Emami; Douglas A Corley; Lawrence H Kushi; Elad Ziv; Stephen K Van Den Eeden; Eric Jorgenson; Thomas J Hoffmann; Laurel A Habel; John S Witte; Lori C Sakoda
Journal:  Nat Commun       Date:  2021-02-12       Impact factor: 14.919
  4 in total

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