Literature DB >> 21614091

Principles for the post-GWAS functional characterization of cancer risk loci.

Matthew L Freedman1, Alvaro N A Monteiro, Simon A Gayther, Gerhard A Coetzee, Angela Risch, Christoph Plass, Graham Casey, Mariella De Biasi, Chris Carlson, David Duggan, Michael James, Pengyuan Liu, Jay W Tichelaar, Haris G Vikis, Ming You, Ian G Mills.   

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Year:  2011        PMID: 21614091      PMCID: PMC3325768          DOI: 10.1038/ng.840

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   38.330


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  57 in total

Review 1.  Finding genes that underlie complex traits.

Authors:  Anne M Glazier; Joseph H Nadeau; Timothy J Aitman
Journal:  Science       Date:  2002-12-20       Impact factor: 47.728

2.  ChIP-Seq identification of weakly conserved heart enhancers.

Authors:  Matthew J Blow; David J McCulley; Zirong Li; Tao Zhang; Jennifer A Akiyama; Amy Holt; Ingrid Plajzer-Frick; Malak Shoukry; Crystal Wright; Feng Chen; Veena Afzal; James Bristow; Bing Ren; Brian L Black; Edward M Rubin; Axel Visel; Len A Pennacchio
Journal:  Nat Genet       Date:  2010-08-22       Impact factor: 38.330

3.  Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions.

Authors:  Zhihu Zhao; Gholamreza Tavoosidana; Mikael Sjölinder; Anita Göndör; Piero Mariano; Sha Wang; Chandrasekhar Kanduri; Magda Lezcano; Kuljeet Singh Sandhu; Umashankar Singh; Vinod Pant; Vijay Tiwari; Sreenivasulu Kurukuti; Rolf Ohlsson
Journal:  Nat Genet       Date:  2006-10-08       Impact factor: 38.330

4.  Depletion of BRCA1 impairs differentiation but enhances proliferation of mammary epithelial cells.

Authors:  Saori Furuta; Xianzhi Jiang; Bingnan Gu; Eric Cheng; Phang-Lang Chen; Wen-Hwa Lee
Journal:  Proc Natl Acad Sci U S A       Date:  2005-06-20       Impact factor: 11.205

5.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.

Authors:  Lucia A Hindorff; Praveen Sethupathy; Heather A Junkins; Erin M Ramos; Jayashri P Mehta; Francis S Collins; Teri A Manolio
Journal:  Proc Natl Acad Sci U S A       Date:  2009-05-27       Impact factor: 11.205

6.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

7.  Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS.

Authors:  Dan L Nicolae; Eric Gamazon; Wei Zhang; Shiwei Duan; M Eileen Dolan; Nancy J Cox
Journal:  PLoS Genet       Date:  2010-04-01       Impact factor: 5.917

8.  Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes.

Authors:  Hua Zhong; John Beaulaurier; Pek Yee Lum; Cliona Molony; Xia Yang; Douglas J Macneil; Drew T Weingarth; Bin Zhang; Danielle Greenawalt; Radu Dobrin; Ke Hao; Sangsoon Woo; Christine Fabre-Suver; Su Qian; Michael R Tota; Mark P Keller; Christina M Kendziorski; Brian S Yandell; Victor Castro; Alan D Attie; Lee M Kaplan; Eric E Schadt
Journal:  PLoS Genet       Date:  2010-05-06       Impact factor: 5.917

9.  A distal single nucleotide polymorphism alters long-range regulation of the PU.1 gene in acute myeloid leukemia.

Authors:  Ulrich Steidl; Christian Steidl; Alexander Ebralidze; Björn Chapuy; Hye-Jung Han; Britta Will; Frank Rosenbauer; Annegret Becker; Katharina Wagner; Steffen Koschmieder; Susumu Kobayashi; Daniel B Costa; Thomas Schulz; Karen B O'Brien; Roel G W Verhaak; Ruud Delwel; Detlef Haase; Lorenz Trümper; Jürgen Krauter; Terumi Kohwi-Shigematsu; Frank Griesinger; Daniel G Tenen
Journal:  J Clin Invest       Date:  2007-09       Impact factor: 14.808

10.  In search of causal variants: refining disease association signals using cross-population contrasts.

Authors:  Nancy L Saccone; Scott F Saccone; Alison M Goate; Richard A Grucza; Anthony L Hinrichs; John P Rice; Laura J Bierut
Journal:  BMC Genet       Date:  2008-08-29       Impact factor: 2.797

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  221 in total

Review 1.  RNA-Seq and human complex diseases: recent accomplishments and future perspectives.

Authors:  Valerio Costa; Marianna Aprile; Roberta Esposito; Alfredo Ciccodicola
Journal:  Eur J Hum Genet       Date:  2012-06-27       Impact factor: 4.246

2.  Transcriptional output in a prospective design conditionally on follow-up and exposure: the multistage model of cancer.

Authors:  Eiliv Lund; Sandra Plancade
Journal:  Int J Mol Epidemiol Genet       Date:  2012-05-10

3.  eQTL analysis links inflammatory bowel disease associated 1q21 locus to ECM1 gene.

Authors:  Katja Repnik; Uroš Potočnik
Journal:  J Appl Genet       Date:  2016-01-06       Impact factor: 3.240

4.  Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types.

Authors:  Siddhartha P Kar; Jonathan Beesley; Ali Amin Al Olama; Kyriaki Michailidou; Jonathan Tyrer; ZSofia Kote-Jarai; Kate Lawrenson; Sara Lindstrom; Susan J Ramus; Deborah J Thompson; Adam S Kibel; Agnieszka Dansonka-Mieszkowska; Agnieszka Michael; Aida K Dieffenbach; Aleksandra Gentry-Maharaj; Alice S Whittemore; Alicja Wolk; Alvaro Monteiro; Ana Peixoto; Andrzej Kierzek; Angela Cox; Anja Rudolph; Anna Gonzalez-Neira; Anna H Wu; Annika Lindblom; Anthony Swerdlow; Argyrios Ziogas; Arif B Ekici; Barbara Burwinkel; Beth Y Karlan; Børge G Nordestgaard; Carl Blomqvist; Catherine Phelan; Catriona McLean; Celeste Leigh Pearce; Celine Vachon; Cezary Cybulski; Chavdar Slavov; Christa Stegmaier; Christiane Maier; Christine B Ambrosone; Claus K Høgdall; Craig C Teerlink; Daehee Kang; Daniel C Tessier; Daniel J Schaid; Daniel O Stram; Daniel W Cramer; David E Neal; Diana Eccles; Dieter Flesch-Janys; Digna R Velez Edwards; Dominika Wokozorczyk; Douglas A Levine; Drakoulis Yannoukakos; Elinor J Sawyer; Elisa V Bandera; Elizabeth M Poole; Ellen L Goode; Elza Khusnutdinova; Estrid Høgdall; Fengju Song; Fiona Bruinsma; Florian Heitz; Francesmary Modugno; Freddie C Hamdy; Fredrik Wiklund; Graham G Giles; Håkan Olsson; Hans Wildiers; Hans-Ulrich Ulmer; Hardev Pandha; Harvey A Risch; Hatef Darabi; Helga B Salvesen; Heli Nevanlinna; Henrik Gronberg; Hermann Brenner; Hiltrud Brauch; Hoda Anton-Culver; Honglin Song; Hui-Yi Lim; Iain McNeish; Ian Campbell; Ignace Vergote; Jacek Gronwald; Jan Lubiński; Janet L Stanford; Javier Benítez; Jennifer A Doherty; Jennifer B Permuth; Jenny Chang-Claude; Jenny L Donovan; Joe Dennis; Joellen M Schildkraut; Johanna Schleutker; John L Hopper; Jolanta Kupryjanczyk; Jong Y Park; Jonine Figueroa; Judith A Clements; Julia A Knight; Julian Peto; Julie M Cunningham; Julio Pow-Sang; Jyotsna Batra; Kamila Czene; Karen H Lu; Kathleen Herkommer; Kay-Tee Khaw; Keitaro Matsuo; Kenneth Muir; Kenneth Offitt; Kexin Chen; Kirsten B Moysich; Kristiina Aittomäki; Kunle Odunsi; Lambertus A Kiemeney; Leon F A G Massuger; Liesel M Fitzgerald; Linda S Cook; Lisa Cannon-Albright; Maartje J Hooning; Malcolm C Pike; Manjeet K Bolla; Manuel Luedeke; Manuel R Teixeira; Marc T Goodman; Marjanka K Schmidt; Marjorie Riggan; Markus Aly; Mary Anne Rossing; Matthias W Beckmann; Matthieu Moisse; Maureen Sanderson; Melissa C Southey; Michael Jones; Michael Lush; Michelle A T Hildebrandt; Ming-Feng Hou; Minouk J Schoemaker; Montserrat Garcia-Closas; Natalia Bogdanova; Nazneen Rahman; Nhu D Le; Nick Orr; Nicolas Wentzensen; Nora Pashayan; Paolo Peterlongo; Pascal Guénel; Paul Brennan; Paula Paulo; Penelope M Webb; Per Broberg; Peter A Fasching; Peter Devilee; Qin Wang; Qiuyin Cai; Qiyuan Li; Radka Kaneva; Ralf Butzow; Reidun Kristin Kopperud; Rita K Schmutzler; Robert A Stephenson; Robert J MacInnis; Robert N Hoover; Robert Winqvist; Roberta Ness; Roger L Milne; Ruth C Travis; Sara Benlloch; Sara H Olson; Shannon K McDonnell; Shelley S Tworoger; Sofia Maia; Sonja Berndt; Soo Chin Lee; Soo-Hwang Teo; Stephen N Thibodeau; Stig E Bojesen; Susan M Gapstur; Susanne Krüger Kjær; Tanja Pejovic; Teuvo L J Tammela; Thilo Dörk; Thomas Brüning; Tiina Wahlfors; Tim J Key; Todd L Edwards; Usha Menon; Ute Hamann; Vanio Mitev; Veli-Matti Kosma; Veronica Wendy Setiawan; Vessela Kristensen; Volker Arndt; Walther Vogel; Wei Zheng; Weiva Sieh; William J Blot; Wojciech Kluzniak; Xiao-Ou Shu; Yu-Tang Gao; Fredrick Schumacher; Matthew L Freedman; Andrew Berchuck; Alison M Dunning; Jacques Simard; Christopher A Haiman; Amanda Spurdle; Thomas A Sellers; David J Hunter; Brian E Henderson; Peter Kraft; Stephen J Chanock; Fergus J Couch; Per Hall; Simon A Gayther; Douglas F Easton; Georgia Chenevix-Trench; Rosalind Eeles; Paul D P Pharoah; Diether Lambrechts
Journal:  Cancer Discov       Date:  2016-07-17       Impact factor: 39.397

5.  Networks of intergenic long-range enhancers and snpRNAs drive castration-resistant phenotype of prostate cancer and contribute to pathogenesis of multiple common human disorders.

Authors:  Anna B Glinskii; Shuang Ma; Jun Ma; Denise Grant; Chang-Uk Lim; Ian Guest; Stewart Sell; Ralph Buttyan; Gennadi V Glinsky
Journal:  Cell Cycle       Date:  2011-10-15       Impact factor: 4.534

Review 6.  Genetics of sudden cardiac death caused by ventricular arrhythmias.

Authors:  Roos F Marsman; Hanno L Tan; Connie R Bezzina
Journal:  Nat Rev Cardiol       Date:  2013-12-10       Impact factor: 32.419

Review 7.  The rise of regulatory RNA.

Authors:  Kevin V Morris; John S Mattick
Journal:  Nat Rev Genet       Date:  2014-04-29       Impact factor: 53.242

8.  Genetic Modifiers of Progression-Free Survival in Never-Smoking Lung Adenocarcinoma Patients Treated with First-Line Tyrosine Kinase Inhibitors.

Authors:  I-Shou Chang; Shih Sheng Jiang; James Chih-Hsin Yang; Wu-Chou Su; Li-Hsin Chien; Chin-Fu Hsiao; Jih-Hsiang Lee; Chih-Yi Chen; Chung-Hsing Chen; Gee-Chen Chang; Zhaoming Wang; Fang-Yi Lo; Kuan-Yu Chen; Wen-Chang Wang; Yuh-Min Chen; Ming-Shyan Huang; Ying-Huang Tsai; Yu-Chun Su; Wan-Shan Hsieh; Wen-Chi Shih; Shwn-Huey Shieh; Tsung-Ying Yang; Qing Lan; Nathaniel Rothman; Chien-Jen Chen; Stephen J Chanock; Pan-Chyr Yang; Chao A Hsiung
Journal:  Am J Respir Crit Care Med       Date:  2017-03-01       Impact factor: 21.405

9.  Comprehensive functional annotation of susceptibility variants associated with asthma.

Authors:  Yadu Gautam; Yashira Afanador; Sudhir Ghandikota; Tesfaye B Mersha
Journal:  Hum Genet       Date:  2020-04-02       Impact factor: 4.132

10.  Architecture of pharmacogenomic associations: structures with functional foundations or castles made of sand?

Authors:  Dylan M Glubb; Federico Innocenti
Journal:  Pharmacogenomics       Date:  2013-01       Impact factor: 2.533

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