Literature DB >> 26358132

Collaborative science in the next-generation sequencing era: a viewpoint on how to combine exome sequencing data across sites to identify novel disease susceptibility genes.

Steven N Hart, Kara N Maxwell, Tinu Thomas, Vignesh Ravichandran, Bradley Wubberhorst, Robert J Klein, Kasmintan Schrader, Csilla Szabo, Jeffrey N Weitzel, Susan L Neuhausen, Katherine Nathanson, Kenneth Offit, Fergus J Couch, Joseph Vijai.   

Abstract

The purpose of this article is to inform readers about technical challenges that we encountered when assembling exome sequencing data from the 'Simplifying Complex Exomes' (SIMPLEXO) consortium-whose mandate is the discovery of novel genes predisposing to breast and ovarian cancers. Our motivation is to share these obstacles-and our solutions to them-as a means of communicating important technical details that should be discussed early in projects involving massively parallel sequencing.
© The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Entities:  

Keywords:  exome; genomics

Mesh：

Year:  2015        PMID： 26358132      PMCID： PMC4945829          DOI： 10.1093/bib/bbv075

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN： 1467-5463            Impact factor:   11.622


  28 in total

1.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Authors:  Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo
Journal:  Genome Res       Date:  2010-07-19       Impact factor: 9.043

2.  A large-scale screen for coding variants predisposing to psoriasis.

Authors:  Huayang Tang; Xin Jin; Yang Li; Hui Jiang; Xianfa Tang; Xu Yang; Hui Cheng; Ying Qiu; Gang Chen; Junpu Mei; Fusheng Zhou; Renhua Wu; Xianbo Zuo; Yong Zhang; Xiaodong Zheng; Qi Cai; Xianyong Yin; Cheng Quan; Haojing Shao; Yong Cui; Fangzhen Tian; Xia Zhao; Hong Liu; Fengli Xiao; Fengping Xu; Jianwen Han; Dongmei Shi; Anping Zhang; Cheng Zhou; Qibin Li; Xing Fan; Liya Lin; Hongqing Tian; Zaixing Wang; Huiling Fu; Fang Wang; Baoqi Yang; Shaowei Huang; Bo Liang; Xuefeng Xie; Yunqing Ren; Qingquan Gu; Guangdong Wen; Yulin Sun; Xueli Wu; Lin Dang; Min Xia; Junjun Shan; Tianhang Li; Lin Yang; Xiuyun Zhang; Yuzhen Li; Chundi He; Aie Xu; Liping Wei; Xiaohang Zhao; Xinghua Gao; Jinhua Xu; Furen Zhang; Jianzhong Zhang; Yingrui Li; Liangdan Sun; Jianjun Liu; Runsheng Chen; Sen Yang; Jun Wang; Xuejun Zhang
Journal:  Nat Genet       Date:  2013-11-10       Impact factor: 38.330

3.  Association of exome sequences with plasma C-reactive protein levels in >9000 participants.

Authors:  Ursula M Schick; Paul L Auer; Joshua C Bis; Honghuang Lin; Peng Wei; Nathan Pankratz; Leslie A Lange; Jennifer Brody; Nathan O Stitziel; Daniel S Kim; Christopher S Carlson; Myriam Fornage; Jeffery Haessler; Li Hsu; Rebecca D Jackson; Charles Kooperberg; Suzanne M Leal; Bruce M Psaty; Eric Boerwinkle; Russell Tracy; Diego Ardissino; Svati Shah; Cristen Willer; Ruth Loos; Olle Melander; Ruth Mcpherson; Kees Hovingh; Muredach Reilly; Hugh Watkins; Domenico Girelli; Pierre Fontanillas; Daniel I Chasman; Stacey B Gabriel; Richard Gibbs; Deborah A Nickerson; Sekar Kathiresan; Ulrike Peters; Josée Dupuis; James G Wilson; Stephen S Rich; Alanna C Morrison; Emelia J Benjamin; Myron D Gross; Alex P Reiner
Journal:  Hum Mol Genet       Date:  2014-09-03       Impact factor: 6.150

4.  Loss-of-function mutations in SLC30A8 protect against type 2 diabetes.

Authors:  Jason Flannick; Gudmar Thorleifsson; Nicola L Beer; Suzanne B R Jacobs; Niels Grarup; Noël P Burtt; Anubha Mahajan; Christian Fuchsberger; Gil Atzmon; Rafn Benediktsson; John Blangero; Don W Bowden; Ivan Brandslund; Julia Brosnan; Frank Burslem; John Chambers; Yoon Shin Cho; Cramer Christensen; Desirée A Douglas; Ravindranath Duggirala; Zachary Dymek; Yossi Farjoun; Timothy Fennell; Pierre Fontanillas; Tom Forsén; Stacey Gabriel; Benjamin Glaser; Daniel F Gudbjartsson; Craig Hanis; Torben Hansen; Astradur B Hreidarsson; Kristian Hveem; Erik Ingelsson; Bo Isomaa; Stefan Johansson; Torben Jørgensen; Marit Eika Jørgensen; Sekar Kathiresan; Augustine Kong; Jaspal Kooner; Jasmina Kravic; Markku Laakso; Jong-Young Lee; Lars Lind; Cecilia M Lindgren; Allan Linneberg; Gisli Masson; Thomas Meitinger; Karen L Mohlke; Anders Molven; Andrew P Morris; Shobha Potluri; Rainer Rauramaa; Rasmus Ribel-Madsen; Ann-Marie Richard; Tim Rolph; Veikko Salomaa; Ayellet V Segrè; Hanna Skärstrand; Valgerdur Steinthorsdottir; Heather M Stringham; Patrick Sulem; E Shyong Tai; Yik Ying Teo; Tanya Teslovich; Unnur Thorsteinsdottir; Jeff K Trimmer; Tiinamaija Tuomi; Jaakko Tuomilehto; Fariba Vaziri-Sani; Benjamin F Voight; James G Wilson; Michael Boehnke; Mark I McCarthy; Pål R Njølstad; Oluf Pedersen; Leif Groop; David R Cox; Kari Stefansson; David Altshuler
Journal:  Nat Genet       Date:  2014-03-02       Impact factor: 38.330

5.  Identification of a BRCA2-specific modifier locus at 6p24 related to breast cancer risk.

Authors:  Mia M Gaudet; Karoline B Kuchenbaecker; Joseph Vijai; Robert J Klein; Tomas Kirchhoff; Lesley McGuffog; Daniel Barrowdale; Alison M Dunning; Andrew Lee; Joe Dennis; Sue Healey; Ed Dicks; Penny Soucy; Olga M Sinilnikova; Vernon S Pankratz; Xianshu Wang; Ronald C Eldridge; Daniel C Tessier; Daniel Vincent; Francois Bacot; Frans B L Hogervorst; Susan Peock; Dominique Stoppa-Lyonnet; Paolo Peterlongo; Rita K Schmutzler; Katherine L Nathanson; Marion Piedmonte; Christian F Singer; Mads Thomassen; Thomas v O Hansen; Susan L Neuhausen; Ignacio Blanco; Mark H Greene; Judith Garber; Jeffrey N Weitzel; Irene L Andrulis; David E Goldgar; Emma D'Andrea; Trinidad Caldes; Heli Nevanlinna; Ana Osorio; Elizabeth J van Rensburg; Adalgeir Arason; Gad Rennert; Ans M W van den Ouweland; Annemarie H van der Hout; Carolien M Kets; Cora M Aalfs; Juul T Wijnen; Margreet G E M Ausems; Debra Frost; Steve Ellis; Elena Fineberg; Radka Platte; D Gareth Evans; Chris Jacobs; Julian Adlard; Marc Tischkowitz; Mary E Porteous; Francesca Damiola; Lisa Golmard; Laure Barjhoux; Michel Longy; Muriel Belotti; Sandra Fert Ferrer; Sylvie Mazoyer; Amanda B Spurdle; Siranoush Manoukian; Monica Barile; Maurizio Genuardi; Norbert Arnold; Alfons Meindl; Christian Sutter; Barbara Wappenschmidt; Susan M Domchek; Georg Pfeiler; Eitan Friedman; Uffe Birk Jensen; Mark Robson; Sohela Shah; Conxi Lazaro; Phuong L Mai; Javier Benitez; Melissa C Southey; Marjanka K Schmidt; Peter A Fasching; Julian Peto; Manjeet K Humphreys; Qin Wang; Kyriaki Michailidou; Elinor J Sawyer; Barbara Burwinkel; Pascal Guénel; Stig E Bojesen; Roger L Milne; Hermann Brenner; Magdalena Lochmann; Kristiina Aittomäki; Thilo Dörk; Sara Margolin; Arto Mannermaa; Diether Lambrechts; Jenny Chang-Claude; Paolo Radice; Graham G Giles; Christopher A Haiman; Robert Winqvist; Peter Devillee; Montserrat García-Closas; Nils Schoof; Maartje J Hooning; Angela Cox; Paul D P Pharoah; Anna Jakubowska; Nick Orr; Anna González-Neira; Guillermo Pita; M Rosario Alonso; Per Hall; Fergus J Couch; Jacques Simard; David Altshuler; Douglas F Easton; Georgia Chenevix-Trench; Antonis C Antoniou; Kenneth Offit
Journal:  PLoS Genet       Date:  2013-03-27       Impact factor: 5.917

6.  COMPLEXO: identifying the missing heritability of breast cancer via next generation collaboration.

Authors:  Melissa C Southey; Daniel J Park; Tu Nguyen-Dumont; Ian Campbell; Ella Thompson; Alison H Trainer; Georgia Chenevix-Trench; Jacques Simard; Martine Dumont; Penny Soucy; Mads Thomassen; Lars Jønson; Inge S Pedersen; Thomas Vo Hansen; Heli Nevanlinna; Sofia Khan; Olga Sinilnikova; Sylvie Mazoyer; Fabienne Lesueur; Francesca Damiola; Rita Schmutzler; Alfons Meindl; Eric Hahnen; Michael R Dufault; Tl Chris Chan; Ava Kwong; Rosa Barkardóttir; Paolo Radice; Paolo Peterlongo; Peter Devilee; Florentine Hilbers; Javier Benitez; Anders Kvist; Therese Törngren; Douglas Easton; David Hunter; Sara Lindstrom; Peter Kraft; Wei Zheng; Yu-Tang Gao; Jirong Long; Susan Ramus; Bing-Jian Feng; Jeffrey N Weitzel; Katherine Nathanson; Kenneth Offit; Vijai Joseph; Mark Robson; Kasmintan Schrader; San Wang; Yeong C Kim; Henry Lynch; Carrie Snyder; Sean Tavtigian; Susan Neuhausen; Fergus J Couch; David E Goldgar
Journal:  Breast Cancer Res       Date:  2013-06-21       Impact factor: 6.466

7.  GEMINI: integrative exploration of genetic variation and genome annotations.

Authors:  Umadevi Paila; Brad A Chapman; Rory Kirchner; Aaron R Quinlan
Journal:  PLoS Comput Biol       Date:  2013-07-18       Impact factor: 4.475

8.  Evaluation of SNP calling using single and multiple-sample calling algorithms by validation against array base genotyping and Mendelian inheritance.

Authors:  Pankaj Kumar; Mashael Al-Shafai; Wadha Ahmed Al Muftah; Nader Chalhoub; Mahmoud F Elsaid; Alice Abdel Aleem; Karsten Suhre
Journal:  BMC Res Notes       Date:  2014-10-22

9.  Genome-wide association study identifies novel breast cancer susceptibility loci.

Authors:  Douglas F Easton; Karen A Pooley; Alison M Dunning; Paul D P Pharoah; Deborah Thompson; Dennis G Ballinger; Jeffery P Struewing; Jonathan Morrison; Helen Field; Robert Luben; Nicholas Wareham; Shahana Ahmed; Catherine S Healey; Richard Bowman; Kerstin B Meyer; Christopher A Haiman; Laurence K Kolonel; Brian E Henderson; Loic Le Marchand; Paul Brennan; Suleeporn Sangrajrang; Valerie Gaborieau; Fabrice Odefrey; Chen-Yang Shen; Pei-Ei Wu; Hui-Chun Wang; Diana Eccles; D Gareth Evans; Julian Peto; Olivia Fletcher; Nichola Johnson; Sheila Seal; Michael R Stratton; Nazneen Rahman; Georgia Chenevix-Trench; Stig E Bojesen; Børge G Nordestgaard; Christen K Axelsson; Montserrat Garcia-Closas; Louise Brinton; Stephen Chanock; Jolanta Lissowska; Beata Peplonska; Heli Nevanlinna; Rainer Fagerholm; Hannaleena Eerola; Daehee Kang; Keun-Young Yoo; Dong-Young Noh; Sei-Hyun Ahn; David J Hunter; Susan E Hankinson; David G Cox; Per Hall; Sara Wedren; Jianjun Liu; Yen-Ling Low; Natalia Bogdanova; Peter Schürmann; Thilo Dörk; Rob A E M Tollenaar; Catharina E Jacobi; Peter Devilee; Jan G M Klijn; Alice J Sigurdson; Michele M Doody; Bruce H Alexander; Jinghui Zhang; Angela Cox; Ian W Brock; Gordon MacPherson; Malcolm W R Reed; Fergus J Couch; Ellen L Goode; Janet E Olson; Hanne Meijers-Heijboer; Ans van den Ouweland; André Uitterlinden; Fernando Rivadeneira; Roger L Milne; Gloria Ribas; Anna Gonzalez-Neira; Javier Benitez; John L Hopper; Margaret McCredie; Melissa Southey; Graham G Giles; Chris Schroen; Christina Justenhoven; Hiltrud Brauch; Ute Hamann; Yon-Dschun Ko; Amanda B Spurdle; Jonathan Beesley; Xiaoqing Chen; Arto Mannermaa; Veli-Matti Kosma; Vesa Kataja; Jaana Hartikainen; Nicholas E Day; David R Cox; Bruce A J Ponder
Journal:  Nature       Date:  2007-06-28       Impact factor: 49.962

10.  An integrated map of genetic variation from 1,092 human genomes.

Authors:  Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean
Journal:  Nature       Date:  2012-11-01       Impact factor: 49.962
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  3 in total

1.  Evaluation of ACMG-Guideline-Based Variant Classification of Cancer Susceptibility and Non-Cancer-Associated Genes in Families Affected by Breast Cancer.

Authors:  Kara N Maxwell; Steven N Hart; Joseph Vijai; Kasmintan A Schrader; Thomas P Slavin; Tinu Thomas; Bradley Wubbenhorst; Vignesh Ravichandran; Raymond M Moore; Chunling Hu; Lucia Guidugli; Brandon Wenz; Susan M Domchek; Mark E Robson; Csilla Szabo; Susan L Neuhausen; Jeffrey N Weitzel; Kenneth Offit; Fergus J Couch; Katherine L Nathanson
Journal:  Am J Hum Genet       Date:  2016-05-05       Impact factor: 11.025

2.  Interdisciplinary approach towards a systems medicine toolbox using the example of inflammatory diseases.

Authors:  Christian R Bauer; Carolin Knecht; Christoph Fretter; Benjamin Baum; Sandra Jendrossek; Malte Rühlemann; Femke-Anouska Heinsen; Nadine Umbach; Bodo Grimbacher; Andre Franke; Wolfgang Lieb; Michael Krawczak; Marc-Thorsten Hütt; Ulrich Sax
Journal:  Brief Bioinform       Date:  2017-05-01       Impact factor: 11.622

3.  Toward automation of germline variant curation in clinical cancer genetics.

Authors:  Vignesh Ravichandran; Zarina Shameer; Yelena Kemel; Michael Walsh; Karen Cadoo; Steven Lipkin; Diana Mandelker; Liying Zhang; Zsofia Stadler; Mark Robson; Kenneth Offit; Joseph Vijai
Journal:  Genet Med       Date:  2019-02-21       Impact factor: 8.822
  3 in total

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