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Literature DB >> 20507892

Evoker: a visualization tool for genotype intensity data.

James A Morris¹, Joshua C Randall, Julian B Maller, Jeffrey C Barrett.

Abstract

SUMMARY: Genome-wide association studies (GWAS), which produce huge volumes of data, are now being carried out by many groups around the world, creating a need for user-friendly tools for data quality control (QC) and analysis. One critical aspect of GWAS QC is evaluating genotype cluster plots to verify sensible genotype calling in putatively associated single nucleotide polymorphisms (SNPs). Evoker is a tool for visualizing genotype cluster plots, and provides a solution to the computational and storage problems related to working with such large datasets. AVAILABILITY: http://www.sanger.ac.uk/resources/software/evoker/

Entities: Disease Gene Species

Mesh：

Year: 2010 PMID： 20507892 PMCID： PMC3073232 DOI： 10.1093/bioinformatics/btq280

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

7 in total

1. PLINK: a tool set for whole-genome association and population-based linkage analyses.

Authors: Shaun Purcell; Benjamin Neale; Kathe Todd-Brown; Lori Thomas; Manuel A R Ferreira; David Bender; Julian Maller; Pamela Sklar; Paul I W de Bakker; Mark J Daly; Pak C Sham
Journal: Am J Hum Genet Date: 2007-07-25 Impact factor: 11.025

2. Genomewide association studies--illuminating biologic pathways.

Authors: Joel N Hirschhorn
Journal: N Engl J Med Date: 2009-04-15 Impact factor: 91.245

3. Practical aspects of imputation-driven meta-analysis of genome-wide association studies.

Authors: Paul I W de Bakker; Manuel A R Ferreira; Xiaoming Jia; Benjamin M Neale; Soumya Raychaudhuri; Benjamin F Voight
Journal: Hum Mol Genet Date: 2008-10-15 Impact factor: 6.150

4. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs.

Authors: Joshua M Korn; Finny G Kuruvilla; Steven A McCarroll; Alec Wysoker; James Nemesh; Simon Cawley; Earl Hubbell; Jim Veitch; Patrick J Collins; Katayoon Darvishi; Charles Lee; Marcia M Nizzari; Stacey B Gabriel; Shaun Purcell; Mark J Daly; David Altshuler
Journal: Nat Genet Date: 2008-09-07 Impact factor: 38.330

5. Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.

Authors: Jeffrey C Barrett; James C Lee; Charles W Lees; Natalie J Prescott; Carl A Anderson; Anne Phillips; Emma Wesley; Kirstie Parnell; Hu Zhang; Hazel Drummond; Elaine R Nimmo; Dunecan Massey; Kasia Blaszczyk; Timothy Elliott; Lynn Cotterill; Helen Dallal; Alan J Lobo; Craig Mowat; Jeremy D Sanderson; Derek P Jewell; William G Newman; Cathryn Edwards; Tariq Ahmad; John C Mansfield; Jack Satsangi; Miles Parkes; Christopher G Mathew; Peter Donnelly; Leena Peltonen; Jenefer M Blackwell; Elvira Bramon; Matthew A Brown; Juan P Casas; Aiden Corvin; Nicholas Craddock; Panos Deloukas; Audrey Duncanson; Janusz Jankowski; Hugh S Markus; Christopher G Mathew; Mark I McCarthy; Colin N A Palmer; Robert Plomin; Anna Rautanen; Stephen J Sawcer; Nilesh Samani; Richard C Trembath; Anath C Viswanathan; Nicholas Wood; Chris C A Spencer; Jeffrey C Barrett; Céline Bellenguez; Daniel Davison; Colin Freeman; Amy Strange; Peter Donnelly; Cordelia Langford; Sarah E Hunt; Sarah Edkins; Rhian Gwilliam; Hannah Blackburn; Suzannah J Bumpstead; Serge Dronov; Matthew Gillman; Emma Gray; Naomi Hammond; Alagurevathi Jayakumar; Owen T McCann; Jennifer Liddle; Marc L Perez; Simon C Potter; Radhi Ravindrarajah; Michelle Ricketts; Matthew Waller; Paul Weston; Sara Widaa; Pamela Whittaker; Panos Deloukas; Leena Peltonen; Christopher G Mathew; Jenefer M Blackwell; Matthew A Brown; Aiden Corvin; Mark I McCarthy; Chris C A Spencer; Antony P Attwood; Jonathan Stephens; Jennifer Sambrook; Willem H Ouwehand; Wendy L McArdle; Susan M Ring; David P Strachan
Journal: Nat Genet Date: 2009-11-15 Impact factor: 38.330

6. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.

Authors:
Journal: Nature Date: 2007-06-07 Impact factor: 49.962

7. A genotype calling algorithm for the Illumina BeadArray platform.

Authors: Yik Y Teo; Michael Inouye; Kerrin S Small; Rhian Gwilliam; Panagiotis Deloukas; Dominic P Kwiatkowski; Taane G Clark
Journal: Bioinformatics Date: 2007-09-10 Impact factor: 6.937

7 in total

20 in total

1. A genome-wide association study on common SNPs and rare CNVs in anorexia nervosa.

Authors: K Wang; H Zhang; C S Bloss; V Duvvuri; W Kaye; N J Schork; W Berrettini; H Hakonarson
Journal: Mol Psychiatry Date: 2010-11-16 Impact factor: 15.992

2. optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants.

Authors: T S Shah; J Z Liu; J A B Floyd; J A Morris; N Wirth; J C Barrett; C A Anderson
Journal: Bioinformatics Date: 2012-04-12 Impact factor: 6.937

3. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.

Authors: Jimmy Z Liu; Suzanne van Sommeren; Hailiang Huang; Siew C Ng; Rudi Alberts; Atsushi Takahashi; Stephan Ripke; James C Lee; Luke Jostins; Tejas Shah; Shifteh Abedian; Jae Hee Cheon; Judy Cho; Naser E Dayani; Lude Franke; Yuta Fuyuno; Ailsa Hart; Ramesh C Juyal; Garima Juyal; Won Ho Kim; Andrew P Morris; Hossein Poustchi; William G Newman; Vandana Midha; Timothy R Orchard; Homayon Vahedi; Ajit Sood; Joseph Y Sung; Reza Malekzadeh; Harm-Jan Westra; Keiko Yamazaki; Suk-Kyun Yang; Jeffrey C Barrett; Behrooz Z Alizadeh; Miles Parkes; Thelma Bk; Mark J Daly; Michiaki Kubo; Carl A Anderson; Rinse K Weersma
Journal: Nat Genet Date: 2015-07-20 Impact factor: 41.307

4. Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.

Authors: George F Mells; James A B Floyd; Katherine I Morley; Heather J Cordell; Christopher S Franklin; So-Youn Shin; Michael A Heneghan; James M Neuberger; Peter T Donaldson; Darren B Day; Samantha J Ducker; Agnes W Muriithi; Elizabeth F Wheater; Christopher J Hammond; Muhammad F Dawwas; David E Jones; Leena Peltonen; Graeme J Alexander; Richard N Sandford; Carl A Anderson
Journal: Nat Genet Date: 2011-03-13 Impact factor: 38.330

5. Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis.

Authors: Jimmy Z Liu; Mohamed A Almarri; Daniel J Gaffney; George F Mells; Luke Jostins; Heather J Cordell; Samantha J Ducker; Darren B Day; Michael A Heneghan; James M Neuberger; Peter T Donaldson; Andrew J Bathgate; Andrew Burroughs; Mervyn H Davies; David E Jones; Graeme J Alexander; Jeffrey C Barrett; Richard N Sandford; Carl A Anderson
Journal: Nat Genet Date: 2012-09-09 Impact factor: 38.330

6. Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis.

Authors: Jimmy Z Liu; Johannes Roksund Hov; Trine Folseraas; Eva Ellinghaus; Simon M Rushbrook; Nadezhda T Doncheva; Ole A Andreassen; Rinse K Weersma; Tobias J Weismüller; Bertus Eksteen; Pietro Invernizzi; Gideon M Hirschfield; Daniel Nils Gotthardt; Albert Pares; David Ellinghaus; Tejas Shah; Brian D Juran; Piotr Milkiewicz; Christian Rust; Christoph Schramm; Tobias Müller; Brijesh Srivastava; Georgios Dalekos; Markus M Nöthen; Stefan Herms; Juliane Winkelmann; Mitja Mitrovic; Felix Braun; Cyriel Y Ponsioen; Peter J P Croucher; Martina Sterneck; Andreas Teufel; Andrew L Mason; Janna Saarela; Virpi Leppa; Ruslan Dorfman; Domenico Alvaro; Annarosa Floreani; Suna Onengut-Gumuscu; Stephen S Rich; Wesley K Thompson; Andrew J Schork; Sigrid Næss; Ingo Thomsen; Gabriele Mayr; Inke R König; Kristian Hveem; Isabelle Cleynen; Javier Gutierrez-Achury; Isis Ricaño-Ponce; David van Heel; Einar Björnsson; Richard N Sandford; Peter R Durie; Espen Melum; Morten H Vatn; Mark S Silverberg; Richard H Duerr; Leonid Padyukov; Stephan Brand; Miquel Sans; Vito Annese; Jean-Paul Achkar; Kirsten Muri Boberg; Hanns-Ulrich Marschall; Olivier Chazouillères; Christopher L Bowlus; Cisca Wijmenga; Erik Schrumpf; Severine Vermeire; Mario Albrecht; John D Rioux; Graeme Alexander; Annika Bergquist; Judy Cho; Stefan Schreiber; Michael P Manns; Martti Färkkilä; Anders M Dale; Roger W Chapman; Konstantinos N Lazaridis; Andre Franke; Carl A Anderson; Tom H Karlsen
Journal: Nat Genet Date: 2013-04-21 Impact factor: 38.330

7. A colorectal cancer genome-wide association study in a Spanish cohort identifies two variants associated with colorectal cancer risk at 1p33 and 8p12.

Authors: Ceres Fernandez-Rozadilla; Jean-Baptiste Cazier; Ian P Tomlinson; Luis G Carvajal-Carmona; Claire Palles; María J Lamas; Montserrat Baiget; Luis A López-Fernández; Alejandro Brea-Fernández; Anna Abulí; Luis Bujanda; Juan Clofent; Dolors Gonzalez; Rosa Xicola; Montserrat Andreu; Xavier Bessa; Rodrigo Jover; Xavier Llor; Víctor Moreno; Antoni Castells; Ángel Carracedo; Sergi Castellvi-Bel; Clara Ruiz-Ponte
Journal: BMC Genomics Date: 2013-01-26 Impact factor: 3.969

8. A genome-wide association analysis of a broad psychosis phenotype identifies three loci for further investigation.

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Journal: Biol Psychiatry Date: 2013-07-17 Impact factor: 13.382

9. Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci.

Authors: David Ellinghaus; Luke Jostins; Sarah L Spain; Adrian Cortes; Jörn Bethune; Buhm Han; Yu Rang Park; Soumya Raychaudhuri; Jennie G Pouget; Matthias Hübenthal; Trine Folseraas; Yunpeng Wang; Tonu Esko; Andres Metspalu; Harm-Jan Westra; Lude Franke; Tune H Pers; Rinse K Weersma; Valerie Collij; Mauro D'Amato; Jonas Halfvarson; Anders Boeck Jensen; Wolfgang Lieb; Franziska Degenhardt; Andreas J Forstner; Andrea Hofmann; Stefan Schreiber; Ulrich Mrowietz; Brian D Juran; Konstantinos N Lazaridis; Søren Brunak; Anders M Dale; Richard C Trembath; Stephan Weidinger; Michael Weichenthal; Eva Ellinghaus; James T Elder; Jonathan N W N Barker; Ole A Andreassen; Dermot P McGovern; Tom H Karlsen; Jeffrey C Barrett; Miles Parkes; Matthew A Brown; Andre Franke
Journal: Nat Genet Date: 2016-03-14 Impact factor: 41.307

10. A genome-wide association study of anorexia nervosa.

Authors: V Boraska; C S Franklin; J A B Floyd; L M Thornton; L M Huckins; L Southam; N W Rayner; I Tachmazidou; K L Klump; J Treasure; C M Lewis; U Schmidt; F Tozzi; K Kiezebrink; J Hebebrand; P Gorwood; R A H Adan; M J H Kas; A Favaro; P Santonastaso; F Fernández-Aranda; M Gratacos; F Rybakowski; M Dmitrzak-Weglarz; J Kaprio; A Keski-Rahkonen; A Raevuori; E F Van Furth; M C T Slof-Op 't Landt; J I Hudson; T Reichborn-Kjennerud; G P S Knudsen; P Monteleone; A S Kaplan; A Karwautz; H Hakonarson; W H Berrettini; Y Guo; D Li; N J Schork; G Komaki; T Ando; H Inoko; T Esko; K Fischer; K Männik; A Metspalu; J H Baker; R D Cone; J Dackor; J E DeSocio; C E Hilliard; J K O'Toole; J Pantel; J P Szatkiewicz; C Taico; S Zerwas; S E Trace; O S P Davis; S Helder; K Bühren; R Burghardt; M de Zwaan; K Egberts; S Ehrlich; B Herpertz-Dahlmann; W Herzog; H Imgart; A Scherag; S Scherag; S Zipfel; C Boni; N Ramoz; A Versini; M K Brandys; U N Danner; C de Kovel; J Hendriks; B P C Koeleman; R A Ophoff; E Strengman; A A van Elburg; A Bruson; M Clementi; D Degortes; M Forzan; E Tenconi; E Docampo; G Escaramís; S Jiménez-Murcia; J Lissowska; A Rajewski; N Szeszenia-Dabrowska; A Slopien; J Hauser; L Karhunen; I Meulenbelt; P E Slagboom; A Tortorella; M Maj; G Dedoussis; D Dikeos; F Gonidakis; K Tziouvas; A Tsitsika; H Papezova; L Slachtova; D Martaskova; J L Kennedy; R D Levitan; Z Yilmaz; J Huemer; D Koubek; E Merl; G Wagner; P Lichtenstein; G Breen; S Cohen-Woods; A Farmer; P McGuffin; S Cichon; I Giegling; S Herms; D Rujescu; S Schreiber; H-E Wichmann; C Dina; R Sladek; G Gambaro; N Soranzo; A Julia; S Marsal; R Rabionet; V Gaborieau; D M Dick; A Palotie; S Ripatti; E Widén; O A Andreassen; T Espeseth; A Lundervold; I Reinvang; V M Steen; S Le Hellard; M Mattingsdal; I Ntalla; V Bencko; L Foretova; V Janout; M Navratilova; S Gallinger; D Pinto; S W Scherer; H Aschauer; L Carlberg; A Schosser; L Alfredsson; B Ding; L Klareskog; L Padyukov; P Courtet; S Guillaume; I Jaussent; C Finan; G Kalsi; M Roberts; D W Logan; L Peltonen; G R S Ritchie; J C Barrett; X Estivill; A Hinney; P F Sullivan; D A Collier; E Zeggini; C M Bulik
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