Literature DB >> 26395054

WGSA: an annotation pipeline for human genome sequencing studies.

Xiaoming Liu1, Simon White2, Bo Peng3, Andrew D Johnson4, Jennifer A Brody5, Alexander H Li6, Zhuoyi Huang2, Andrew Carroll7, Peng Wei8, Richard Gibbs2, Robert J Klein9, Eric Boerwinkle10.   

Abstract

Entities:  

Keywords:  Genetics; Genome-wide

Mesh：

Year:  2015        PMID： 26395054      PMCID： PMC5124490          DOI： 10.1136/jmedgenet-2015-103423

Source DB:  PubMed          Journal:  J Med Genet        ISSN： 0022-2593            Impact factor:   6.318


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  8 in total

1.  A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.

Authors:  Pablo Cingolani; Adrian Platts; Le Lily Wang; Melissa Coon; Tung Nguyen; Luan Wang; Susan J Land; Xiangyi Lu; Douglas M Ruden
Journal:  Fly (Austin)       Date:  2012 Apr-Jun       Impact factor: 2.160

2.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.

Authors:  Kai Wang; Mingyao Li; Hakon Hakonarson
Journal:  Nucleic Acids Res       Date:  2010-07-03       Impact factor: 16.971

3.  dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations.

Authors:  Xiaoming Liu; Xueqiu Jian; Eric Boerwinkle
Journal:  Hum Mutat       Date:  2013-07-10       Impact factor: 4.878

4.  Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.

Authors:  William McLaren; Bethan Pritchard; Daniel Rios; Yuan Chen; Paul Flicek; Fiona Cunningham
Journal:  Bioinformatics       Date:  2010-06-18       Impact factor: 6.937

5.  dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions.

Authors:  Xiaoming Liu; Xueqiu Jian; Eric Boerwinkle
Journal:  Hum Mutat       Date:  2011-08       Impact factor: 4.878

6.  RefSeq: an update on mammalian reference sequences.

Authors:  Kim D Pruitt; Garth R Brown; Susan M Hiatt; Françoise Thibaud-Nissen; Alexander Astashyn; Olga Ermolaeva; Catherine M Farrell; Jennifer Hart; Melissa J Landrum; Kelly M McGarvey; Michael R Murphy; Nuala A O'Leary; Shashikant Pujar; Bhanu Rajput; Sanjida H Rangwala; Lillian D Riddick; Andrei Shkeda; Hanzhen Sun; Pamela Tamez; Raymond E Tully; Craig Wallin; David Webb; Janet Weber; Wendy Wu; Michael DiCuccio; Paul Kitts; Donna R Maglott; Terence D Murphy; James M Ostell
Journal:  Nucleic Acids Res       Date:  2013-11-19       Impact factor: 16.971

7.  Ensembl 2015.

Authors:  Fiona Cunningham; M Ridwan Amode; Daniel Barrell; Kathryn Beal; Konstantinos Billis; Simon Brent; Denise Carvalho-Silva; Peter Clapham; Guy Coates; Stephen Fitzgerald; Laurent Gil; Carlos García Girón; Leo Gordon; Thibaut Hourlier; Sarah E Hunt; Sophie H Janacek; Nathan Johnson; Thomas Juettemann; Andreas K Kähäri; Stephen Keenan; Fergal J Martin; Thomas Maurel; William McLaren; Daniel N Murphy; Rishi Nag; Bert Overduin; Anne Parker; Mateus Patricio; Emily Perry; Miguel Pignatelli; Harpreet Singh Riat; Daniel Sheppard; Kieron Taylor; Anja Thormann; Alessandro Vullo; Steven P Wilder; Amonida Zadissa; Bronwen L Aken; Ewan Birney; Jennifer Harrow; Rhoda Kinsella; Matthieu Muffato; Magali Ruffier; Stephen M J Searle; Giulietta Spudich; Stephen J Trevanion; Andy Yates; Daniel R Zerbino; Paul Flicek
Journal:  Nucleic Acids Res       Date:  2014-10-28       Impact factor: 16.971

8.  Choice of transcripts and software has a large effect on variant annotation.

Authors:  Davis J McCarthy; Peter Humburg; Alexander Kanapin; Manuel A Rivas; Kyle Gaulton; Jean-Baptiste Cazier; Peter Donnelly
Journal:  Genome Med       Date:  2014-03-31       Impact factor: 11.117
  8 in total
  55 in total

1.  Gene-based segregation method for identifying rare variants in family-based sequencing studies.

Authors:  Dandi Qiao; Christoph Lange; Nan M Laird; Sungho Won; Craig P Hersh; Jarrett Morrow; Brian D Hobbs; Sharon M Lutz; Ingo Ruczinski; Terri H Beaty; Edwin K Silverman; Michael H Cho
Journal:  Genet Epidemiol       Date:  2017-02-13       Impact factor: 2.135

2.  Practical Approaches for Whole-Genome Sequence Analysis of Heart- and Blood-Related Traits.

Authors:  Alanna C Morrison; Zhuoyi Huang; Bing Yu; Ginger Metcalf; Xiaoming Liu; Christie Ballantyne; Josef Coresh; Fuli Yu; Donna Muzny; Elena Feofanova; Navin Rustagi; Richard Gibbs; Eric Boerwinkle
Journal:  Am J Hum Genet       Date:  2017-01-12       Impact factor: 11.025

3.  Human Prehistoric Demography Revealed by the Polymorphic Pattern of CpG Transitions.

Authors:  Xiaoming Liu
Journal:  Mol Biol Evol       Date:  2020-09-01       Impact factor: 16.240

4.  Impact of Rare and Common Genetic Variants on Diabetes Diagnosis by Hemoglobin A1c in Multi-Ancestry Cohorts: The Trans-Omics for Precision Medicine Program.

Authors:  Chloé Sarnowski; Aaron Leong; Laura M Raffield; Peitao Wu; Paul S de Vries; Daniel DiCorpo; Xiuqing Guo; Huichun Xu; Yongmei Liu; Xiuwen Zheng; Yao Hu; Jennifer A Brody; Mark O Goodarzi; Bertha A Hidalgo; Heather M Highland; Deepti Jain; Ching-Ti Liu; Rakhi P Naik; Jeffrey R O'Connell; James A Perry; Bianca C Porneala; Elizabeth Selvin; Jennifer Wessel; Bruce M Psaty; Joanne E Curran; Juan M Peralta; John Blangero; Charles Kooperberg; Rasika Mathias; Andrew D Johnson; Alexander P Reiner; Braxton D Mitchell; L Adrienne Cupples; Ramachandran S Vasan; Adolfo Correa; Alanna C Morrison; Eric Boerwinkle; Jerome I Rotter; Stephen S Rich; Alisa K Manning; Josée Dupuis; James B Meigs
Journal:  Am J Hum Genet       Date:  2019-09-26       Impact factor: 11.025

5.  VIPdb, a genetic Variant Impact Predictor Database.

Authors:  Zhiqiang Hu; Changhua Yu; Mabel Furutsuki; Gaia Andreoletti; Melissa Ly; Roger Hoskins; Aashish N Adhikari; Steven E Brenner
Journal:  Hum Mutat       Date:  2019-08-17       Impact factor: 4.878

6.  Identifying Putative Susceptibility Genes and Evaluating Their Associations with Somatic Mutations in Human Cancers.

Authors:  Zhishan Chen; Wanqing Wen; Alicia Beeghly-Fadiel; Xiao-Ou Shu; Virginia Díez-Obrero; Jirong Long; Jiandong Bao; Jing Wang; Qi Liu; Qiuyin Cai; Victor Moreno; Wei Zheng; Xingyi Guo
Journal:  Am J Hum Genet       Date:  2019-08-08       Impact factor: 11.025

7.  Analysis of causal effect of APOA5 variants on premature coronary artery disease.

Authors:  Fan Wang; Isabel Z Wang; Stephen Ellis; Stephen Archacki; John Barnard; Carlos Hubbard; Eric J Topol; Qiuyun Chen; Qing K Wang
Journal:  Ann Hum Genet       Date:  2018-07-19       Impact factor: 1.670

8.  Association of kidney structure-related gene variants with type 2 diabetes-attributed end-stage kidney disease in African Americans.

Authors:  Meijian Guan; Jun Ma; Jacob M Keaton; Latchezar Dimitrov; Poorva Mudgal; Mary Stromberg; Jason A Bonomo; Pamela J Hicks; Barry I Freedman; Donald W Bowden; Maggie C Y Ng
Journal:  Hum Genet       Date:  2016-07-26       Impact factor: 4.132

9.  Analysis commons, a team approach to discovery in a big-data environment for genetic epidemiology.

Authors:  Jennifer A Brody; Alanna C Morrison; Joshua C Bis; Jeffrey R O'Connell; Michael R Brown; Jennifer E Huffman; Darren C Ames; Andrew Carroll; Matthew P Conomos; Stacey Gabriel; Richard A Gibbs; Stephanie M Gogarten; Namrata Gupta; Cashell E Jaquish; Andrew D Johnson; Joshua P Lewis; Xiaoming Liu; Alisa K Manning; George J Papanicolaou; Achilleas N Pitsillides; Kenneth M Rice; William Salerno; Colleen M Sitlani; Nicholas L Smith; Susan R Heckbert; Cathy C Laurie; Braxton D Mitchell; Ramachandran S Vasan; Stephen S Rich; Jerome I Rotter; James G Wilson; Eric Boerwinkle; Bruce M Psaty; L Adrienne Cupples
Journal:  Nat Genet       Date:  2017-10-27       Impact factor: 38.330

10.  dbMTS: A comprehensive database of putative human microRNA target site SNVs and their functional predictions.

Authors:  Chang Li; Chengcheng Mou; Michael D Swartz; Bing Yu; Yongsheng Bai; Yicheng Tu; Xiaoming Liu
Journal:  Hum Mutat       Date:  2020-04-06       Impact factor: 4.878
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