PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
Shaun Purcell,Shaun Purcell,Benjamin M. Neale,Benjamin M. Neale,Kathe Todd-Brown,Lori Thomas,Manuel A. R. Ferreira,David Bender,David Bender,Julian Maller,Julian Maller,Pamela Sklar,Pamela Sklar,Paul I.W. de Bakker,Paul I.W. de Bakker,Mark J. Daly,Mark J. Daly,Pak C. Sham +17 more
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TLDR
This work introduces PLINK, an open-source C/C++ WGAS tool set, and describes the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation, which focuses on the estimation and use of identity- by-state and identity/descent information in the context of population-based whole-genome studies.Abstract:
Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis.read more
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A genome-wide association study identifies a locus for nonsyndromic cleft lip with or without cleft palate on 8q24
Struan F.A. Grant,Struan F.A. Grant,Kai Wang,Haitao Zhang,Wendy Glaberson,Kiran Annaiah,Cecilia E. Kim,Jonathan P. Bradfield,Joseph T. Glessner,Kelly A. Thomas,Maria Garris,Edward C. Frackelton,F. George Otieno,Rosetta M. Chiavacci,Hyun-Duck Nah,Richard E. Kirschner,Hakon Hakonarson,Hakon Hakonarson +17 more
TL;DR: The results strongly suggest that a locus on 8q24 is involved in the pathogenesis of NSCL/P, and this previous report acts as a de novo replication for the independent observation outlined here.
A Resource for Population, Disease, and Pharmacological Genetics Research
Matthew R. Nelson,Katarzyna Bryc,Karen S. King,Amit Indap,Adam R. Boyko,John Novembre,Linda P. Briley,Yuka Maruyama,Dawn M. Waterworth,Peter Vollenweider,Jorge R. Oksenberg,Stephen L. Hauser,Heide A. Stirnadel,Jaspal S. Kooner,John C. Chambers,Brendan Jones,Vincent Mooser,Carlos Bustamante,Allen D. Roses,Daniel K. Burns,Margaret G. Ehm,Eric H. Lai +21 more
TL;DR: It is found that matching based on country of origin, identity-by-state distance, and multidimensional PCA do similarly well to control the type I error rate in a genome-wide analysis of abacavir-associated hypersensitivity reaction.
Journal ArticleDOI
HLA-DQA1*02:01 Is a Major Risk Factor for Lapatinib-Induced Hepatotoxicity in Women With Advanced Breast Cancer
Colin F. Spraggs,Laura R. Budde,Linda P. Briley,Nan Bing,Charles J. Cox,Karen S. King,John C. Whittaker,Vincent Mooser,A. Preston,S. Stein,Lon R. Cardon +10 more
TL;DR: The results support a role for immune mechanisms in lapatinib-induced hepatotoxicity and further work is required to determine whether testing for DQA1*02:01 allele carriage is clinically useful in managing liver safety risk during Lapatinib treatment.
Journal ArticleDOI
Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility
Towfique Raj,Yang I. Li,Garrett Wong,Jack Humphrey,Minghui Wang,Satesh Ramdhani,Ying-Chih Wang,Bryan C. Ng,Ishaan Gupta,Vahram Haroutunian,Vahram Haroutunian,Eric E. Schadt,Tracy L. Young-Pearse,Sara Mostafavi,Bin Zhang,Pamela Sklar,David A. Bennett,Philip L. De Jager,Philip L. De Jager +18 more
TL;DR: This study of the transcriptome of the aging brain provides evidence that dysregulation of mRNA splicing is a feature of Alzheimer’s disease and is, in some cases, genetically driven.
Journal ArticleDOI
Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits
Iona M. MacLeod,Iona M. MacLeod,Phil J. Bowman,Phil J. Bowman,C. J. Vander Jagt,Mekonnen Haile-Mariam,Kathryn E. Kemper,Amanda J. Chamberlain,Chris Schrooten,Ben J. Hayes,Ben J. Hayes,Michael E. Goddard,Michael E. Goddard +12 more
TL;DR: The results suggest that the new BayesRC method was equal to or more powerful than BayesR for detecting candidate causal variants and for genomic prediction of milk traits.
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