Genetic Epidemiology, Psychiatric Genetics, Asthma Genetics and Statistical Genetics Laboratories investigate the pattern of disease in families, particularly identical and non-identical twins, to assess the relative importance of genes and environment in a variety of important health problems.
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PMID
17701901
TITLE
PLINK: a tool set for whole-genome association and population-based linkage analyses.
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.
DATE PUBLISHED
2007 Sep
HISTORY
PUBSTATUS PUBSTATUSDATE
received 2007/02/06
accepted 2007/05/02
aheadofprint 2007/07/25
pubmed 2007/08/19 09:00
medline 2007/10/05 09:00
entrez 2007/08/19 09:00
AUTHORS
NAME COLLECTIVENAME LASTNAME FORENAME INITIALS AFFILIATION AFFILIATIONINFO
Purcell S Purcell Shaun S Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA. shaun@pngu.mgh.harvard.edu
Neale B Neale Benjamin B
Todd-Brown K Todd-Brown Kathe K
Thomas L Thomas Lori L
Ferreira MA Ferreira Manuel A R MA
Bender D Bender David D
Maller J Maller Julian J
Sklar P Sklar Pamela P
de Bakker PI de Bakker Paul I W PI
Daly MJ Daly Mark J MJ
Sham PC Sham Pak C PC
INVESTIGATORS
JOURNAL
VOLUME: 81
ISSUE: 3
TITLE: American journal of human genetics
ISOABBREVIATION: Am. J. Hum. Genet.
YEAR: 2007
MONTH: Sep
DAY:
MEDLINEDATE:
SEASON:
CITEDMEDIUM: Print
ISSN: 0002-9297
ISSNTYPE: Print
MEDLINE JOURNAL
MEDLINETA: Am J Hum Genet
COUNTRY: United States
ISSNLINKING: 0002-9297
NLMUNIQUEID: 0370475
PUBLICATION TYPE
PUBLICATIONTYPE TEXT
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
COMMENTS AND CORRECTIONS
REFTYPE REFSOURCE REFPMID NOTE
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GRANTS
GRANTID AGENCY COUNTRY
EY-12562 NEI NIH HHS United States
R03 MH73806-01A1 NIMH NIH HHS United States
U01 HG004171 NHGRI NIH HHS United States
GENERAL NOTE
KEYWORDS
MESH HEADINGS
DESCRIPTORNAME QUALIFIERNAME
Genetic Linkage genetics
Genome, Human genetics
Humans genetics
Polymorphism, Single Nucleotide genetics
Population genetics
Software genetics
SUPPLEMENTARY MESH
GENE SYMBOLS
CHEMICALS
OTHER ID's
OTHERID SOURCE
PMC1950838 NLM