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| PLINK: A tool set for whole-genome association and population-based linkage analyses |
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| Author(s): Purcell S (Purcell, Shaun), Neale B (Neale, Benjamin), Todd-Brown K (Todd-Brown, Kathe), Thomas L (Thomas, Lori), Ferreira MAR (Ferreira, Manuel A. R.), Bender D (Bender, David), Maller J (Maller, Julian), Sklar P (Sklar, Pamela), de Bakker PIW (de Bakker, Paul I. W.), Daly MJ (Daly, Mark J.), Sham PC (Sham, Pak C.) |
| Source: AMERICAN JOURNAL OF HUMAN GENETICS Volume: 81 Issue: 3 Pages: 559-575 Published: SEP 2007 |
| Times Cited: 658 References: 39 |
| 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. |
| Document Type: Article |
| Language: English |
| Reprint Address: Purcell, S (reprint author), Massachusetts Gen Hosp, Ctr Human Genet Res, Room 6-254,CPZ N,185 Cambridge St, Boston, MA 02114 USA |
Addresses:
1. Massachusetts Gen Hosp, Ctr Human Genet Res, Boston, MA 02114 USA
2. Harvard & Massachusetts Inst Technol, Broad Inst, Cambridge, MA USA
3. Univ London, Inst Psychiat, London, England
4. Univ Hong Kong, Ctr Gene Res, Hong Kong, Hong Kong Peoples R China |
| Publisher: UNIV CHICAGO PRESS, 1427 E 60TH ST, CHICAGO, IL 60637-2954 USA |
| Subject Category: Genetics & Heredity |
| IDS Number: 205PX |
| ISSN: 0002-9297 |
| DOI: 10.1086/519795 |
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| | | | | | | | | Record from Web of Science® | | | | | | | | | |