PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
Citations
13,581 citations
Cites methods from "PLINK: A Tool Set for Whole-Genome ..."
...Some software packages (e.g. plink Purcell et al. 2007) have been specifically developed to both handle such huge data sets and to directly perform statistical analyses on the data....
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7,038 citations
Cites background from "PLINK: A Tool Set for Whole-Genome ..."
...9’s core functional domains are unchanged from that of its predecessor—data management, summary statistics, population stratification, association analysis, identity-by-descent estimation [1] —and it is usable as a drop-in replacement in most cases, requiring no changes to existing scripts....
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5,867 citations
Cites methods from "PLINK: A Tool Set for Whole-Genome ..."
...Two estimates have been used: one based on the variance of additive genetic values (diagonal of the SNP-derived GRM) and the other based on SNP homozygosity (implemented in PLINK).(25) Let (1 – pi) 2 þ pi(1 – pi)F, 2pi(1 – pi)(1 – F), and pi 2 þ pi(1 – pi)F be the frequencies of the three genotypes of a SNP i and let hi 1⁄4 2pi(1 – pi)....
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4,573 citations
4,565 citations
References
251 citations
"PLINK: A Tool Set for Whole-Genome ..." refers background in this paper
...However, the strategies of the past decade have met with limited success.(3,4) One possible reason for the lack of identified complextrait disease genes is that studies have still been lacking in sample size and genome coverage....
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213 citations
136 citations
"PLINK: A Tool Set for Whole-Genome ..." refers background in this paper
...PLINK has a simple procedure to find extended stretches of homozygosity in whole-genome data (regions spanning more than a certain number of SNPs and/or kilobases, allowing for a certain amount of missing genotypes and/ or occasional heterozygote calls) that occur relatively frequently, and it can provide a powerful approach to map recessive disease genes.(33,34) Via permutation, an empirical P value can be calculated for each SNP on the basis of a test for whether there is a higher rate of homozygous segments spanning that position in cases versus controls....
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96 citations
"PLINK: A Tool Set for Whole-Genome ..." refers result in this paper
...Rather than directly test frequency differences of a variant, we propose examining ancestral sharing at a locus, following ideas from previous work on haplotype sharing methods.(14,15) That is, given ascertainment based on disease, we might expect to see multiple copies of even very rare variants that are moderately or highly penetrant among the descendants of the founder in whom the mutational events occurred....
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74 citations
"PLINK: A Tool Set for Whole-Genome ..." refers background in this paper
...Information about parental phenotypes can also be combined in these analyses.(25,26) There is support for haplotype-based case/control and quantitative trait tests and TDTs based on the expected haplotype distribution for each individual obtained from expectation-maximization phasing....
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