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Chunk #30 — 4 Test data generation

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FINEMAP: efficient variable selection using summary data from genome-wide association studies.
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We obtained real genotype data on 18 834 individuals from the National FINRISK study (Borodulin et al., 2015). The genotype data comprise a 500 kilobase region centered on rs11591147 in PCSK9 gene on chromosome 1 with 1920 polymorphic SNPs with pairwise absolute correlations less than 0.99. To assess the computational efficiency and fine-mapping accuracy, we considered the following scenarios: Scenario AIncreasing number of SNPs (m=750,1000,1250,1500) considering causal configurations with up to K = 3 or K = 5 SNPs. Scenario BFixed number of m = 150 SNPs considering causal configurations with increasing maximum number of SNPs (K=1,2,3,4,5).