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Chunk #19 — Methods — Analysis Plan — Developmentally-Informative GWAS

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A Developmentally-Informative Genome-wide Association Study of Alcohol Use Frequency.
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Linkage disequilibrium score regression (LDSC; Bulik-Sullivan, Loh, et al. 2015), was performed on the meta-analyzed GWAS summary statistics to construct a genetic covariance matrix using the Genomic SEM package (Grotzinger et al. 2019). Previous work indicates that LDSC is robust to sample overlap (Bulik-Sullivan, Finucane, et al. 2015), facilitating the analysis of repeated measures across developmental periods. LD scores were drawn from the 1000 Genomes reference panel (McVean et al. 2012) and restricted to HapMap3 SNPS (Altshuler et al. 2010), which are well characterized in terms of LD structure. 1,193,613, 1,193,617, and 1,170,827 HapMap3 SNPs were included in the LD score regression after matching meta-analyzed summary statistics to the reference panel and LD scores for adolescence, early adulthood, and adulthood, respectively. We fit a common factor model to the genetic covariance matrix using the Genomic SEM package (Grotzinger et al. 2019) in R (R Core Team, 2017). A diagram of the common factor genomic structural equation model (gSEM) is included in Figure 1. The variance of the common factor was fixed to 1 to identify the model without SNPs. Loadings