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Chunk #17 — Materials and methods — SNP-chip heritability and genetic correlation estimation with LDSC

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Largest GWAS of PTSD (N=20 070) yields genetic overlap with schizophrenia and sex differences in heritability.
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LDSC33, 34 was used on the SNP-level summary statistics from the 7 EA data sets for which raw genotype data were available. With raw data we could rule out population stratification and the presence of related individuals, and consequently the constrained version of LDSC could be used, affording greater power for heritability estimation. By constraining the LDSC regression intercept to be 1 (that is, the expected χ2 for a single SNP with LD score equal to zero and with no influence from population stratification), there is one less parameter to estimate in the LDSC regression and standard error of the heritability estimate is reduced. For genetic correlation, we report both constrained and unconstrained results. As with GCTA, we use population prevalence estimates of 11% (female), 5% (male) and 8% (combined). Separate male and female heritability estimates were calculated using sex-specific subsamples of the data. General instructions for LDSC are provided here: https://github.com/bulik/ldsc