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Chunk #23 — 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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Statistical power was not adequate to estimate genetic correlations between the model residuals and a series of phenotypes from other studies. Interpretable heritability estimates have a range of zero (0% heritable) to one (100% heritable); however, LDSC heritability estimates are not bound to the range of interpretable values. LDSC heritability estimates can sometimes fall below this range and be negative if the true value of the heritability is close to zero or statistical power is low enough that sampling variance produces a point estimate below zero. Negative heritability estimates are not interpretable and prevent the calculation of genetic correlations with the phenotype that has negative heritability. The residual parameterization produced negative heritability estimates in early adulthood and adulthood (early adult H2SNP = −6e-04, adult H2SNP = −4e-04), preventing the calculation of genetic correlations. The total variance parameterization of the gSEM GWAS model, which omits the path from SNP to the common factor, was used for this component of the analysis plan. Negative LDSC heritability estimates do not prevent polygenic risk scoring. The residual parameterization was used to construct polygenic scores