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Chunk #20 — Materials and Methods — Follow-up SNP/indel association testing with nicotine dependence in independent samples

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Genome-wide meta-analysis reveals common splice site acceptor variant in CHRNA4 associated with nicotine dependence.
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build 37 [hg19] coordinates) at the Institute for Molecular Medicine Finland. After imputation, FTC samples were merged together. Standardized residuals of the categorical FTND phenotype, regressed against SNP dosages, age, sex, birth cohort and the 10 first principal components (calculated from genome-wide genotype data), were used in QFAM association test in PLINK.17 The resulting regression coefficients are mathematically equivalent to regression coefficients when using raw phenotypes that are linearly regressed on SNP genotypes and covariates, enabling us to combine the FTC results with the others in meta-analysis as done elsewhere.39