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Chunk #18 — 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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proportions did not match their reported genetic relationship were assigned to two different families and pairs of individuals who shared >25% of their alleles identity-by-state were assigned to the same family. Participants with gender discordance (FST<0.2 for chromosome X SNPs to confirm females and FST >0.8 to confirm males) were also removed, unless their true identity could be determined. To verify and correct potential misclassification of self-reported race, we compared the GWAS data from all participants with HapMap phase III reference genotypes. Association tests were performed on N=2116 using linear regression models adjusted for age, sex and the first three principal component eigenvectors computed using Eigensoft and embedded in generalized estimating equations to correct for correlations among relatives.