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Chunk #10 — Methods — Genotyping and Genotype Imputation

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A protocadherin gene cluster regulatory variant is associated with nicotine withdrawal and the urge to smoke.
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allelic discrimination assay (Applied Biosystems, Foster City, CA, USA). We considered rs31746 to be the “best” SNP to select for follow-up studies in the laboratory sample because in contrast to the other two SNPS, rs31746 was directly genotyped by all arrays and it was positioned in a regulatory element. The majority of laboratory subjects (n=124) were assigned to either EA or AA ancestry groups based on a previously described ancestry informative genetic marker method.32,42 Subjects not assigned by a genetic ancestry were assigned based on their self-reported ancestry. Four subjects with a genetic assignment that was discordant with the self-report were re-assigned to the ancestry group defined by the genetic markers.