Chunk #12 — MATERIALS AND METHODS — Explaining phenotypic variation

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Rare, low frequency and common coding variants in CHRNA5 and their contribution to nicotine dependence in European and African Americans.

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To examine the variation in nicotine dependence explained by CHRNA5 coding variants, we used Nagelkerke’s adjusted R2 from logistic regression of case-control status.25 The variance in phenotype attributed to selected variants was derived as the R2 attributable to the full model minus the R2 attributable to the base model, including age, sex, and first ancestry-specific PC as predictors of outcome. European and African American samples were analyzed separately.