Genotypic data that passed initial quality control at CIDR were released to the Quality Assurance/Quality Control analysis team at the University of Washington Genetics Coordinating Center. CHRNA5 coding variants were identified by ANNOVAR19 and then manually reviewed. This review involved examining summary statistics of the quality control metrics, comparing the quality of novel variants with known variants from dbSNP and HapMap, as well as inspecting alignments of selected samples with non-reference calls to pass or fail variant sites. Large genetic databases20 and protein prediction programs21 were also used to evaluate identified coding variants.
