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Chunk #6 — Methods — Stage 1 meta-analysis (expanded in Supplementary Methods)

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Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
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We repeated the meta-analysis combining evidence for association based solely on the p value. Specifically, for each study we converted the two-sided p value to a z-statistic which was signed to reflect the direction of the association given the reference allele. Each z-score was then weighted; the squared weights were chosen to sum to 1 and each sample-specific weight was proportional to the square root of the effective number of individuals in the sample. Weighted z-statistics were summed across studies and the summary z-score converted to a two-sided p value.