Chunk #34 — Materials and Methods — Genotyping and quality control

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A systematic mapping approach of 16q12.2/FTO and BMI in more than 20,000 African Americans narrows in on the underlying functional variation: results from the Population Architecture using Genomics and Epidemiology (PAGE) study.

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excluded SNPs based on Mendelian errors in 30 YRI trios >1, replication errors >2 with discordant calls (when comparing across studies) in 90 YRI samples >3, and discordant calls for 90 YRI genotyped in PAGE versus HapMap database >3. In total, we successfully genotyped 1,694 out of 1,818 variants in the 16q12.2/FTO region. After excluding 165 SNPs that were monomorphic or had very low allele frequency (<0.01%) we included 1,529 variants in the analysis.