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Chunk #13 — Materials and methods — Statistical analysis — Discovery sample

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Large-scale genome-wide association study of Asian population reveals genetic factors in FRMD4A and other loci influencing smoking initiation and nicotine dependence.
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To find supporting evidence for the 12 associated SNPs, we performed imputation analysis for untyped SNPs within ±500 kb of these SNPs. Imputation was carried out using the IMPUTE program on the basis of the NCBI (build 36) and dbSNP (build 126) databases. We initially used 90 individuals from JPT and CHB founders in HapMap as a reference panel comprising 3.99 million SNPs (release 22) (Marchini et al. 2007). We removed the imputed SNPs with <0.5 genotype information content, posterior probability scores <0.90, and low call rates (<0.90), MAF < 0.01, and HWE (p < 1 × 10−7).