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Imputation analysis of the UBAC2 gene region

KY Kyoko Yamazoe
AM Akira Meguro
MT Masaki Takeuchi
ES Etsuko Shibuya
SO Shigeaki Ohno
NM Nobuhisa Mizuki
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To evaluate potential associations with un-genotyped SNPs within the region encompassing the UBAC2 gene, we performed imputation analysis. The genotypes of our Japanese GWAS set were imputed based on the 58 genotyped SNPs using MACH v1.0 (http://www.sph.umich.edu/csg/abecasis/MACH/index.html)28, 29. The reference panel comprised the 1000 Genomes Phase 3 datasets of 315 East Asian samples, which included a set of Japanese samples from Tokyo (JPT, N = 104), Han Chinese samples from Beijing (CHB, N = 103), and Southern Han Chinese samples (CHS, N = 108)) (http://www.1000genomes.org/)30. All imputed SNPs were filtered with the following quality control settings: HWE P > 0.001, minor allele frequency >1%, and a squared correlation between imputed and true genotypes (Rsq) of >0.90. A total of 562 imputed SNPs were included in further analysis.

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