Infinium Asian Screening Array Kit KAPA Hyper Prep Kit TruSeq DNA PCR-Free Library Prep Kit
プラットフォーム
Illumina HiSeq 2500 Illumina HiSeq 3000 Illumina HiSeq X Illumina Infinium Asian Screening Array Illumina NovaSeq 6000
参照ゲノム
GRCh37
QC・フィルタリング
・SNP array data： サンプル QC：We excluded individuals with low genotyping call rates (call rate < 98%). We included individuals of the estimated Asian ancestry using PCA. バリアント QC：We excluded variants with (1) genotyping call rate < 99%, (2) minor allele count < 5, (3) P-value for Hardy-Weinberg equilibrium < 1.0 × 10^−10, and (4) > 5% allele frequency difference compared with the imputation reference panel or the allele frequency panel of Tohoku Medical Megabank Project. インピュテーション後のQC：We excluded imputed variants with Rsq < 0.7 and minor allele frequency < 1%. ・WGS： We excluded variants with genotype call rate <90%, ExcessHet > 60, Hardy-Weinberg P<1.0×10−10 After imputation with Beagle v5.1, we excluded imputed variants with minor allele frequency < 1%.
