For our replication study, we used the pre-imputed dataset released by the TMM32 (link),33 (link). Within this dataset, we used the subsets genotyped using Omni2.5 SNP array (Illumina Inc., San Diego, CA, USA) as well as the customized genotyping array designed by the TMM based on the Axiom platform (Thermo Fisher Scientific, Waltham, MA USA), denoted as Japonica array version 2 (JPAv2). The genotyped data were pre-phased using SHAPEIT version 2 r837 and imputed using IMPUTE2 version 2.2.2 and 2KJPN with an allele frequency panel of ~ 2000 Japanese individuals34 (link)–36 (link). After conducting the same quality control with the main dataset, 4,935,024 and 5,686,147 variants in the JPAv2 and Omni2.5 datasets, respectively, were selected for further analysis.
Replication analysis was conducted using the same exclusion criteria as those for the main analysis. Additionally, we excluded the Miyagi population in the subjects genotyped by JPAv2, because of small sample size (n = 678). The all subjects in the dataset genotyped by Omni2.5 belonged in the Miyagi population. Ultimately, 2791 and 1597 individuals for the JPAv2 and Omni2.5 dataset, respectively, were selected for replication analysis.
Replication analysis was conducted using the same exclusion criteria as those for the main analysis. Additionally, we excluded the Miyagi population in the subjects genotyped by JPAv2, because of small sample size (n = 678). The all subjects in the dataset genotyped by Omni2.5 belonged in the Miyagi population. Ultimately, 2791 and 1597 individuals for the JPAv2 and Omni2.5 dataset, respectively, were selected for replication analysis.
Free full text: Click here
