title: Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals.
abstract: The Tohoku Medical Megabank Organization constructed the reference panel (referred to as the 1KJPN panel), which contains >20 million single nucleotide polymorphisms (SNPs), from whole-genome sequence data from 1070 Japanese individuals. The 1KJPN panel contains the largest number of haplotypes of Japanese ancestry to date. Here, from the 1KJPN panel, we designed a novel custom-made SNP array, named the Japonica array, which is suitable for whole-genome imputation of Japanese individuals. The array contains 659,253 SNPs, including tag SNPs for imputation, SNPs of Y chromosome and mitochondria, and SNPs related to previously reported genome-wide association studies and pharmacogenomics. The Japonica array provides better imputation performance for Japanese individuals than the existing commercially available SNP arrays with both the 1KJPN panel and the International 1000 genomes project panel. For common SNPs (minor allele frequency (MAF)>5%), the genomic coverage of the Japonica array (r(2)>0.8) was 96.9%, that is, almost all common SNPs were covered by this array. Nonetheless, the coverage of low-frequency SNPs (0.5%<MAF⩽5%) of the Japonica array reached 67.2%, which is higher than those of the existing arrays. In addition, we confirmed the high quality genotyping performance of the Japonica array using the 288 samples in 1KJPN; the average call rate 99.7% and the average concordance rate 99.7% to the genotypes obtained from high-throughput sequencer. As demonstrated in this study, the creation of custom-made SNP arrays based on a population-specific reference panel is a practical way to facilitate further association studies through genome-wide genotype imputations.
authors.affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.|Graduate School of Medicine, Tohoku University, Sendai, Japan.
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Kawai
authors.affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
authors.forename: Takahiro
authors.initials: T
authors.lastname: Mimori
authors.affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.|Graduate School of Medicine, Tohoku University, Sendai, Japan.|Department of Cohort Genome Information Analysis, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
authors.forename: Kaname
authors.initials: K
authors.lastname: Kojima
authors.affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.|Graduate School of Medicine, Tohoku University, Sendai, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Nariai
authors.affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
authors.forename: Inaho
authors.initials: I
authors.lastname: Danjoh
authors.affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
authors.forename: Rumiko
authors.initials: R
authors.lastname: Saito
authors.affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.|Graduate School of Medicine, Tohoku University, Sendai, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Yasuda
authors.affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.|Graduate School of Medicine, Tohoku University, Sendai, Japan.
authors.forename: Masayuki
authors.initials: M
authors.lastname: Yamamoto
authors.affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.|Graduate School of Medicine, Tohoku University, Sendai, Japan.|Department of Cohort Genome Information Analysis, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.|Graduate School of Information Sciences, Tohoku University, Sendai, Japan.
authors.forename: Masao
authors.initials: M
authors.lastname: Nagasaki
mesh_terms: D044466:Asian People; D041322:Chromosomes, Human, Y / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D005260:Female; D055106:Genome-Wide Association Study; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D006239:Haplotypes; D006801:Humans; D007564:Japan; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide
chemical_list: D004272:DNA, Mitochondrial