Custom-Designed SNP Array Facilitates Japanese Genomic Studies

By LabMedica International staff writers
Posted on 16 Sep 2015

$Image: The \"Japonica Array\" contains 659,253 SNPs, including tag SNPs for imputation, SNPs of Y chromosome and mitochondria, and SNPs related to previously reported genome-wide association studies and pharmacogenomics (Photo courtesy of Tohoku Medical Megabank Organization).$

Image: The \"Japonica 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 (Photo courtesy of Tohoku Medical Megabank Organization).

Japanese genomic researchers have created a single nucleotide polymorphism (SNP) array optimized for studies on the Japanese population.

The so-called "Japonica Array" was designed by investigators at the Tohoku University Tohoku Medical Megabank Organization (Sendai, Japan). As source material, the investigators used the Tohoku Medical Megabank Organization's reference panel (referred to as the 1KJPN panel), which contains more than 20 million SNPs from whole-genome sequence data from 1070 Japanese individuals. The 1KJPN panel contains the largest number of haplotypes of Japanese ancestry to date.

Beginning with the 1KJPN panel, the investigators designed a novel custom-made SNP array, containing 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 was found to provide better imputation performance for Japanese individuals than the existing commercially available SNP arrays. Imputation is an information science technique for estimating the genotype of several millions of unmeasured SNPs with a SNP array by combining it with a reference panel.

The genomic coverage of the Japonica Array was 96.9% for common SNPs; that is, almost all common SNPs were covered by this array. Furthermore, the coverage of low-frequency SNPs reached 67.2%, which was higher than those of other existing arrays.

The investigators confirmed the high quality genotyping performance of the Japonica array using the 288 samples from the 1KJPN reference panel. Results obtained from genotype screening with a high-throughput sequencer yielded an average call rate of 99.7% and an average concordance rate of 99.7%. Thus, the creation of custom-made SNP arrays based on a population-specific reference panel was shown to be a practical way to facilitate further association studies through genome-wide genotype imputations.

The study was published in the June 25, 2015, online edition of the Journal of Human Genetics.

Related Links:
Tohoku University Tohoku Medical Megabank Organization