Making Sense Of SNPs With The Japonica Array

Developed from samples from the Tohoku Medical Megabank Organization, the Japonica array is the first SNP array optimized for the Japanese population.

AsianScientist (Sep. 10, 2015) – In a study published in the Journal of Human Genetics, researchers from the Tohoku University describe the first ever single nucleotide polymorphism (SNP) array optimized for the Japanese population.

A SNP is a single-nucleotide substitution of one base for another that occurs commonly within a population. Roughly 50 million SNPs are scattered throughout the human genome, in both coding and non-coding regions. The challenge for scientists is determining which SNPs are linked to disease and which are harmless variation.

The new SNP array, called the ‘Japonica Array’, covers the whole-genome region from which the SNPs possessed by Japanese people can be obtained with a high degree of accuracy.

The Japonica Array was designed by a research group led by Professor Masao Nagasaki and Senior Assistant Professor Yosuke Kawai at Tohoku University. The team developed and implemented a unique SNP selection algorithm, using a supercomputer to analyze the genomic information from the 1,070 individuals who participated in the cohort studies of the Tohoku Medical Megabank Project.

By using genotype imputation technology, information on a maximum of 20 million SNPs are presumed from only 659,253 SNPs on the Japonica Array.

The Japonica Array has an imputation accuracy that is at least 10 percent better than other existing SNP arrays that contain an equivalent number of SNPs, and offers a level of performance that is equivalent to or higher than existing SNP arrays that contain three or more times the number of SNPs.

This research has produced a basic analysis tool for the large-scale identification and study of the genes related to the physical constitution and diseases that are peculiar to the Japanese. It has so far yielded important results that can accelerate the research of personalized healthcare and medicine.

The article can be found at: Kawai et al. (2015) Japonica Array: Improved Genotype Imputation by Designing a Population-Specific SNP Array with 1070 Japanese Individuals.


Source: Tokohu University.
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