Professor Masayuki Yamamoto and his colleagues published an article on the journal "BMC Genomics". They verified 1KJPN performance for genotype imputation of Japanese people and compared with other reference panels, and it showed higher accuracy than others.

The dataset of 1,070 genomes containing haplotype information was produced as part of the Tohoku Medical Megabank project. Launched in the aftermath of the 2011 earthquake, the project aims to develop tailor-made medical diagnosis and treatment using people’s genetic information in Miyagi and Iwate prefectures. The data, known as the ‘1KJPN’ reference panel, was created based on samples from Miyagi.

In a present study, a research team from the Tohoku Medical Megabank Organization at Tohoku University investigated how accurately Miyagi samples represent the diversity of genome variations of the entire Japanese mainland population. They compared the 1KJPN panel with 144, 39 and 35 genome samples from the areas of Iwate, Nagahama and Aki, respectively.
The results showed that while the Miyagi data was a sufficient representative of the entire population, combining the 1KJPN dataset with genome samples from Iwate, Nagahama and Aki improved the efficiency of the genotype imputation, particularly in identifying rare variants or SNPs on a nationwide scale. The combined data was also more accurate than Japanese samples in the other international project.

Please see below for more details on the article.

Article information

Title: Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project

Published journal:BMC Genomics 2018  19:551

Authors:
Jun Yasuda, Fumiki Katsuoka, Inaho Danjoh, Yosuke Kawai, Kaname Kojima, Masao Nagasaki, Sakae Saito, Yumi Yamaguchi-Kabata, Shu Tadaka, Ikuko N. Motoike, Kazuki Kumada, Mika Sakurai-Yageta, Osamu Tanabe, Nobuo Fuse, Gen Tamiya, Koichiro Higasa, Fumihiko Matsuda, Nobufumi Yasuda, Motoki Iwasaki, Makoto Sasaki, Atsushi Shimizu, Kengo Kinoshita, Masayuki Yamamoto

Published date:24 July 2018

Doi: https://doi.org/10.1186/s12864-018-4942-0

Related link

Polishing Japanese genome data with distant relatives (Asia Research News: ResearchSea)

Polishing Japanese genome data with distant relatives （Tohoku University website)