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BMC Genomics. 2018 Jul 24;19(1):551. doi: 10.1186/s12864-018-4942-0.

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

Author information

1
Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan. jyasuda@megabank.tohoku.ac.jp.
2
Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan.
3
Present address: Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, 113-0033, Tokyo, Japan.
4
Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Sakyo-ku, Japan.
5
Department of Public Health, Kochi University Medical School, Nankoku-shi, 783-8505, Kochi, Japan.
6
Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, 104-0045, Chuo-ku, Japan.
7
Division of Ultrahigh Field MRI, Institute for Biomedical Sciences, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Shiwa, Iwate, 028-3694, Japan.
8
Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Shiwa, Iwate, 028-3694, Japan.
9
Graduate School of Information Sciences, Tohoku University, Aoba-ku, Sendai, 980-8579, Miyagi, Japan.
10
Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan. masiyamamoto@med.tohoku.ac.jp.
11
Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Miyagi, Japan. masiyamamoto@med.tohoku.ac.jp.

Abstract

BACKGROUND:

Genotype imputation from single-nucleotide polymorphism (SNP) genotype data using a haplotype reference panel consisting of thousands of unrelated individuals from populations of interest can help to identify strongly associated variants in genome-wide association studies. The Tohoku Medical Megabank (TMM) project was established to support the development of precision medicine, together with the whole-genome sequencing of 1070 human genomes from individuals in the Miyagi region (Northeast Japan) and the construction of the 1070 Japanese genome reference panel (1KJPN). Here, we investigated the performance of 1KJPN for genotype imputation of Japanese samples not included in the TMM project and compared it with other population reference panels.

RESULTS:

We found that the 1KJPN population was more similar to other Japanese populations, Nagahama (south-central Japan) and Aki (Shikoku Island), than to East Asian populations in the 1000 Genomes Project other than JPT, suggesting that the large-scale collection (more than 1000) of Japanese genomes from the Miyagi region covered many of the genetic variations of Japanese in mainland Japan. Moreover, 1KJPN outperformed the phase 3 reference panel of the 1000 Genomes Project (1KGPp3) for Japanese samples, and IKJPN showed similar imputation rates for the TMM and other Japanese samples for SNPs with minor allele frequencies (MAFs) higher than 1%.

CONCLUSIONS:

1KJPN covered most of the variants found in the samples from areas of the Japanese mainland outside the Miyagi region, implying 1KJPN is representative of the Japanese population's genomes. 1KJPN and successive reference panels are useful genome reference panels for the mainland Japanese population. Importantly, the addition of whole genome sequences not included in the 1KJPN panel improved imputation efficiencies for SNPs with MAFs under 1% for samples from most regions of the Japanese archipelago.

KEYWORDS:

Genome reference panel; Genotype imputation; Japan; Population genetics

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