Format

Send to

Choose Destination
J Hum Genet. 2018 Feb;63(2):213-230. doi: 10.1038/s10038-017-0347-1. Epub 2017 Dec 1.

Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals.

Author information

1
Tohoku Medical Megabank Organization, Tohoku University, Aoba-ku, Sendai, 980-8573, Japan. yamaguchi@megabank.tohoku.ac.jp.
2
Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Japan. yamaguchi@megabank.tohoku.ac.jp.
3
Tohoku Medical Megabank Organization, Tohoku University, Aoba-ku, Sendai, 980-8573, Japan.
4
Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Japan.
5
Ageo Central General Hospital, Ageo, 362-8588, Japan.
6
Graduate School of Information Sciences, Tohoku University, Aoba-ku, Sendai, 980-8579, Japan.
7
Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Chuo-ku, Tokyo, 103-0027, Japan.
8
International Research Institute of Disaster Science, Tohoku University, Aoba-ku, Sendai, 980-0845, Japan.
9
Japan Agency for Medical Research and Development (AMED), Chiyodaku, Tokyo, 100-0004, Japan.
10
Tohoku Medical Megabank Organization, Tohoku University, Aoba-ku, Sendai, 980-8573, Japan. kengo@ecei.tohoku.ac.jp.
11
Graduate School of Information Sciences, Tohoku University, Aoba-ku, Sendai, 980-8579, Japan. kengo@ecei.tohoku.ac.jp.
12
Institute of Development, Aging and Cancer, Tohoku University, Aoba-ku, Sendai, 980-8575, Japan. kengo@ecei.tohoku.ac.jp.

Abstract

Clarifying allele frequencies of disease-related genetic variants in a population is important in genomic medicine; however, such data is not yet available for the Japanese population. To estimate frequencies of actionable pathogenic variants in the Japanese population, we examined the reported pathological variants in genes recommended by the American College of Medical Genetics and Genomics (ACMG) in our reference panel of genomic variations, 2KJPN, which was created by whole-genome sequencing of 2049 individuals of the resident cohort of the Tohoku Medical Megabank Project. We searched for pathogenic variants in 2KJPN for 57 autosomal ACMG-recommended genes responsible for 26 diseases and then examined their frequencies. By referring to public databases of pathogenic variations, we identified 143 reported pathogenic variants in 2KJPN for the 57 ACMG recommended genes based on a classification system. At the individual level, 21% of the individuals were found to have at least one reported pathogenic allele. We then conducted a literature survey to review the variants and to check for evidence of pathogenicity. Our results suggest that a substantial number of people have reported pathogenic alleles for the ACMG genes, and reviewing variants is indispensable for constructing the information infrastructure of genomic medicine for the Japanese population.

PMID:
29192238
DOI:
10.1038/s10038-017-0347-1
[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for Nature Publishing Group
Loading ...
Support Center