Human genetic variation database, a reference database of genetic variations in the Japanese population.

Higasa K1, Miyake N2, Yoshimura J3, Okamura K4, Niihori T5, Saitsu H2, Doi K3, Shimizu M1, Nakabayashi K6, Aoki Y5, Tsurusaki Y2, Morishita S3, Kawaguchi T1, Migita O6,7, Nakayama K8, Nakashima M2, Mitsui J9, Narahara M10, Hayashi K6, Funayama R8, Yamaguchi D11, Ishiura H9, Ko WY10, Hata K6, Nagashima T8, Yamada R10, Matsubara Y5, Umezawa A12, Tsuji S9, Matsumoto N2, Matsuda F1.

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Abstract

Whole-genome and -exome resequencing using next-generation sequencers is a powerful approach for identifying genomic variations that are associated with diseases. However, systematic strategies for prioritizing causative variants from many candidates to explain the disease phenotype are still far from being established, because the population-specific frequency spectrum of genetic variation has not been characterized. Here, we have collected exomic genetic variation from 1208 Japanese individuals through a collaborative effort, and aggregated the data into a prevailing catalog. In total, we identified 156 622 previously unreported variants. The allele frequencies for the majority (88.8%) were lower than 0.5% in allele frequency and predicted to be functionally deleterious. In addition, we have constructed a Japanese-specific major allele reference genome by which the number of unique mapping of the short reads in our data has increased 0.045% on average. Our results illustrate the importance of constructing an ethnicity-specific reference genome for identifying rare variants. All the collected data were centralized to a newly developed database to serve as useful resources for exploring pathogenic variations. Public access to the database is available at http://www.genome.med.kyoto-u.ac.jp/SnpDB/.Journal of Human Genetics advance online publication, 25 February 2016; doi:10.1038/jhg.2016.12.