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J Hum Genet. 2016 Jun;61(6):547-53. doi: 10.1038/jhg.2016.12. Epub 2016 Feb 25.

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

Author information

1
Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
2
Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
3
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
4
Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan.
5
Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan.
6
Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan.
7
Department of Pediatrics, St Marianna University School of Medicine, Kanagawa, Japan.
8
Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.
9
Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
10
Statistical Genetics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
11
Bits Co., Ltd., Tokyo, Japan.
12
Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan.

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/.

PMID:
26911352
PMCID:
PMC4931044
DOI:
10.1038/jhg.2016.12
[Indexed for MEDLINE]
Free PMC Article
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