Is the population of Sado Island genetically close to the population of western Japan?

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Abstract

To explore the effect of aging, a cohort study is being performed on Sado Island, which is located in the Sea of Japan. Sado Island is close to the eastern coast of Japan, yet its population speaks the western Japanese dialect. Consequently, the genetic background of the population of Sado Island is of interest. Based on Nei’s genetic distance, we compared the allele frequencies of people from Sado Island to those of people from Nagahama and Miyagi, which are located in the western and northeastern parts of Honshu, respectively. The results showed that the populations of Miyagi and Nagahama are genetically closer to each other than to the population of Sado Island. Because the Sado and Honshu Islands are isolated by a channel, it is possible that genetic drift occurred within Sado Island, which would explain the uniqueness of the people of this region.

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Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals

Masao Nagasaki, Jun Yasuda, Fumiki Katsuoka … (2015)

The Tohoku Medical Megabank Organization reports the whole-genome sequences of 1,070 healthy Japanese individuals and construction of a Japanese population reference panel (1KJPN). Here we identify through this high-coverage sequencing (32.4 × on average), 21.2 million, including 12 million novel, single-nucleotide variants (SNVs) at an estimated false discovery rate of <1.0%. This detailed analysis detected signatures for purifying selection on regulatory elements as well as coding regions. We also catalogue structural variants, including 3.4 million insertions and deletions, and 25,923 genic copy-number variants. The 1KJPN was effective for imputing genotypes of the Japanese population genome wide. These data demonstrate the value of high-coverage sequencing for constructing population-specific variant panels, which covers 99.0% SNVs of minor allele frequency ≥0.1%, and its value for identifying causal rare variants of complex human disease phenotypes in genetic association studies.

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

Koichiro Higasa, Noriko Miyake, Jun-ichi Yoshimura … (2016)

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/.

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Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals

Yosuke Kawai, Takahiro Mimori, Kaname Kojima … (2015)

The Tohoku Medical Megabank Organization constructed the reference panel (referred to as the 1KJPN panel), which contains >20 million single nucleotide polymorphisms (SNPs), from whole-genome sequence data from 1070 Japanese individuals. The 1KJPN panel contains the largest number of haplotypes of Japanese ancestry to date. Here, from the 1KJPN panel, we designed a novel custom-made SNP array, named the Japonica array, which is suitable for whole-genome imputation of Japanese individuals. The array contains 659 253 SNPs, including tag SNPs for imputation, SNPs of Y chromosome and mitochondria, and SNPs related to previously reported genome-wide association studies and pharmacogenomics. The Japonica array provides better imputation performance for Japanese individuals than the existing commercially available SNP arrays with both the 1KJPN panel and the International 1000 genomes project panel. For common SNPs (minor allele frequency (MAF)>5%), the genomic coverage of the Japonica array (r 2>0.8) was 96.9%, that is, almost all common SNPs were covered by this array. Nonetheless, the coverage of low-frequency SNPs (0.5%

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Author and article information

Contributors

Kazuharu Misawa:

ORCID: http://orcid.org/0000-0002-6277-4330

+81-72-804-2623 , kazu_misawa@hotmail.com

Journal

Journal ID (nlm-ta): Hum Genome Var

Journal ID (iso-abbrev): Hum Genome Var

Title: Human Genome Variation

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2054-345X

Publication date (Electronic): 4 June 2019

Publication date PMC-release: 4 June 2019

Publication date Collection: 2019

Volume: 6

Electronic Location Identifier: 26

Affiliations

[1 ]ISNI 0000 0001 2248 6943, GRID grid.69566.3a, Department of Integrative Genomics, Tohoku Medical Megabank Organization, , Tohoku University, ; Sendai, Miyagi Japan

[2 ]ISNI 0000 0001 0671 5144, GRID grid.260975.f, Department of Cardiovascular Biology and Medicine, , Niigata University Graduate School of Medical and Dental Sciences, ; Niigata, Japan

[3 ]ISNI 0000 0001 0671 5144, GRID grid.260975.f, Department of Inter-Organ Communication Research, , Niigata University Graduate School of Medical and Dental Sciences, ; Niigata, Japan

[4 ]ISNI 0000 0001 0671 5144, GRID grid.260975.f, Division of Comprehensive Geriatrics in Community, , Niigata University Graduate School of Medical and Dental Sciences, ; Niigata, Japan

[5 ]ISNI 0000 0001 0671 5144, GRID grid.260975.f, Department of Neurology, Brain Research Institute, , Niigata University, ; Niigata, Japan

[6 ]ISNI 0000 0001 0671 5144, GRID grid.260975.f, Division of Clinical Nephrology and Rheumatology, , Niigata University Graduate School of Medical and Dental Sciences, ; Niigata, Japan

[7 ]GRID grid.452773.0, Sado General Hospital, ; Niigata, Japan

[8 ]ISNI 0000 0001 0671 5144, GRID grid.260975.f, Division of Orthopedic Surgery, Department of Regenerative and Transplant Medicine, , Niigata University Graduate School of Medical and Dental Sciences, ; Niigata, Japan

[9 ]ISNI 0000 0001 2172 5041, GRID grid.410783.9, Present Address: Kansai Medical University, ; 2-5-1 Shin-machi, Hirakata, 573-1010 Osaka Japan

Author information

Kazuharu Misawa http://orcid.org/0000-0002-6277-4330

Minako Wakasugi http://orcid.org/0000-0003-1555-7736

Osamu Onodera http://orcid.org/0000-0003-3354-5472

Article

Publisher ID: 58

DOI: 10.1038/s41439-019-0058-6

PMC ID: 6547765

SO-VID: 61365a58-8589-425e-9620-0292f0c225f2

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 31 March 2019

Date revision received : 19 April 2019

Date accepted : 15 May 2019

Funding

Funded by: FundRef https://doi.org/10.13039/501100001691, MEXT | Japan Society for the Promotion of Science (JSPS);

Award ID: JP17K08682

Award Recipient : Kazuharu Misawa

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Keywords: genetic variation,evolutionary biology

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Keywords: genetic variation, evolutionary biology

Is the population of Sado Island genetically close to the population of western Japan?

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Most cited references 6

Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals

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

Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals

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