OpenLB
Open Library of Bioscience
Advanced Search
Journal of human genetics
Jun, 2016;61 (6): 547-53.

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

Koichiro Higasa, Noriko Miyake, Jun Yoshimura, Kohji Okamura, Tetsuya Niihori, Hirotomo Saitsu, Koichiro Doi, Masakazu Shimizu, Kazuhiko Nakabayashi, Yoko Aoki, Yoshinori Tsurusaki, Shinichi Morishita, Takahisa Kawaguchi, Osuke Migita, Keiko Nakayama, Mitsuko Nakashima, Jun Mitsui, Maiko Narahara, Keiko Hayashi, Ryo Funayama, Daisuke Yamaguchi, Hiroyuki Ishiura, Wen-Ya Ko, Kenichiro Hata, Takeshi Nagashima, Ryo Yamada, Yoichi Matsubara, Akihiro Umezawa, Shoji Tsuji, Naomichi Matsumoto, Fumihiko Matsuda
Author Information
  1. Koichiro Higasa: Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
  2. Noriko Miyake: Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
  3. Jun Yoshimura: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
  4. Kohji Okamura: Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan.
  5. Tetsuya Niihori: Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan.
  6. Hirotomo Saitsu: Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
  7. Koichiro Doi: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
  8. Masakazu Shimizu: Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
  9. Kazuhiko Nakabayashi: Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan.
  10. Yoko Aoki: Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan.
  11. Yoshinori Tsurusaki: Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
  12. Shinichi Morishita: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
  13. Takahisa Kawaguchi: Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
  14. Osuke Migita: Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan.
  15. Keiko Nakayama: Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.
  16. Mitsuko Nakashima: Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
  17. Jun Mitsui: Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
  18. Maiko Narahara: Statistical Genetics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
  19. Keiko Hayashi: Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan.
  20. Ryo Funayama: Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.
  21. Daisuke Yamaguchi: Bits Co., Ltd., Tokyo, Japan.
  22. Hiroyuki Ishiura: Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
  23. Wen-Ya Ko: Statistical Genetics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
  24. Kenichiro Hata: Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan.
  25. Takeshi Nagashima: Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.
  26. Ryo Yamada: Statistical Genetics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
  27. Yoichi Matsubara: Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan.
  28. Akihiro Umezawa: Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan.
  29. Shoji Tsuji: Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
  30. Naomichi Matsumoto: Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
  31. Fumihiko Matsuda: Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
PMID: 26911352 DOI: 10.1038/jhg.2016.12

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/.

References

  1. Genetics. 1989 Nov;123(3):585-95 [PMID: 2513255]
  2. Mol Biol Evol. 2013 Dec;30(12):2654-65 [PMID: 24045876]
  3. Theor Popul Biol. 1975 Apr;7(2):256-76 [PMID: 1145509]
  4. Nature. 2015 Oct 1;526(7571):68-74 [PMID: 26432245]
  5. Nucleic Acids Res. 2000 Jan 1;28(1):27-30 [PMID: 10592173]
  6. Nat Genet. 2006 Aug;38(8):904-9 [PMID: 16862161]
  7. Nature. 2015 Oct 1;526(7571):82-90 [PMID: 26367797]
  8. Science. 2012 Jul 6;337(6090):64-9 [PMID: 22604720]
  9. Nat Genet. 2014 Aug;46(8):818-25 [PMID: 24974849]
  10. Nat Genet. 2015 May;47(5):435-44 [PMID: 25807286]
  11. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61 [PMID: 14681407]
  12. Nature. 2004 Oct 21;431(7011):931-45 [PMID: 15496913]
  13. Hypertension. 2014 Dec;64(6):1212-8 [PMID: 25201894]
  14. Nucleic Acids Res. 2001 Jan 1;29(1):308-11 [PMID: 11125122]
  15. Nat Genet. 2013 Apr;45(4):406-14, 414e1-2 [PMID: 23435088]
  16. PLoS Genet. 2013 Mar;9(3):e1003372 [PMID: 23555287]
  17. Pigment Cell Melanoma Res. 2015 Mar;28(2):233-5 [PMID: 25469862]
  18. Am J Hum Genet. 2007 Apr;80(4):588-604 [PMID: 17357067]
  19. Bioinformatics. 2009 Aug 15;25(16):2078-9 [PMID: 19505943]
  20. Genome Res. 2002 Dec;12(12):1805-14 [PMID: 12466284]
  21. Nat Methods. 2010 Apr;7(4):248-9 [PMID: 20354512]
  22. PLoS Genet. 2011 Sep;7(9):e1002280 [PMID: 21935354]
  23. Science. 2012 Jul 6;337(6090):100-4 [PMID: 22604722]
  24. PLoS One. 2013;8(2):e55089 [PMID: 23405114]
  25. Nat Genet. 2011 May;43(5):491-8 [PMID: 21478889]
  26. Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5 [PMID: 17130148]
  27. Hum Mutat. 2011 Aug;32(8):894-9 [PMID: 21520341]
  28. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W186-92 [PMID: 17526521]
  29. Nat Commun. 2015 Aug 21;6:8018 [PMID: 26292667]
  30. Genome Biol. 2010;11(8):R88 [PMID: 20796305]
  31. Nature. 2009 Oct 8;461(7265):747-53 [PMID: 19812666]
  32. BMC Bioinformatics. 2014;15 Suppl 11:S6 [PMID: 25350283]
  33. Am J Hum Genet. 2007 Sep;81(3):559-75 [PMID: 17701901]
  34. Nat Protoc. 2009;4(7):1073-81 [PMID: 19561590]
  35. PLoS One. 2014 Jun 23;9(6):e100924 [PMID: 24956270]
  36. Blood. 2003 Oct 15;102(8):3035-42 [PMID: 12829588]
  37. Nature. 2010 Oct 28;467(7319):1061-73 [PMID: 20981092]
  38. Bioinformatics. 2009 Jul 15;25(14):1754-60 [PMID: 19451168]
  39. Genome Biol. 2011 Sep 14;12(9):R84 [PMID: 21917140]
  40. Am J Hum Genet. 2013 Jan 10;92(1):52-66 [PMID: 23290073]
  41. Science. 2015 May 8;348(6235):648-60 [PMID: 25954001]
  42. Nature. 2001 Feb 15;409(6822):860-921 [PMID: 11237011]
  43. Theor Popul Biol. 1995 Oct;48(2):172-97 [PMID: 7482370]

MeSH Term

Alleles
Databases, Genetic
Exome
Gene Frequency
Genetic Variation
Genetics, Population
Genome, Human
Genomics
Genotype
High-Throughput Nucleotide Sequencing
Humans
Japan
Quality Control
Selection, Genetic
Web Browser
Journal Article

Links to CNCB-NGDC Resources

Database Commons: DBC003825 (HGVD)
Article has an altmetric score of 125

Word Cloud

Created with Highcharts 10.0.0geneticdatabasevariationsvariantsvariationdataallelereferencegenomeidentifyingfrequencycollectedJapanese0Whole-genome-exomeresequencingusingnext-generationsequencerspowerfulapproachgenomicassociateddiseasesHoweversystematicstrategiesprioritizingcausativemanycandidatesexplaindiseasephenotypestillfarestablishedpopulation-specificspectrumcharacterizedexomic1208individualscollaborativeeffortaggregatedprevailingcatalogtotalidentified156 622previouslyunreportedfrequenciesmajority888%lower5%predictedfunctionallydeleteriousadditionconstructedJapanese-specificmajornumberuniquemappingshortreadsincreased045%averageresultsillustrateimportanceconstructingethnicity-specificrarecentralizednewlydevelopedserveusefulresourcesexploringpathogenicPublicaccessavailablehttp://wwwmedkyoto-uacjp/SnpDB/Humanpopulation

Similar Articles

Cited By