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

Journal of Human Genetics

Volumn 61, Issue 6, 2016, Pages 547-553

  Higasa, Koichiro ^a   Miyake, Noriko ^b   Yoshimura, Jun ^c   Okamura, Kohji ^d   Niihori, Tetsuya ^e   Saitsu, Hirotomo ^b   Doi, Koichiro ^c   Shimizu, Masakazu ^a   Nakabayashi, Kazuhiko ^d   Aoki, Yoko ^e   Tsurusaki, Yoshinori ^b   Morishita, Shinichi ^c   Kawaguchi, Takahisa ^a   Migita, Osuke ^d,f   Nakayama, Keiko ^e   Nakashima, Mitsuko ^b   Mitsui, Jun ^g   Narahara, Maiko ^a   Hayashi, Keiko ^d   Funayama, Ryo ^e   Yamaguchi, Daisuke ^h   Ishiura, Hiroyuki ^g   Ko, Wen Ya ^a,i   Hata, Kenichiro ^d   Nagashima, Takeshi ^e   Yamada, Ryo ^a   Matsubara, Yoichi ^e,j   Umezawa, Akihiro ^d   Tsuji, Shoji ^g   Matsumoto, Naomichi ^b   Matsuda, Fumihiko ^a   more..

^a KYOTO UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^b YOKOHAMA CITY UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d NATIONAL RESEARCH INSTITUTE FOR CHILD HEALTH AND DEVELOPMENT   (Japan)

^e TOHOKU UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^f ST MARIANNA UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^g UNIVERSITY OF TOKYO   (Japan)

^h BITS Company Limited   (Japan)

ⁱ NATIONAL YANG MING UNIVERSITY   (Taiwan)

^j NATIONAL CENTER FOR CHILD HEALTH AND DEVELOPMENT   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ETHNICITY; EXOME; GENE CONSTRUCT; GENE FREQUENCY; GENE MAPPING; GENE SEQUENCE; GENETIC DATABASE; GENETIC VARIATION; GENOME ANALYSIS; HUMAN; JAPANESE (PEOPLE); MAJOR CLINICAL STUDY; POPULATION GENETICS; REFERENCE DATABASE; ALLELE; GENETIC SELECTION; GENOMICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; JAPAN; PROCEDURES; QUALITY CONTROL; WEB BROWSER;

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;

EID: 84976541585     PISSN: 14345161     EISSN: 1435232X     Source Type: Journal    
DOI: 10.1038/jhg.2016.12     Document Type: Article

References (45)

1. Genome of the Netherlands Consortium. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat. Genet. 46, 818-825 (2014).
2. 1000 Genomes Project Consortium, Auton, A., Brooks, L. D., Durbin, R. M., Garrison, E. P., Kang, H. M. et al. A global reference for human genetic variation. Nature 526, 68-74 (2015).
3. Gudbjartsson, D. F., Helgason, H., Gudjonsson, S. A., Zink, F., Oddson, A., Gylfason, A. et al. Large-scale whole-genome sequencing of the Icelandic population. Nat. Genet. 47, 435-444 (2015).
4. Nagasaki, M., Yasuda, J., Katsuoka, F., Nariai, N., Kojima, K., Kawai, Y. et al. Rare variant discovery by deep whole-genome sequencing of 1, 070 Japanese individuals. Nat. Commun. 6, 8018 (2015).
5. Tennessen, J. A., Bigham, A. W., O'Connor, T. D., Fu, W., Kenny, E. E., Gravel, S. et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337, 64-69 (2012).
6. UK10K Consortium, Walter, K., Min, J. L., Huang, J., Crooks, L., Memari, Y. et al. The UK10K project identifies rare variants in health and disease. Nature 526, 82-90 (2015).
7. Wong, L. P., Ong, R. T., Poh, W. T., Liu, X., Chen, P., Li, R. et al. Deep whole-genome sequencing of 100 southeast Asian Malays. Am. J. Hum. Genet. 92, 52-66 (2013).
8. Zhang, W., Meehan, J., Su, Z., Ng, H. W., Shu, M., Luo, H. et al. Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population. BMC Bioinformatics 15 (Suppl 11), S6 (2014).
9. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
10. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
11. DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
12. Sherry, S. T., Ward, M. H., Kholodov, M., Baker, J., Phan, L., Smigielski, E. M. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308-311 (2001).
13. Durbin, R. M., Abecasis, G. R., Altshuler, D. L., Auton, A., Brooks, L. D., Gibbs, R. A. et al. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010).
14. Reese, M. G., Moore, B., Batchelor, C., Salas, F., Cunningham, F., Marth, G. T. et al. A standard variation file format for human genome sequences. Genome Biol. 11, R88 (2010).
15. Pruitt, K. D., Tatusova, T. & Maglott, D. R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35, D61-D65 (2007).
16. Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P. et al. A method and server for predicting damaging missense mutations. Nat. Methods. 7, 248-249 (2010).
17. Kumar, P., Henikoff, S. & Ng, P. C. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc. 4, 1073-1081 (2009).
18. Siepel, A., Pollard, K. & Haussler, D. New methods for detecting lineage-specific selection. Proceedings of the 10th international conference on research in computational molecular biology (RECOMB 2006), 3909, 190-205 (2006).
19. Liu, X., Jian, X. & Boerwinkle, E. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum. Mutat. 32, 894-899 (2011).
20. Fu, Y. X. Statistical properties of segregating sites. Theor. Popul. Biol. 48, 172-197 (1995).
21. Watterson, G. A. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7, 256-276 (1975).
22. Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595 (1989).
23. Akey, J. M., Zhang, G., Zhang, K., Jin, L. & Shriver, M. D. Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 12, 1805-1814 (2002).
24. Backes, C., Keller, A., Kuentzer, J., Kneissl, B., Comtesse, N., Elnakady, Y. A. et al. GeneTrail-advanced gene set enrichment analysis. Nucleic Acids Res. 35, W186-W192 (2007).
25. Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30 (2000).
26. McKusick, V. A. Mendelian Inheritance in Man and its online version, OMIM. Am. J. Hum. Genet. 80, 588-604 (2007).
27. Harris, M. A., Clark, J., Ireland, A., Lomax, J., Ashburner, M., Foulger, R. et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258-D261 (2004).
28. Tabara, Y., Takahashi, Y., Kawaguchi, T., Setoh, K., Terao, C., Yamada, R. et al. Association of serum-free fatty acid level with reduced reflection pressure wave magnitude and central blood pressure: the Nagahama study. Hypertension 64, 1212-1218 (2014).
29. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007).
30. Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A. & Reich, D. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904-909 (2006).
31. Marth, G. T., Yu, F., Indap, A. R., Garimella, K., Gravel, S., Leong, W. F. et al. The functional spectrum of low-frequency coding variation. Genome Biol. 12, R84 (2011).
32. Nelson, M. R., Wegmann, D., Ehm, M. G., Kessner, D. St, Jean, P., Verzilli, C. et al. An abundance of rare functional variants in 202 drug target genes sequenced in 14, 002 people. Science 337, 100-104 (2012).
33. Weir, B. S. Population Substructure. Genetic Data Analysis II, Sinauer Associates, Sunderland, MA., (1996).
34. Beleza, S., Johnson, N. A., Candille, S. I., Absher, D. M., Coram, M. A., Lopes, J. et al. Genetic architecture of skin and eye color in an african-European admixed population. PLoS Genet. 9, e1003372 (2013).
35. Martinez-Cadenas, C., Lopez, S., Ribas, G., Flores, C., Garcia, O., Sevilla, A. et al. Simultaneous purifying selection on the ancestral MC1R allele and positive selection on the melanoma-risk allele V60L in south Europeans. Mol. Biol. Evol. 30, 2654-2665 (2013).
36. Shimanuki, M., Abe, Y., Tamiya, G., Ueki, M., Hozumi, Y. & Suzuki, T. Positive selection with diversity in oculocutaneous albinisms type 2 gene (OCA2) among Japanese. Pigment Cell Melanoma Res. 28, 233-235 (2015).
37. Seltsam, A., Hallensleben, M., Kollmann, A. & Blasczyk, R. The nature of diversity and diversification at the ABO locus. Blood 102, 3035-3042 (2003).
38. Dewey, F. E., Chen, R., Cordero, S. P., Ormond, K. E., Caleshu, C., Karczewski, K. J. et al. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet. 7, e1002280 (2011).
39. Narahara, M., Higasa, K., Nakamura, S., Tabara, Y., Kawaguchi, T., Ishii, M. et al. Large-scale East-Asian eQTL mapping reveals novel candidate genes for LD mapping and the genomic landscape of transcriptional effects of sequence variants. PLoS ONE 9, e100924 (2014).
40. The GTEx Consortium. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348, 648-660 (2015).
41. Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J. et al. Finding the missing heritability of complex diseases. Nature 461, 747-753 (2009).
42. Ratan, A., Miller, W., Guillory, J., Stinson, J., Seshagiri, S. & Schuster, S. C. Comparison of sequencing platforms for single nucleotide variant calls in a human sample. PLoS ONE 8, e55089 (2013).
43. Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
44. Genovese, G., Handsaker, R. E., Li, H., Altemose, N., Lindgren, A. M., Chambert, K. et al. Using population admixture to help complete maps of the human genome. Nat. Genet. 45, 406-414 (2013).
45. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931-945 (2004).