Journal of Genetics

, Volume 93, Supplement 1, pp 1–11 | Cite as

Analysis of indel variations in the human disease-associated genes CDKN2AIP, WDR66, USP20 and OR7C2 in a Korean population

  • RYONG NAM KIM
  • AERI KIM
  • DONG-WOOK KIM
  • SANG-HAENG CHOI
  • DAE-SOO KIM
  • SEONG-HYEUK NAM
  • ARAM KANG
  • MIN-YOUNG KIM
  • KUN-HYANG PARK
  • BYOUNG-HA YOON
  • KANG SEON LEE
  • HONG-SEOG PARK
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  • 159 Downloads

Keywords

insertion–deletion variations haematological disease tumours human genetics 

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References

  1. Ahn S. M., Kim T. H., Lee S., Kim D., Ghang H., Kim D. S. et al. 2009 The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 19, 1622–1629.CrossRefPubMedPubMedCentralGoogle Scholar
  2. Bentley D. R., Balasubramanian S., Swerdlow H. P., Smith G. P., Milton J., Brown C. G. et al. 2008 Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53–59.CrossRefPubMedPubMedCentralGoogle Scholar
  3. Berthouze M., Venkataramanan V., Li Y. and Shenoy S. K. 2009 The deubiquitinases USP33 and USP20 coordinate beta2 adrenergic receptor recycling and resensitization. EMBO J. 28, 1684–1696.CrossRefPubMedPubMedCentralGoogle Scholar
  4. Cheung C. T., Hasan M. K., Widodo N., Kaul S. C. and Wadhwa R. 2009 CARF: an emerging regulator of p53 tumor suppressor and senescence pathway. Mech. Ageing Dev. 130, 18–23.CrossRefPubMedGoogle Scholar
  5. Collins F. S., Drumm M. L., Cole J. L., Lockwood W. K., Vande Woude G. F. and Iannuzzi M. C. 1987 Construction of a general human chromosome jumping library, with application to cystic fibrosis. Science 235, 1046–1049.CrossRefPubMedGoogle Scholar
  6. Durbin R. M., Abecasis G. R., Altshuler D. L., Auton A., Brooks L. D., Gibbs R. A. et al. 2010 A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073.CrossRefPubMedGoogle Scholar
  7. Goldsmith D. J. and Thomas P. 1999 Images in clinical medicine. von Hippel-Lindau disease. N. Engl. J. Med. 340, 1880.CrossRefPubMedGoogle Scholar
  8. Hajirasouliha I., Hormozdiari F., Alkan C., Kidd J. M., Birol I., Eichler E. E. and Sahinalp S. C. 2010 Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics 26, 1277–1283.CrossRefPubMedPubMedCentralGoogle Scholar
  9. Kelley L. A. and Sternberg M. J. 2009 Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 4, 363–371.CrossRefPubMedGoogle Scholar
  10. Kim D. W., Nam S. H., Kim R. N., Choi S. H. and Park H. S. 2010 Whole human exome capture for high-throughput sequencing. Genome 53, 568–574.CrossRefPubMedGoogle Scholar
  11. Kim J. I., Ju Y. S., Park H., Kim S., Lee S., Yi J. H. et al. 2009 A highly annotated whole-genome sequence of a Korean individual. Nature 460, 1011–1015.PubMedPubMedCentralGoogle Scholar
  12. Li D. and Roberts R. 2001 WD-repeat proteins: structure characteristics, biological function, and their involvement in human diseases. Cell Mol. Life Sci. 58, 2085–2097.CrossRefPubMedGoogle Scholar
  13. Li Z., Wang D., Na X., Schoen S. R., Messing E. M. and Wu G. 2002 Identification of a deubiquitinating enzyme subfamily as substrates of the von Hippel-Lindau tumor suppressor. Biochem. Biophys. Res. Commun. 294, 700–709.CrossRefPubMedGoogle Scholar
  14. Li Z., Wang D., Messing E. M. and Wu G. 2005 VHL protein-interacting deubiquitinating enzyme 2 deubiquitinates and stabilizes HIF-1alpha. EMBO Rep. 6, 373–378.CrossRefPubMedPubMedCentralGoogle Scholar
  15. Malnic B., Godfrey P. A. and Buck L. B. 2004 The human olfactory receptor gene family. Proc. Natl. Acad. Sci. USA 101, 2584–2589.CrossRefPubMedPubMedCentralGoogle Scholar
  16. McCarroll S. A., Kuruvilla F. G., Korn J. M., Cawley S., Nemesh J. and Wysoker A. 2008 Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet. 40, 1166–1174.CrossRefPubMedGoogle Scholar
  17. Meisinger C., Prokisch H., Gieger C., Soranzo N., Mehta D., Rosskopf D. et al. 2009 A genome-wide association study identifies three loci associated with mean platelet volume. Am. J. Hum. Genet. 84, 66–71.CrossRefPubMedPubMedCentralGoogle Scholar
  18. Mills R. E., Luttig C. T., Larkins C. E., Beauchamp A., Tsui C., Pittard W. S. and Devine S. E. 2006 An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 16, 1182–1190.CrossRefPubMedPubMedCentralGoogle Scholar
  19. Mullaney J. M., Mills R. E., Pittard W. S. and Devine S. E. 2010 Small insertions and deletions (INDELs) in human genomes. Hum. Mol. Genet. 19, R131–R136.CrossRefGoogle Scholar
  20. Ngo V. N., Young R. M., Schmitz R., Jhavar S., Xiao W., Lim K. H. et al. 2011 Oncogenically active MYD88 mutations in human lymphoma. Nature 470, 115–119.CrossRefPubMedGoogle Scholar
  21. Ostertag E. M. and Kazazian Jr H. H. 2001 Biology of mammalian L1 retrotransposons. Annu. Rev. Genet. 35, 501–538.CrossRefPubMedGoogle Scholar
  22. Soranzo N., Spector T. D., Mangino M., Kuhnel B., Rendon A., Teumer A. et al. 2009 A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium. Nat. Genet. 41, 1182–1190.CrossRefPubMedPubMedCentralGoogle Scholar
  23. The International HapMap Project 2003 Nature 426, 789–796.CrossRefGoogle Scholar
  24. Varela I., Tarpey P., Raine K., Huang D., Ong C. K., Stephens P. et al. 2011 Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 469, 539–542.CrossRefPubMedPubMedCentralGoogle Scholar
  25. Wang J., Wang W., Li R., Li Y., Tian G., Goodman L. et al. 2008 The diploid genome sequence of an Asian individual. Nature 456, 60–65.CrossRefPubMedPubMedCentralGoogle Scholar
  26. Warren S. T., Zhang F., Licameli G. R. and Peters J. F. 1987 The fragile X site in somatic cell hybrids: an approach for molecular cloning of fragile sites. Science 237, 420–423.CrossRefPubMedGoogle Scholar
  27. Wheeler D. A., Srinivasan M., Egholm M., Shen Y., Chen L., McGuire A. et al. 2008 The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872–876.CrossRefPubMedGoogle Scholar
  28. Ye K., Schulz M. H., Long Q., Apweiler R. and Ning Z. 2009 Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865–2871.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Indian Academy of Sciences 2012

Authors and Affiliations

  • RYONG NAM KIM
    • 1
  • AERI KIM
    • 1
    • 2
  • DONG-WOOK KIM
    • 1
  • SANG-HAENG CHOI
    • 1
  • DAE-SOO KIM
    • 1
  • SEONG-HYEUK NAM
    • 1
  • ARAM KANG
    • 1
    • 2
  • MIN-YOUNG KIM
    • 1
  • KUN-HYANG PARK
    • 1
  • BYOUNG-HA YOON
    • 1
    • 2
  • KANG SEON LEE
    • 1
  • HONG-SEOG PARK
    • 1
    • 2
  1. 1.Genome Resource CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)DaejeonRepublic of Korea
  2. 2.University of Science and Technology (UST)DaejeonRepublic of Korea

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