UNDERSTANDING OF EPIGENETICS AND DNA METHYLATION

인간 게놈의 Copy Number Variation과 유전자 질환

  • Oh, Jung-Hwan (Department of Oral and Maxillofacial Surgery, School of Dentistry, Kyung-Hee University) ;
  • Nishimura, Ichiro (The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, Department of Advanced Prothodontics, School of Dentistry, UCLA)
  • 오정환 (경희대학교 치의학전문대학원 구강악안면외과학교실) ;
  • Published : 2008.03.31

Abstract

Genetic variation in the human genome occurs on various levels; from the single nucleotide polymorphism to large, microscopically visible chromosome anomalies. It can be present in many forms, including variable number of tandem repeat (VNTRs; e.g., mini- and microsatellites), presence/absence of transposable elements (e.g., Alu elements), single nucleotide polymorphisms, and structural alterations (e.g., copy number variation, segmental duplication, inversion, translocation). Until recently SNPs were thought to be the main source of genetic and phenotypic human variation. However, the use of methods such as array comparative genomic hybridization (array CGH) and fluorescence in situ hybridization (FISH) have revealed the presence of copy number variations(CNVs) ranging from kilobases (kb) to megabases (Mb) in the human genome. There is great interest in the possibility that CNVs playa role in the etiology of common disease such as HIV-1/AIDS, diabetes, autoimmune disease, heart disease and cancer. The discovery of widespread copy number variation in human provides insights into genetic variability among populations and provides a foundation for studies of the contribution of CNVs to evolution and disease.

인간 게놈의 DNA서열의 차이는 개개인의 특이성을 의미하기 때문에 염기서열의 변화는 질병에 대한 감수성, 약물에 대한 반응 등 개인의 성향에 큰 영향을 미치게 된다. 인간 게놈에는 여러 가지 형태의 유전적 변이가 존재하지만 그 중 단일염기다형성이 인간의 유전적, 표현형의 다양성을 설명하는 주된 유전적 변이로 생각되었으나 최근 유전체 전체 분석법의 발전으로 1 kb 이상 크기의 CNV의 발견으로 개체간의 유전적 다양성에 대한 더 많은 이해가 가능하게 되었고, 진화와 유전 질환에 대한 CNV의 역할을 조사하는 연구의 기초를 제공하게 되었다. 현재 인간게놈의 CNV를 찾아내고 특성화 작업을 목표로 하는 The Copy Number Variation Project를 위해 The Wellcome Trust Institute (Hinxton, United Kingdom), Hospital for Sick Children (Toronto), University of Tokyo (Tokyo), Affymetrix (Santa Clara, CA), 그리고 Harvard Medical School/Brigham and Women's Hospital (Boston, MA) 등이 참여하는 international consortium이 구성되어 보다 심도 있는 연구가 진행되고, 또한 향후 진보된 DNA microarray-based technology와 서열화 기술의 개발로 인간 게놈 상의 모든 유전적 변이를 발견하게 되고 포괄적인 CNV 지도를 완성하고 인간 유전자 다양성 인간의 진화, 유전적 질환 개인 맞춤형 의학에 대한 새로운 이해와 연구가 가능하게 될 것으로 기대된다.

Keywords

References

  1. Venter JC, Adams MD, Myers EW et al : The sequence of the human genome. Science 291 : 1304, 2001 https://doi.org/10.1126/science.1058040
  2. Thorisson GA, Stein LD: The SNP consortium website : past, present and future. Nucleic Acids Res 31(1) : 124, 2003 https://doi.org/10.1093/nar/gkg052
  3. The International HapMap Consortium. The International HapMap Project. Nature 426 : 789, 2003 https://doi.org/10.1038/nature02168
  4. The International HapMap Consortium. A haplotype map of the human genome. Nature 437 : 1299, 2005 https://doi.org/10.1038/nature04226
  5. The International SNP Map Working Group. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409 : 928, 2001 https://doi.org/10.1038/35057149
  6. Iafrate AJ, Feuk L, Rivera MN et al : Detection of largescale variation in the human genome. Nat Genet 36 : 949, 2004 https://doi.org/10.1038/ng1416
  7. Sebat J, Lakshmi B, Troge J et al : Large-scale copy number polymorphism I the human genome. Science 305 : 525, 2004 https://doi.org/10.1126/science.1098918
  8. Sharp AJ, Locke DP, McGrath SD et al : Segmental duplications and copy-number variation in the hman genome. Am J Hum Genet 77 : 78,2005 https://doi.org/10.1086/431652
  9. Tuzun E, Sharp AJ, Bailey JA et al : Fine-scale structural variation of the human genome. Nat Genet 37 : 727, 2005 https://doi.org/10.1038/ng1562
  10. Clark P. David. Molecular biology: Understanding the genetic revolution. 1st Ed. Burlington : Elsevier Inc. 2005
  11. Freeman JL, Perry GH, Feuk L et al: Copy number variation : New insights in genome diversity. Genome Res 949, 2007
  12. Feuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat Rev Genet 7:85, 2006
  13. Sherer SW, Cheung J, MacDonald JR et al : Human chromosome 7: DNA sequence and biology. Science 300: 767, 2003 https://doi.org/10.1126/science.1083423
  14. Conrad DF, Andrews TD, Carter NP et al : A high-resolution survey of deletion polymorphism in the human genome. Nat Genet 38 : 75, 2006 https://doi.org/10.1038/ng1697
  15. McCarroll SA, Hadnott TN, Perry GH et al : Common deletion polymorphisms in the human genome. Nat Genet 38 : 86, 2006 https://doi.org/10.1038/ng1696
  16. Hinds DA, Klock AP, Jen M et al : Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet 38 : 82, 2006 https://doi.org/10.1038/ng1695
  17. Nadeau JH, Lee C: Copies count. Nature 439 : 798, 2006 https://doi.org/10.1038/439798a
  18. Eichler EE: Widening the spectrum of human genetic variation. Nat Genet 38(1) : 9, 2006 https://doi.org/10.1038/ng0106-9
  19. Redon R, Ishikawa S, Fitch KR et al : Global variation in copy number in the human genome. Nature 444 : 444, 2006 https://doi.org/10.1038/nature05329
  20. Shaw CJ, Lupski JR: Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease. Hum Mol Genet. 13(1) : 57, 2004 https://doi.org/10.1093/hmg/ddh073
  21. Gonzalez E, Quinones MP, Barnshad MJ et al : The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307 : 1434, 2005 https://doi.org/10.1126/science.1101160
  22. Yang Y, Chung EK, Savelli SL et al : Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE) : low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. Am J Hum Genet 80(6) : 1037, 2007 https://doi.org/10.1086/518257
  23. Sebat J, Lakshmi B, Malhotra D et al : Strong association of de novo copy number mutations with autism. Science 20(316) : 445, 2007
  24. Christiansen J, Dyck JD, Elyas BG et al : Chromosome 1q21.1 contiguous gene deletion is associated with congenital heart disease. Circ Res 92 : 1492, 2004
  25. Gal TJ, Huang WY, Chen C et al : DNA repair gene polymorphisms and risk of second primary neoplasms and mortality in oral cancer patients. Laryngoscope 115 : 2221, 2005 https://doi.org/10.1097/01.mlg.0000183736.96004.f7
  26. Albertson DG, Pinkel D: Genomic microarrays in human genetic disease and Cancer. Hum Mol Genet 12(2) : 145, 2003 https://doi.org/10.1093/hmg/ddg016
  27. Bejjani B, Shaffer LG: Application of array-based comparative genomic hybridization to clinical diagnostics. J Mol Diagnostics 8(5) : 528, 2006 https://doi.org/10.2353/jmoldx.2006.060029
  28. Pinkel D, Albertson DG: Array comparative genomic hybridization and its applications in cancer. Nat Genet 37:11, 2005 https://doi.org/10.1038/ng0105-11
  29. Braude I, Vukovic B, Prasad M et al: Large scale copy number variation (CNV) at 14q12 is associated with the presence of genomic abnormalities in neoplasia. BMC Genomics 7 : 138, 2006 https://doi.org/10.1186/1471-2164-7-138