Journal of the Korean Association of Oral and Maxillofacial Surgeons

The Korean Association of Oral and Maxillofacial Surgeons (대한구강악안면외과학회)
권호 표지

UNDERSTANDING OF SINGLE NUCLEOTIDE POLYMORPHISM OF HUMAN GENOME

인간 게놈의 단일염기변형 (Single Nucleotide Polymorphism; SNP)에 대한 이해

  • Oh, Jung-Hwan (Dept. of Oral and Maxillofacial Surgery, School of Dentistry, Kyung-Hee University) ;
  • Yoon, Byung-Wook (Dept. of Oral and Maxillofacial Surgery, School of Dentistry, Kyung-Hee University)
  • 오정환 (경희대학교 치의학전문대학원 구강악안면외과학교실) ;
  • 윤병욱 (경희대학교 치의학전문대학원 구강악안면외과학교실)
  • Published : 2008.08.29
Download PDF
⟨ Previous Next ⟩

Abstract

A Single Nucleotide Polymorphism (SNP) is a small genetic change or variation that can occur within a DNA sequence. It's the difference of one base at specific base pair position. SNP variation occurs when a single nucleotide, such as an A, replaces one of the other three nucleotide letters-C, G, or T. On average, SNP occur in the human population more than 1 percent of the time. They occur once in every 300 nucleotides on average, which means there are roughly 10 million SNPs in the human genome. Because SNPs occur frequently throughout the genome and tend to be relatively stable genetically, they serve as excellent biological markers. They can help scientists locate genes that are associated with disease such as heart disease, cancer, diabetes. They can also be used to track the inheritance of disease genes within families. SNPs may also be associated with absorbance and clearance of therapeutic agents. In the future, the most appropriate drug for an individual could be determined in advance of treatment by analyzing a patient's SNP profile. This pharmacogenetic strategy heralds an era in which the choice of drugs for a particular patient will be based on evidence rather than trial and error (so called "personalized medicine").

Keywords

References

  1. Clark P. David. Molecular biology: Understanding the genetic revolution. 1st Ed. Burlington: Elsevier Inc. 2005
  2. Venter JC, Adams MD, Myers EW et al: The sequence of the human genome. Science 2001;291:1304-1353 https://doi.org/10.1126/science.1058040
  3. Sachidanandam R, Weissman D, Schmidt S et al: The International SNP Map Working Group: A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 2001;409:928-933 https://doi.org/10.1038/35057149
  4. Thorisson GA, Stein LD: The SNP consortium website:past, present and future. Nucleic Acids Res 2003;31(1):124-127 https://doi.org/10.1093/nar/gkg052
  5. The International HapMap Consortium. The International HapMap Project. Nature 2003;426: 789-796 https://doi.org/10.1038/nature02168
  6. The International HapMap Consortium. A haplotype map of the human genome. Nature 2005;437:1299-1320 https://doi.org/10.1038/nature04226
  7. The International SNP Map Working Group. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 2001;409:928-933 https://doi.org/10.1038/35057149
  8. Bayani J, Selvarajah S, Maire G et al: Genomic mechanisms and measurement of structural and numerical instability in cancer cells. Seminars in Cancer Biol 2007;17:5-18
  9. Zho G, Zhai Y, Cui Y et al: MDM2 promoter SNP309 is associated with risk of occurrence and advanced lymph node metastasis of nasopharygeal carcinoma in china population. Clin Cancer Res 2007:13(9):2627-33 https://doi.org/10.1158/1078-0432.CCR-06-2281
  10. Girard L, Zoechbauer-Mueller S, Virmani AK et al: Genomewide allelotyping of lung cancer identifies new regions of allelic loss, difference between small cell lung cancer and non-small cell lung cancer, and loci clustering. Cancer Res 2000;60:4894-4906
  11. Harding AH, Loos RJ, Luan J et al: Polymorphisms in the gene encoding sterol requlatory element-binding factor-1c are associated with type 2 diabetes. Diabetetlolgia 2006;49(11):2642-2648 https://doi.org/10.1007/s00125-006-0430-1
  12. Jung CH, Rhee EJ, Kim SY et al: Associatios between two single nucleotide polymorphisms of Adiponetin gene and coronary artery diseases. Endocrine J 2006;53(5):671-677 https://doi.org/10.1507/endocrj.K06-020
  13. Oscarson M: Pharmacogenetics of drug metabolizing enzyme: importance for personalized medicine. Clin Chem Lab Med 2003;41(4):573-580 https://doi.org/10.1515/CCLM.2003.087
  14. De La Vega FM, Dailey D, Ziegle J et al: New generation pharmacogenomic tools: a SNP linkage disequlibrium Map, validated SNP assay resource, and high-throughput instrumentation system for large-scale genetic studies. Biotechniques 2002;suppl:48-50
  15. Deeken JF, Figg WD, Bates SE, Sparreboom A: Toward indivisualized treatment: prediction of anticancer drug disposition and toxicity with pharmacogenetics. Anticancer Drugs 2007;18(2):111-126 https://doi.org/10.1097/CAD.0b013e3280109411
  16. 이종극. 질병 유전체 분석법, 서울: 월드사이언스, 2006
  17. Cargill M, Altshuler D, Ireland J et al. Characterization of singlenucleotide polymorphisms in coding regions of human genes. Nat Genet 1999;22(3):231-238 https://doi.org/10.1038/10290
  18. Ardlie KG, Kruglyak L, Seielstad M: Patterns of linkage disequilibrium in the human genome. Nature Reviews Genet 2002;3(4):299-309 https://doi.org/10.1038/nrg777
  19. Wall JD, Pritchard JK: Haplotype blocks and linkage disequlilbrium in the human genome. Nature Reviews Genet;4:587-597
  20. Conrad DF, Jakobsson M, Coop G: A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet 2006:38(11):1227-1228 https://doi.org/10.1038/ng1106-1227
  21. McGuigan FE, Ralston SH: Single nucleotide polymorphism detection: allelic discrimination using TaqMan. Psychiatr Genet 2002;12(3):133-6 https://doi.org/10.1097/00041444-200209000-00003
  22. Livak KJ: Allelic discrimination using fluorogenic probes and the 5'nuclease assay. Genet Anal 1999;14(5-6):143-9 https://doi.org/10.1016/S1050-3862(98)00019-9
  23. Tost J, Gut IG: DNA methylation analysis by pyrosequencing. Nat Protocol 2007;2(9):2265-2275 https://doi.org/10.1038/nprot.2007.314
  24. Xiao Y, Segal MR, Yeh RF: A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays. Bioinformatics 2007;23(12):1459-1467 https://doi.org/10.1093/bioinformatics/btm131
  25. Stephens M, Smith NJ, Donnelly P: A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001;68:978-989 https://doi.org/10.1086/319501
  26. Barrett JC, Fry B, Maller J, Daly MJ: Haploview:analysis and visulalization of LD and haplotype maps. Bioinformatics 2005;1:263-265
  27. Gabriel SB et. al.: The structure of Haplotype blocks in the human genome. Science 2002;296:2225-2229 https://doi.org/10.1126/science.1069424
  28. Shibata T: Function of homologous DNA recombination. Rolem Revoew 2001;41:21-23