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Aspects Influencing Genotyping Method Selection

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Pharmacogenomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 311))

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Abstract

The variety of genotyping methods currently available and the evolution of their capabilities have facilitated an expansion of the field of pharmacogenomics. Traditionally, limited genotyping capabilities have restricted the generation and application of genotyping data for pharmacogenomic studies. With the variety of platforms and chemistries available for flexible, high-throughput genotyping, it is important to keep in mind the limitations imposed by both the polymorphisms that are to be interrogated and the type of pharmacogenomics study for which the data are being generated. This chapter is an overview of the constraints these factors impose on different genotyping methods and describes aspects important to the integration of genotyping into a pharmacogenomics study.

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References

  1. Kwok, P. Y. and Gu, Z. J. (1999) Single Nucleotide polymorphism libraries: why and how are we building them? Mol. Med. Today 5, 538–543.

    Article  PubMed  CAS  Google Scholar 

  2. Wheeler, D. L., Church, D. M., Edgar, R., et al. (2004) Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res. 32, D35–40. Available at: http://www.ncbi.nlm.nih.gov/SNP/.

    Article  PubMed  CAS  Google Scholar 

  3. Birney, E., Andrews, T. D., Bevan, P., et al. (2004) An overview of Ensembl. Genome Res. 5, 925–928. Available at: http://www.ensembl.org.

    Article  Google Scholar 

  4. The international SNP map working group. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933. Available at:http://snp.cshl.org/.

    Article  Google Scholar 

  5. The international hapmap consortium. (2003) The international hapmap project. Nature 426, 349–357. Available at: http://www.hapmap.org.

    Google Scholar 

  6. Packer, B. R., Yeager, M., and Staats, B., et al. (2004) SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes. Nucleic Acids Res. 32, D528–D532. Available at: http://snp500cancer.nci.nih.gov/home_1.cfm?CFID=2241&CFTOKEN=69829203.

    Article  PubMed  CAS  Google Scholar 

  7. Abeysinghe, S. S., Stenson, P. D., Krawczak, M., and Cooper, D. N. (2004) Gross rearrangement breakpoint database (GRaBD). Hum. Mutat. 23, 219–221. Available at: http://www.uwcm.ac.uk/uwcm/mg/grabd/.

    Article  PubMed  CAS  Google Scholar 

  8. Kwok, P. Y. (ed.) (2003) Single Nucleotide Polymorphisms. Humana, Totowa, NJ.

    Google Scholar 

  9. Mitchelson, K. R. and Cheng, J., (ed.) (2001) Capillary Electrophoresis of Nucleic Acids, Vol II. Humana, Totowa, NJ.

    Google Scholar 

  10. Kwok, P. Y. (2000) High-throughput genotyping assay approaches. Pharmacogenomics. 1, 95–100.

    Article  PubMed  CAS  Google Scholar 

  11. Brooks, L. (2003) SNPs: why do we care, in Single Nucleotide Polymorphisms (Kwok, P. Y., ed.), Humana, Totowa, NJ, pp. 1–14.

    Google Scholar 

  12. Wang, Z. and Moult, J., (2001) SNPs, protein structure, and disease. Hum. Mutat. 17, 263–270.

    Article  PubMed  Google Scholar 

  13. Cargill, M., Sltchuler, D., Ireland, J., et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22, 231–238.

    Article  PubMed  CAS  Google Scholar 

  14. Chakravarti, A. (1999) Population genetics—making sense out of sequence. Nat. Genet. 21, 239–247.

    Article  Google Scholar 

  15. Kruglyak, L. and Nickerson, DA. (2001) Variation is the spice of life. Nat. Genet. 27, 234–236.

    Article  PubMed  CAS  Google Scholar 

  16. Imyanitov, E. N., Togo, A. V., and Hanson, K. P. (2004) Searching for cancer-associated gene polymorphisms: promises and obstacles. Cancer Lett. 2004, 3–14.

    Article  Google Scholar 

  17. Schlotterer, C. (2004) The evolution of molecular markers—just a matter of fashion? Nat. Rev. Genet. 5, 63–69.

    Article  PubMed  Google Scholar 

  18. Jonasdottir, A., Thorlacius, T., Fossdal, R., et al. (2003) A whole genome association study in Icelandic multiple sclerosis patients with 4804 markers. J. Neuroimmunol. 143, 88–92.

    Article  PubMed  CAS  Google Scholar 

  19. Collins, J. R., Stephens, R. M., Gold, B., Long, B., Dean, M., and Burt, S. K. (2003) An exhaustive DNA micro-satellite map of the human genome using high performance computing. Genomics. 82, 10–19.

    Article  PubMed  CAS  Google Scholar 

  20. Nievergelt, C. M., Smith, D. W., Kohlenberg, J. B., and Schork, N. J. (2004) Large-scale integration of human genetic and physical maps. Genome Res. 14, 1199–1205.

    Article  PubMed  CAS  Google Scholar 

  21. Rosenberg, N. A., Li, L. M., Ward, R., and Pritchard, J. K. (2003) Informativeness of genetic markers for inference of ancestry. Am. J. Hum. Genet. 73, 1402–1422.

    Article  PubMed  CAS  Google Scholar 

  22. Monaghan, G., Ryan, M., Seddon, R., Hume, R., and Burchell, B. (1996) Genetic variation in bilirubin UDP-glucuronocyltransferase gene promoter and Gilbert’s syndrome. Lancet 347, 578–581.

    Article  PubMed  CAS  Google Scholar 

  23. Bosma, P. J., Chowdhury, J. R., Bakker, C., et al. (1995) The genetic basis of the reduced expression of bilirubin UDP-glucuronosyltransferase 1 in Gilbert’s syndrome. N. Engl. J. Med. 333, 1171–1175.

    Article  PubMed  CAS  Google Scholar 

  24. Mansfield, E. S., Wilson, R. B., and Fortina, P. (2001) Analysis of short tandem repeat markers by capillary array electrophoresis, in Capillary Electrophoresis of Nucleic Acids, Vol II. (Mitchelson, K. R., and Cheng, J., eds.), Humana, Totowa, NJ, pp. 151–162.

    Chapter  Google Scholar 

  25. Etienne, M. C., Ilc, K., Formento, J. L., et al. (2004) Thymidylate synthase and methylenetetrahydrofolate reductase gene polymorphisms: relationships with 5-fluorouracil sensitivity. Br. J. Cancer 90, 526–534.

    Article  PubMed  CAS  Google Scholar 

  26. Marsh, S., Collie-Duguid, E. S.R., Li, T., Liu, X., and McLeod, H. L. (1999) Ethnic variation in the thymidylate synthase enhancer region polymorphism among Caucasian and Asian populations. Genomics 58, 310–312.

    Article  PubMed  CAS  Google Scholar 

  27. Tsai, M. Y., Bignell, M., Schwichtenberg, K., and Hanson, N. Q. (1996) High prevalence of a mutation in the Cystathionine β-synthase gene. Am. J. Hum. Genet. 59, 1262–1267.

    PubMed  CAS  Google Scholar 

  28. Tsai, M. Y., Bignell, M., Yang, F., Welge, B. G., Graham, K. J., and Hanson, N. Q. (2000) Polygenic influence on plasma homocysteine: association of two prevalent mutations, the 844ins68 of cystathionine β-synthase and A2756G of methionine synthase, with lowered plasma levels. Atherosclerosis 149, 131–137.

    Article  PubMed  CAS  Google Scholar 

  29. Kraus, J. P., Loiveriusova, J., Sokolova, J., et al. (1998) The human cystathionine β-sythase (CBS) gene: complete sequence, alternative splicing, and polymorphisms. Genomics 52, 312–314.

    Article  PubMed  CAS  Google Scholar 

  30. Guo, D. C., Qi, Y., He, R., Gupta, P., and Milewicz, D. M. (2003) High throughput detection of small genomic insertions or deletions by Pyrosequencing. Biotechnol. Lett. 25, 1703–1707.

    Article  PubMed  CAS  Google Scholar 

  31. Huang, X. H., Salomake, A., Malin, R., Koivula, T., Jokela, H., and Lehtimaki, T. (1997) Rapid identification of angiotensin-converting enzyme genotypes by capillary electrophoresis.43, 2195–2196

    Google Scholar 

  32. Wenz, H. M., Dailey, D., and Johnson, M. D. (2001) Development of a highthroughput capillary electrophoresis protocol for DNA fragment analysis, in Capillary Electrophoresis of Nucleic Acids, Vol II. (Mitchelson, K. R., Cheng, J., eds.), Humana, Totowa, NJ, pp. 3–18.

    Chapter  Google Scholar 

  33. Goldstein, D. B., Tate, S. K., and Sisodiya, S. M. (2003) Pharmacogenetics goes genomic. Nat. Rev. Genet. 4, 937–947.

    Article  PubMed  CAS  Google Scholar 

  34. Evans, W. E. and McLoed, H. L. (2003) Pharmacogenomics-drug disposition, drug targets, and side effects. N. Engl. J. Med. 346, 538–549.

    Google Scholar 

  35. Evans, W. E. and Relling, M. V. (1999) Pharmacogenomics: translating functional genomics into rational therapeutics. Science 286, 487–491.

    Article  PubMed  CAS  Google Scholar 

  36. Ulrich, C. M., Robien, K., and McLoed, H. L. (2003) Cancer pharmacogenetics: polymorphisms, pathways and beyond. Nat. Rev. Cancer 3, 912–920.

    Article  PubMed  CAS  Google Scholar 

  37. Johnson, J. A. (2003) Pharmacogenetics: potential for individualized drug therapy through genetics. Trends Genet. 19, 660–666.

    Article  PubMed  CAS  Google Scholar 

  38. McLeod, H. L. and Evans, W. E. (2001) Phamacogenomics: unlocking the human genome for better drug therapy. Annu Rev. Pharmacol. Toxicol. 41, 101–121.

    Article  PubMed  CAS  Google Scholar 

  39. Daly, A. K. (2003) Pharmacogenetics of the major polymorphic metabolizing enzymes. Fundam. Clin. Pharmacol. 17, 27–41.

    Article  PubMed  CAS  Google Scholar 

  40. Hao, K., Xu, X., Laird, N., Wang, X., and Xu, X. (2003) Power estimation of multiple SNP association test of case-control study and application. Genet. Epidemiol. 26, 22–30.

    Article  Google Scholar 

  41. Service, S. K., Sandkuijl, L. A., and Freimer, N. B. (2003) Cost-effective designs for linkage disequilibrium mapping of complex traits. Am. J. Hum. Genet. 72, 1213–1220.

    Article  PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN

    Peter Imle

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  1. Peter Imle
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Editors and Affiliations

  1. Committee on Clinical Pharmacology and Pharmacogenomics, Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL

    Federico Innocenti MD, PhD

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© 2005 Humana Press Inc., Totowa, NJ

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Imle, P. (2005). Aspects Influencing Genotyping Method Selection. In: Innocenti, F. (eds) Pharmacogenomics. Methods in Molecular Biology™, vol 311. Humana Press. https://doi.org/10.1385/1-59259-957-5:063

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  • DOI: https://doi.org/10.1385/1-59259-957-5:063

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-440-1

  • Online ISBN: 978-1-59259-957-8

  • eBook Packages: Springer Protocols

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