Genomics & Informatics

  • 제7권1호
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  • Pages.32-37
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  • 2009
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  • 1598-866X(pISSN)
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  • 2234-0742(eISSN)
한국유전체학회 (Korea Genome Organization)
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Choosing Optimal STR Markers for Quality Assurance of Distributed Biomaterials in Biobanking

  • Chung, Tae-Hoon (Korea Biobank, Center for Genome Science, Korean National Institute of Health, Korea Center for Disease Control and Prevention) ;
  • Lee, Hee-Jung (Korea Biobank, Center for Genome Science, Korean National Institute of Health, Korea Center for Disease Control and Prevention) ;
  • Lee, Mi-Hee (Korea Biobank, Center for Genome Science, Korean National Institute of Health, Korea Center for Disease Control and Prevention) ;
  • Jeon, Jae-Pil (Korea Biobank, Center for Genome Science, Korean National Institute of Health, Korea Center for Disease Control and Prevention) ;
  • Kim, Ki-Sang (Korea Biobank, Center for Genome Science, Korean National Institute of Health, Korea Center for Disease Control and Prevention) ;
  • Han, Bok-Ghee (Korea Biobank, Center for Genome Science, Korean National Institute of Health, Korea Center for Disease Control and Prevention)
  • 발행 : 2009.03.31
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초록

The quality assurance (QA) is of utmost importance in biobanks when archived biomaterials are distributed to biomedical researchers. For sample authentication and cross-contamination detection, the two fundamental elements of QA, STR genotyping is usually utilized. However, the incorporated number of STR markers is highly redundant for biobanking purposes, resulting in time and cost inefficiency. An index to measure the cross-contamination detection capability of an STR marker, the mixture probability (MP), was developed. MP as well as other forensic parameters for STR markers was validated using STR genotyping data on 2328 normal Koreans with the commercial AmpFlSTR kit. For Koreans, 7 STR marker (D2S1338, FGA, D18S51, D8S1179, D13S317, D21S11, vWA) set was sufficient to provide discrimination power of ${\sim}10^{-10}$ and cross-contamination detection probability of ${sim}1$. Interestingly, similar marker sets were obtained from African Americans, Caucasian Americans, and Hispanic Americans under the same level of discrimination power. Only a small subset of commonly used STR markers is sufficient for QA purposes in biobanks. A procedure for selecting optimal STR markers is outlined using STR genotyping results from normal Korean population.

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참고문헌

  1. Ahn, C. (2007). Pharmacogenomics in Drug Discovery and Development. Genomics & Informatics 5, 41-45
  2. Alford, R.L., Hammond, H.A., Coto, I., and Caskey, C.T. (1994). Rapid and efficient resolution of parentage by amplification of short tandem repeats. Am. J. Hum. Genet. 55, 190-195
  3. Ballantyn, J. (1997). Mass disaster genetics. Nat. Genet. 15, 329-331 https://doi.org/10.1038/ng0497-329
  4. Bhak, J., Ghang, H., Reja, R., and Kim, S. (2008). Personal Genomics, Bioinformatics, and Variomics. Genomics & Informatics 6, 161-165 https://doi.org/10.5808/GI.2008.6.4.161
  5. Botstein, D., White, R.L., Skolnick, M., and Davis, R.W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314-331
  6. Brenner, C., and Morris, J. (1990). Paternity index calculations in single locus hypervariable DNA probes: validation and other studies. in Proceedings for the International Symposium on Human Identification 1989. Promega Corporation, Madison, WI pp.21-53
  7. Butler, J.M. (2006). Genetics and genomics of core short tandem repeat loci used in human identity testing. J. Forensic Sci. 51, 253-265 https://doi.org/10.1111/j.1556-4029.2006.00046.x
  8. Butler, J.M., Schoske, R., Vallone, P.M., Redman, J.W., and Kline, M.C. (2003). Allele frequencies for 15 autosomal STR loci on U.S. Caucasian, African American, and Hispanic populations. J. Forensic Sci. 48, 908-911
  9. Downey, P., and Peakman, T.C. (2008). Design and implementation of a high throughput biological sample processing facility using modern manufacturing principles. Int. J. Epidemiol. 37(Suppl 1), i46-i50 https://doi.org/10.1093/ije/dyn031
  10. Elliott, P., and Peakman, T.C. (2008). The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine. Int. J. Epidemiol. 37, 234-244 https://doi.org/10.1093/ije/dym276
  11. Elliott, P., and Peakman, T.C. (2008). The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine. Int. J. Epidemiol. 37, 234-244 https://doi.org/10.1093/ije/dym276
  12. Excoffier, L., Laval, G., and Schneider, S. (2005). Arlequin v3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1, 47-50
  13. Fagan, M., and Ball, P. (2008). Design and implementation of a large-scale liquid nitrogen archive. Int. J. Epidemiol. 37(Suppl 1), i62-i64 https://doi.org/10.1093/ije/dym287
  14. Guo, S.W., and Thompson, E.A. (1992). Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48, 361-372 https://doi.org/10.2307/2532296
  15. Hakonarson, H., Gulcher, J.R., and Stefansson, K. (2003). deCODE genetics, Inc. Pharmacogenomics 4, 209-215 https://doi.org/10.1517/phgs.4.2.209.22627
  16. International Society for Biological Environmental Respositories. (2008). Best practices for repositories: collection, storage, retrieval and distribution of human biological materials for research. Cell. Preserv. Tech. 6, 3-58 https://doi.org/10.1089/cpt.2008.9997
  17. Jobling, M.A., and Gill, P. (2004). Encoded evidence: DNA in forensic analysis. Nat. Rev. Genet. 5, 739-751 https://doi.org/10.1038/nrg1455
  18. Jones, D.A. (1972). Blood samples: probability of discrimination. J. Forensic Sci. 12, 355-359 https://doi.org/10.1016/S0015-7368(72)70695-7
  19. Kim, Y.L., Hwang, J.Y., Kim, Y.J., et al. (2003). Allele frequencies of 15 STR loci using AmpFlSTR identifier kit in a Korean population. Forensic Sci. Int. 136, 92-95 https://doi.org/10.1016/S0379-0738(03)00255-X
  20. LifeGene Sweden. http://lifegene.ki.se/research/index_en.html.
  21. McQuillan, A.C., and Sales, S.D. (2008). Designing an automated blood fractionation system. Int. J. Epidemiol. 37 (Suppl 1), i51-i55 https://doi.org/10.1093/ije/dym286
  22. Nei, M. (1987). Molecular Evolutionary Genetics. Columbia University Press, New York, NY, USA
  23. Owen, J.M. (2008). Designing and implementing a large scale automated -80oC archive. Int. J. Epidemiol. 37 (Suppl 1), i56-i61 https://doi.org/10.1093/ije/dym293
  24. Triendl, R. (2003). Japan launches controversial Biobank project. Nat. Med. 9, 982. https://doi.org/10.1038/nm0803-982b
  25. Troyer, D. (2008). Biorepository standards and protocols for collecting, processing, and storing human tissues. Methods. Mol. Biol. 441, 193-220 https://doi.org/10.1007/978-1-60327-047-2
  26. Waits, L.P., Luikart, G., and Taberlet, P. (2001). Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol. Ecol. 10, 249-256 https://doi.org/10.1046/j.1365-294X.2001.01185.x