Abstract
Although the majority of microarray studies have been directed toward RNA expression profiling (functional genomics) and increasingly toward proteomics, a steady increase in the use of microarrays as platforms for DNA genotyping has occurred over the past 5 yr. Multiple array-based chemistries have been developed in order to genotype single nucleotide polymorphisms. Conceptually, the simplest of these microarray genotyping technologies is based on the dideoxynucleotide chemistry of mini-sequencing by arrayed primer extension, whereby oligonucleotide probes (preprinted on the array) are extended by a single nucleotide base. This enzymecatalyzed single base extension reaction is dependent on the sequence (genotype) of the template nucleic acid (sample) that is temporarily hybridized to the probes. Utilization of all four dideoxynucleotides, each conjugated to a different fluorophore, allows genotyping by spectral differentiation of the single base extension reaction products.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Lander, E. S., Linton, L. M., Birren, B., et al. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860–921.
Venter, J. C., Adams, M. D., Myers, E. W., et al. (2001) The sequence of the human genome. Science 291, 1304–1351.
Risch, N. and Merikangas, K. (1996) The future of genetic studies of complex human diseases. Science 273, 1516–1517.
Lord, P. G. and Papoian, T. (2004) Genomics and drug toxicity. Science 306, 575.
Wang, D. G., Fan, J. B., Siao, C. J., et al. (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077–1082.
Ansell, S. M., Ackerman, M. J., Black, J. L., Roberts, L. R., and Tefferi, A. (2003) Primer on medical genomics. Part VI: genomics and molecular genetics in clinical practice. Mayo Clin. Proc. 78, 307–317.
Hood, L., Heath, J. R., Phelps, M. E., and Lin, B. (2004) Systems biology and new technologies enable predictive and preventative medicine. Science 306, 640–643.
Saiki, R. K., Gelfand, D. H., Stoffel, S., et al. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487–491.
Hirschhorn, J. N., Sklar, P., Lindblad-Toh, K., et al. (2000) SBE-TAGS: an array-based method for efficient single-nucleotide polymorphism genotyping. Proc Natl. Acad. Sci. USA 97, 12,164–12,169.
Oliphant, A., Barker, D. L., Stuelpnagel, J. R., and Chee, M. S. (2002) BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques 56–58, 60–51.
Kennedy, G. C., Matsuzaki, H., Dong, S., et al. (2003) Large-scale genotyping of complex DNA. Nat. Biotechnol. 21, 1233–1237.
Shumaker, J. M., Metspalu, A., and Caskey, C. T. (1996) Mutation detection by solid phase primer extension. Hum. Mutat. 7, 346–354.
Kurg, A., Tonisson, N., Georgiou, I., et al. (2000) Arrayed primer extension: solid-phase four-color DNA resequencing and mutation detection technology. Genet Test 4, 1–7.
Syvanen, A. C. (1999) From gels to chips: “minisequencing” primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum. Mutat. 13, 1–10.
Pastinen, T., Raitio, M., Lindroos, K., et al. (2000) A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res. 10, 1031–1042.
Gemignani, F., Perra, C., Landi, S., et al. (2002) Reliable detection of β-thalassemia and G6PD mutations by a DNA microarray. Clin. Chem. 48, 2051–2054.
Tebbutt, S. J., He, J. Q., Burkett, K. M., et al. (2004) Microarray genotyping resource to determine population stratification in genetic association studies of complex disease. Biotechniques 37, 977–985.
Tonisson, N., Zernant, J., Kurg, A., et al. (2002) Evaluating the arrayed primer extension resequencing assay of TP53 tumor suppressor gene. Proc. Natl. Acad. Sci. USA 99, 5503–5508.
Tonisson, N., Kurg, A., Kaasik, K., Lohmussaar, E., and Metspalu, A. (2000) Unravelling genetic data by arrayed primer extension. Clin. Chem. Lab. Med. 38, 165–170.
Dawson, E., Abecasis, G. R., Bumpstead, S., et al. (2002) A first-generation linkage disequilibrium map of human chromosome 22. Nature 418, 544–548.
Tebbutt, S. J., Rogers, H. J., and Lonsdale, D. M. (1994) Characterization of a tobacco gene encoding a pollen-specific polygalacturonase. Plant. Mol. Biol. 25, 283–297.
Tebbutt, S. J., Opushnyev, I. V., Tripp, B. W., et al. (2005) SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data. Bioinformatics 21, 124–127.
Devlin, B. and Roeder, K. (1999) Genomic control for association studies. Biometrics 55, 997–1004.
Reich, D. E. and Goldstein, D. B. (2001) Detecting association in a case-control study while correcting for population stratification. Genet Epidemiol. 20, 4–16.
Freedman, M. L., Reich, D., Penney, K. L., et al. (2004) Assessing the impact of population stratification on genetic association studies. Nat. Genet. 36, 388–393.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Tebbutt, S.J. (2007). Genotyping of Single Nucleotide Polymorphisms by Arrayed Primer Extension. In: Rampal, J.B. (eds) Microarrays. Methods in Molecular Biology, vol 382. Humana Press. https://doi.org/10.1007/978-1-59745-304-2_10
Download citation
DOI: https://doi.org/10.1007/978-1-59745-304-2_10
Publisher Name: Humana Press
Print ISBN: 978-1-58829-944-4
Online ISBN: 978-1-59745-304-2
eBook Packages: Springer Protocols