Whole-Genome Genotyping on Bead Arrays

  • Kevin L. Gunderson
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 529)

Abstract

In this review, we describe the laboratory implementation of Infinium® whole genome genotyping (WGG) technology for whole genome association studies and copy number studies. Briefly, the Infinium WGG assay employs a single tube whole genome amplification reaction to amplify the entire genome; genomic loci of interest are captured on an array by specific hybridization of picomolar concentrations amplified gDNA. After target capture, single nucleotide polymorphisms (SNPs) are genotyped on the array by a primer extension reaction using hapten-labeled nucleotides. The resultant hapten signal is amplified by immunhistochemical sandwich staining and the array is read out on a high resolution confocal scanner. We have combined this Infinium assay with high-density BeadChips to create the first array platform capable of genotyping over 1 million SNPs per slide. Additionally, the complete Infinium assay is automated using Tecan GenePaintTM slide processing system. Hybridization, washing, array-based primer extension and staining are performed directly in the Tecan capillary gap Te-Flow Through chambers. This automation process greatly increases assay robustness and throughput while enabling Laboratory Information Management System (LIMS) control of sample tracking. Finally, we give several examples of how this advance in genotyping technology is being applied in whole genome association and copy number studies.

Key words

Arrays genotyping SNP whole genome association whole genome amplification (WGA) Infinium® DNA copy number 

References

  1. 1.
    Risch, N., and Merikangas, K. (1996) The future of genetic studies of complex human diseases. Science 273, 1516–7.PubMedCrossRefGoogle Scholar
  2. 2.
    Fan, J. B., Chee, M. S., and Gunderson, K. L. (2006) Highly parallel genomic assays. Nat Rev Genet 7, 632–44.PubMedCrossRefGoogle Scholar
  3. 3.
    Carlson, C. S., Eberle, M. A., Rieder, M. J., Yi, Q., Kruglyak, L., and Nickerson, D. A. (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74, 106–20.PubMedCrossRefGoogle Scholar
  4. 4.
    Consortium, T. I. H. (2003) The International HapMap Project. Nature 426, 789–96.CrossRefGoogle Scholar
  5. 5.
    Gunderson, K. L., Steemers, F. J., Lee, G., Mendoza, L. G., and Chee, M. S. (2005) A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet 37, 549–54.PubMedCrossRefGoogle Scholar
  6. 6.
    Gunderson, K. L., Kruglyak, S., Graige, M. S., Garcia, F., Kermani, B. G., Zhao, C., Che, D., Dickinson, T., Wickham, E., Bierle, J., Doucet, D., Milewski, M., Yang, R., Siegmund, C., Haas, J., Zhou, L., Oliphant, A., Fan, J. B., Barnard, S., and Chee, M. S. (2004) Decoding randomly ordered DNA arrays. Genome Res 14, 870–7.PubMedCrossRefGoogle Scholar
  7. 7.
    Shumaker, J. M., Metspalu, A., and Caskey, C. T. (1996) Mutation detection by solid phase primer extension. Hum Mutat 7, 346–54.PubMedCrossRefGoogle Scholar
  8. 8.
    Pastinen, T., Kurg, A., Metspalu, A., Peltonen, L., and Syvanen, A. C. (1997) Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res 7, 606–14.PubMedGoogle Scholar
  9. 9.
    Pastinen, T., Raitio, M., Lindroos, K., Tainola, P., Peltonen, L., and Syvanen, A. C. (2000) A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res 10, 1031–42.PubMedCrossRefGoogle Scholar
  10. 10.
    Steemers, F., Chang, W., Lee, G., Shen, R., Barker, D. L., and Gunderson, K. L. (2006) Whole genome genotyping (WGG) using single base extension (SBE). Nat Methods 3(1), 31–3. Google Scholar
  11. 11.
    Patil, N., Berno, A. J., Hinds, D. A., Barrett, W. A., Doshi, J. M., Hacker, C. R., Kautzer, C. R., Lee, D. H., Marjoribanks, C., McDonough, D. P., Nguyen, B. T., Norris, M. C., Sheehan, J. B., Shen, N., Stern, D., Stokowski, R. P., Thomas, D. J., Trulson, M. O., Vyas, K. R., Frazer, K. A., Fodor, S. P., and Cox, D. R. (2001) Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294, 1719–23.PubMedCrossRefGoogle Scholar
  12. 12.
    Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., Liu-Cordero, S. N., Rotimi, C., Adeyemo, A., Cooper, R., Ward, R., Lander, E. S., Daly, M. J., and Altshuler, D. (2002) The structure of haplotype blocks in the human genome. Science 296, 2225–9.PubMedCrossRefGoogle Scholar
  13. 13.
    Johnson, G. C., Esposito, L., Barratt, B. J., Smith, A. N., Heward, J., Di Genova, G., Ueda, H., Cordell, H. J., Eaves, I. A., Dudbridge, F., Twells, R. C., Payne, F., Hughes, W., Nutland, S., Stevens, H., Carr, P., Tuomilehto-Wolf, E., Tuomilehto, J., Gough, S. C., Clayton, D. G., and Todd, J. A. (2001) Haplotype tagging for the identification of common disease genes. Nat Genet 29, 233–7.PubMedCrossRefGoogle Scholar
  14. 14.
    Galinsky, V. L. (2003) Automatic registration of microarray images. II. Hexagonal grid. Bioinformatics 19, 1832–6.PubMedCrossRefGoogle Scholar
  15. 15.
    Galinsky, V. L. (2003) Automatic registration of microarray images. I. Rectangular grid. Bioinformatics 19, 1824–31.PubMedCrossRefGoogle Scholar
  16. 16.
    Peiffer, D. A., Le, J. M., Steemers, F. J., Chang, W., Jenniges, T., Garcia, F., Haden, K., Li, J., Shaw, C. A., Belmont, J., Cheung, S. W., Shen, R. M., Barker, D. L., and Gunderson, K. L. (2006) High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res 16, 1136–48.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Kevin L. Gunderson
    • 1
  1. 1.Illumina, IncSan DiegoUSA

Personalised recommendations