Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Large-scale genotyping of complex DNA


Genetic studies aimed at understanding the molecular basis of complex human phenotypes require the genotyping of many thousands of single-nucleotide polymorphisms (SNPs) across large numbers of individuals1. Public efforts have so far identified over two million common human SNPs2; however, the scoring of these SNPs is labor-intensive and requires a substantial amount of automation. Here we describe a simple but effective approach, termed whole-genome sampling analysis (WGSA), for genotyping thousands of SNPs simultaneously in a complex DNA sample without locus-specific primers or automation. Our method amplifies highly reproducible fractions of the genome across multiple DNA samples and calls genotypes at >99% accuracy. We rapidly genotyped 14,548 SNPs in three different human populations and identified a subset of them with significant allele frequency differences between groups. We also determined the ancestral allele for 8,386 SNPs by genotyping chimpanzee and gorilla DNA. WGSA is highly scaleable and enables the creation of ultrahigh density SNP maps for use in genetic studies.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Figure 1: Fragment selection by PCR (FSP).
Figure 2: Hybridized chip images.
Figure 3: Effect of complexity on call rate and concordance.
Figure 4: Percentage ancestral allele as a function of allele frequency in three populations.


  1. Ardlie, K.G., Kruglyak, L. & Seielstad, M. Patterns of linkage disequilibrium in the human genome. Nat. Rev. Genet. 3, 299–309 (2002).

    Article  CAS  Google Scholar 

  2. Sachidanandam, R. et al. The International SNP Map Working Group. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933 (2001).

    Article  CAS  Google Scholar 

  3. Kwok, P.-Y. Methods for genotyping single nucleotide polymorphisms. Annu. Rev. Genomics Hum. Genet. 2, 235–258 (2001).

    Article  CAS  Google Scholar 

  4. Syvanen, A.-C. Accessing genetic variation: genotyping single nucleotide polymorphisms Nat. Rev. Genet. 2, 930–942 (2001).

    Article  CAS  Google Scholar 

  5. Lipshutz, R.J., Fodor, S.P., Gingeras, T.R. & Lockhart, D.J. High density synthetic oligonucleotide arrays. Nat. Genet. 21(1 Suppl), 20–24 (1999).

    Article  CAS  Google Scholar 

  6. Lisitsyn, N., Lisitsyn, N. & Wigler, M. Cloning the differences between two complex genomes. Science 259, 946–51 (1993).

    Article  CAS  Google Scholar 

  7. Lucito, R. et al. Genetic analysis using genomic representations. Proc. Natl. Acad. Sci. USA 95, 4487–4492 (1998).

    Article  CAS  Google Scholar 

  8. Vos, P. et al. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23, 4407–4414 (1995).

    Article  CAS  Google Scholar 

  9. Altshuler, D. et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513–516 (2000).

    Article  CAS  Google Scholar 

  10. Dong, S. et al. Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation. Genome Res. 11, 1418–1424 (2001).

    Article  CAS  Google Scholar 

  11. Liu, W.-m. et al. Algorithms for large scale genotyping microarrays. Bioinformatics, (2003), in the press.

  12. Weir, B.S. Genetic Data Analysis II (Sinauer Associates, Sunderland, Massachusetts, 1996).

    Google Scholar 

  13. Bowcock, A.M. et al. Drift, admixture, and selection in human evolution: a study with DNA polymorphisms. Proc. Nat. Acad. Sci. USA 88, 839–843 (1991).

    Article  CAS  Google Scholar 

  14. Collins-Schramm, H. et al. Ethnic-difference markers for use in mapping by admixture linkage disequilibrium. Am. J. Hum. Genet. 70, 737–750 (2002).

    Article  CAS  Google Scholar 

  15. Briscoe, D., Stephens, J.C. & O'Brien, S.J. Linkage disequilibrium in admixed populations: applications in gene mapping. J. Hered. 85, 59–63 (1994).

    CAS  PubMed  Google Scholar 

  16. Parra, E.J. et al. Estimating African-American admixture proportions by use of population-specific alleles. Am. J. Hum. Genet. 63, 1839–1851 (1998).

    Article  CAS  Google Scholar 

  17. McKeigue, P.M., Carpenter, J.R., Parra, E.J. & Shriver, M.D. Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations. Ann. Hum. Genet. 64, 171–186 (2000).

    Article  CAS  Google Scholar 

  18. Hacia, J.G. Genome of the apes. Trends Genet. 17, 637–645 (2001).

    Article  CAS  Google Scholar 

  19. Hacia, J.G. et al. Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nat. Genet. 22, 164–167 (1999).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  21. Watterson, G.A. & Guess, H.A. Is the most frequent allele the oldest? Theor. Pop. Biol. 11, 141–160 (1977).

    Article  CAS  Google Scholar 

  22. Cavalli-Sforza, L.L., Menozzi, P. & Piazza, A. The History and Geography of Human Genes (Princeton University Press, Princeton, NJ, 1994).

    Google Scholar 

  23. Gabriel, S.B. et al. The structure of haplotype blocks in the human genome. Science 296, 2225–2229 (2002).

    Article  CAS  Google Scholar 

  24. Lindblad-Toh, K. et al. Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat. Biotechnol. 18, 1001–1005 (2000).

    Article  CAS  Google Scholar 

  25. Liu, W.-m. et al. Rank-based algorithms for analysis of microarrays. in Microarrays: Optical Technologies and Informatics (eds. Bittner, M.L., Chen, Y., Dorsel, A.N. & Dougherty, E.R.) Proc. SPIE 4266, 56–67 (2001).

    Book  Google Scholar 

  26. Collins, F.S., Brooks, L.D. & Chakravarti, A. A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 8, 1229–1231 (1998).

    Article  CAS  Google Scholar 

  27. Rousseeuw, P.J. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J. Comput. Appl. Math. 20, 53–65 (1987).

    Article  Google Scholar 

  28. Picoult-Newberg, L. et al. Mining SNPs from EST databases. Genome Res. 9, 167–174 (1999).

    CAS  PubMed  Google Scholar 

  29. Patil, N. et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294, 1719–1723 (2001).

    Article  CAS  Google Scholar 

  30. Fan, J.-B. et al. Paternal origins of complete hydatidiform moles proven by whole genome single-nucleotide phaplotyping. Genomics 79, 58–62 (2002).

    Article  CAS  Google Scholar 

Download references


We thank David Altshuler, Eric Lander, Thomas Gingeras, Richard Rava, Michael Shapero and Jon McAuliffe for helpful suggestions and critical reading of the manuscript.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Giulia C Kennedy.

Ethics declarations

Competing interests

G.C.K., H.M., S.D., W.-M.L., J.H., G.L., X.S., M.C., W.C., J.Z., W.L., G.Y., X.D., T.R., Z.H., S.P.A.F. & K.W.J. are or were employed by Affymetrix, a commercial entity that manufactures and sells synthetic DNA microarrays based on the technology described in this paper.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Kennedy, G., Matsuzaki, H., Dong, S. et al. Large-scale genotyping of complex DNA. Nat Biotechnol 21, 1233–1237 (2003).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing