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Identifying Individuals in a Complex Mixture of DNA with Unknown Ancestry

Author

Listed:
  • Sampson Joshua

    (Yale University)

  • Zhao Hongyu

    (Yale University)

Abstract

A new test was recently developed that could use a high-density set of single nucleotide polymorphisms (SNPs) to determine whether a specific individual contributed to a mixture of DNA. The test statistic compared the genotype for the individual to the allele frequencies in the mixture and to the allele frequencies in a reference group. This test requires the ancestries of the reference group to be nearly identical to those of the contributors to the mixture. Here, we first quantify the bias, the increase in type I and type II error, when the ancestries are not well matched. Then, we show that the test can also be biased if the number of subjects in the two groups differ or if the platforms used to measure SNP intensities differ. We then introduce a new test statistic and a test that only requires the ancestries of the reference group to be similar to the individual of interest, and show that this test is not only robust to the number of subjects and platform, but also has increased power of detection. The two tests are compared on both HapMap and simulated data.

Suggested Citation

  • Sampson Joshua & Zhao Hongyu, 2009. "Identifying Individuals in a Complex Mixture of DNA with Unknown Ancestry," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-29, September.
    • Handle: RePEc:bpj:sagmbi:v:8:y:2009:i:1:n:37
    DOI: 10.2202/1544-6115.1469
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