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Development of SNP-based human identification system

International Journal of Legal Medicine volume 124, pages 125–131 (2010)Cite this article

Abstract

Single nucleotide polymorphisms (SNPs) appeal to the forensic DNA community because of their abundance in the human genome, low mutation rate, small amplicon size, and feasibility of high-throughput genotyping technologies. In an initial screening, we identified six SNP markers of sex determination by resequencing the amelogenin genes and the zinc finger protein genes located on the sex chromosomes. Furthermore, for use in human identification, we selected 30 highly polymorphic autosomal SNP markers from among a human population and examined the potential utility of these SNP markers for human identification. The combined mean match probability of 30 SNP markers was 4.83 × 10−13. Using genotyping data from 8,842 unrelated Korean individuals, we also found that discrimination power increased 10-fold for the addition of every five SNP markers in human identification. In this study, we demonstrated that SNP markers are very useful for sex determination and human identification, even in a very homogeneous population.

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Acknowledgments

This study was supported by a grant from the Korea Centers for Disease Control (2008-S6-E-001) and a grant from the Ministry of Health and Welfare, Republic of Korea (01-PJ10-PG6-01GN15-001).

Author information

Affiliations

  1. Asan Institute for Life Sciences, University of Ulsan College of Medicine, 388-1 Pungnap-2-Dong, Songpa-Gu, Seoul, 138-736, Korea

    Jae-Jung Kim, Hae-In Lee & Jong-Keuk Lee

  2. Center for Genome Science, National Institute of Health, Seoul, Korea

    Bok-Ghee Han

  3. Department of Pediatrics, University of Ulsan College of Medicine, Seoul, Korea

    Han-Wook Yoo

Authors
  1. Jae-Jung Kim
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  2. Bok-Ghee Han
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  3. Hae-In Lee
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  4. Han-Wook Yoo
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  5. Jong-Keuk Lee
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Corresponding author

Correspondence to Jong-Keuk Lee.

Additional information

Jae-Jung Kim and Bok-Ghee Han contributed equally to this work.

Electronic supplementary material

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Supplementary Fig. 1
figure 3

Identification of sex determining SNPs within the amelogenin genes. Highly homologous regions of the amelogenin genes (AMEL-X and AMEL-Y) were resequenced in female (n = 12) and male (n = 12) DNA samples to identify sex-determining SNPs. Three candidate sex-determining SNP sites (i.e., AMEL-1, AMEL-2, and AMEL-3) were identified (GIF 3 kb)

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Supplementary Fig. 2
figure 4

Identification of SNPs in genes encoding zinc finger proteins, for use in sex determination. Highly homologous regions of genes encoding zinc finger proteins (ZFX and ZFY) were resequenced in female (n = 12) and male (n = 12) DNA samples to identify sex-determining SNPs. Three candidate sex-determining SNP sites (i.e., ZF-1, ZF-2 and ZF-3) were identified (GIF 3 kb)

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Supplementary Table 1

Validation of 30 SNP markers in 960 individuals using the Illumina VeraCode GoldenGate assay (DOC 61 kb)

Supplementary Table 2

Validation of 30 highly polymorphic SNP markers in 8,842 unrelated Korean individuals (DOC 61 kb)

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High resolution image (TIFF 3141 kb)

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Kim, JJ., Han, BG., Lee, HI. et al. Development of SNP-based human identification system. Int J Legal Med 124, 125–131 (2010). https://doi.org/10.1007/s00414-009-0389-9

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  • DOI: https://doi.org/10.1007/s00414-009-0389-9

Keywords

  • Single nucleotide polymorphism
  • Human identification
  • Sex determination
  • Korean