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Genome-wide Screen for Individual Identification SNPs (IISNPs) and the Confirmation of Six of Them in Han Chinese with Pyrosequencing Technology

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Single nucleotide polymorphisms (SNPs) offer promise to forensic DNA analysts, but it remains uncertain whether a panel of individual identification SNPs can be as informative as the Combined DNA Index System short tandem repeats. Based on the highly accurate and publicly available HapMap SNP database (r21a) and a minor allele frequency cutoff of ≥0.45, we completed a genome-wide screen through 3,905,819 SNPs with internally modified computer programs and identified 1439 SNPs with high heterozygosity and low Fst values among four populations (Utah Caucasian, Han Chinese, Tokyo Japanese, and Nigerian Yoruba). Using pyrosequencing technology, we studied six loci in a relatively large group of samples to determine whether these loci were as informative as the HapMap data suggest. These SNPs performed as expected in the Han Chinese in terms of heterozygosity and Fst. The 1439 identified SNPs should provide a comprehensive and reliable set of loci for identity and relationship testing.
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Keywords: Han Chinese; HapMap database; SNP; forensic sciences; individual identification; minor allele frequency (MAF)

Document Type: Research Article

Affiliations: 1: Center of Forensic Identification, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China. 2: Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China. 3: Department of Clinical Laboratories, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China.

Publication date: 2010-07-01

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