Kinship Analysis Based on SNP Data from the HID-Ion AmpliSeqTM Identity Panel
Journal Title: Journal of Forensic Investigation - Year 2015, Vol 3, Issue 2
Abstract
Next generation sequencing supports extensive single nucleotide polymorphism (SNP) analysis owing to its comprehensive sequencing capacity. In the present study, a number of 20 parent–child pairs and 17 full siblings were genotyped for SNPs taken from the HIDIon AmpliSeqTM Identity Panel, which includes 90 sites on autosomal chromosomes. Kinship analyses of parent–child pairs and full siblings were carried out using the combined likelihood ratio principle based on the product rule. Eight SNPs (rs7520386, rs876724, rs7704770, rs214955, rs727811, rs6955448, rs445251, and rs1523537) were eliminated because of lower depth and allelic imbalance. The combined likelihood ratio values of 82 sites ranged from 1.15 × 103 to 1.26 × 108 for parent–child (n = 20), and from 1.00 × 102 to 9.40 × 1010 for full siblings (n = 17). To evaluate the likelihood ratio distribution more precisely, genotypes were constructed for 10,000 simulated parent–child pairs and full siblings based on allelic frequencies in the Japanese population. As the definitive threshold, likelihood ratio values of less than 1000 were found for 165 (1.7%) parent–child pairs and 243 (2.4%) full siblings. In two inconclusive cases of short tandem repeat analysis, the addition of SNP assays provided conclusive results. Better estimation power was achieved using the set of 82 sites than that in the conventional IdentifilerTM system. Because of the benefits of analyzing degraded samples present in small DNA quantities, the Ion PGMTM system will be favored to obtain informative SNP markers in forensic analyses.
Authors and Affiliations
Motoki Osawa
Keywords
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- EP ID EP202520
- DOI 10.13188/2330-0396.1000027
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