SNP typing of forensic samples with the GenPlex™ HID system: A collaborative study

Abstract

We report the results of an inter-laboratory exercise on typing autosomal single nucleotide polymorphisms (SNPs) with the GenPlex™ HID system (Applied Biosystems—AB). A total of 12 European and US forensic genetic laboratories typed 10 reference DNA samples and 3 samples with partly degraded DNA that only gave strong reactions with amplicons shorter than approximately 135 bp and weak reactions up to 185 bp. The samples and the critical reagents were sent to the participating laboratories from Copenhagen. In addition, the laboratories typed the three degraded DNA samples with one or more STR kits. When 500 pg degraded DNA was used, the success rates of SNP typing in the laboratories varied from 15.6% to 98.6% (median: 94.6%). Only 1.6% of the unsuccessful SNP types were due to wrong SNP calling, while the remaining 98.4% were due to lack of amplification and uncertain results. Two laboratories counted for more than two-thirds of the non-successful results while seven laboratories reported no wrong SNP types. Two laboratories typed the degraded DNA samples successfully with the MiniFiler kit, while other commonly used kits gave incomplete STR profiles in all laboratories. Titration of the degraded DNA showed that the SNP typing results became less reliable with 100 pg DNA and less. The median success rate of SNP typing of 10 reference samples with 50 pg reference DNA was 86% (range: 44.5–99.2% among laboratories). The success rate of SNP typing of the reference samples decreased with smaller amounts of DNA. SNP typing with the GenPlex™ HID system provided more information from degraded DNA samples than any of the commercially available kits used by the participating laboratories.