Highly efficient nuclear DNA typing of the World War II skeletal remains using three new autosomal short tandem repeat amplification kits with the extended European Standard Set of loci

Aim

To perform an efficiency study of three new amplification kits with the extended European Standard Set (ESS) of loci for autosomal short tandem repeat (STR) typing of skeletal remains excavated from the World War II mass graves in Slovenia.

Methods

In the beginning of the 2011, we analyzed 102 bones and teeth using the PowerPlex ESX 17 System (Promega), AmpFiSTR NGM PCR Amplification Kit (Applied Biosystems), and Investigator ESSplex Kit (Qiagen). We cleaned the bones and teeth, removed surface contamination, and ground them into a powder using liquid nitrogen. Prior to DNA isolation with Biorobot EZ1 (Qiagen), 0.5 g bone or tooth powder was decalcified. Nuclear DNA of the samples was quantified using real-time polymerase chain reaction. All three kits used the same extract with the amplification conditions recommended by the manufacturers.

Results

We extracted up to 131 ng DNA/g of powder from the bones and teeth. All three amplification kits showed very similar efficiency, since DNA typing was successful with all amplification kits in 101 out of 102 bones and teeth, which represents a 99% success rate.

Conclusion

The commercially available ESX 17, ESSplex, and NGM kits are highly reliable for STR typing of World War II skeletal remains with the DNA extraction method optimized in our laboratory.DNA typing of bone and tooth samples has been successfully used in anthropological studies and forensic identification analysis (1,2). Nuclear DNA is the preferred genome of amplification for forensic purposes as it is individually specific and provides bi-parental kinship information (3). The success of DNA typing in old bones and teeth is often limited by small amounts of endogenous DNA, presence of polymerase chain reaction (PCR) inhibitors, DNA degradation, and an exceptional risk of contamination (4-6). Mitochondrial DNA testing has been regularly employed in the forensic identification of aged skeletal remains (7-10). Recently, some articles have reported a successful typing of nuclear short tandem repeats (STR) from ancient material using an increased number of cycles (11-18). In 2009 and 2010, new amplification kits were developed to meet the European Network of Forensic Institutes and the European DNA Profiling group recommendations for increasing the European Standard Set (ESS) of loci to improve its discrimination power and to fulfill the increasing requirements regarding sensitivity and reproducibility for the analysis of minute amounts of DNA by adopting five additional mini-STRs: D2S441, D10S1248, D22S1045, D1S1656, and D12S391 (19,20). Some validation, concordance, and population studies (21-28) have been published for new amplification kits with the extended ESS of loci. It was shown that the new kits are robust enough to genotype degraded DNA samples through the use of mini STR loci and have increased tolerance to common inhibitors and increased sensitivity to obtain full profiles from low-level DNA samples from casework (27,29,30). However, no study has been performed using new amplification kits on old skeletal remains. We attempted to obtain autosomal STR profiles from the World War II bones and teeth with three new commercially available amplification kits with the extended ESS of loci using the PCR protocols recommended by the manufacturers without increasing the number of cycles or any other modification of protocols.