The use of enhanced PCR techniques for nuclear DNA analysis of compromised forensic samples

Biological samples encountered in the forensic laboratory are often received in compromised conditions. DNA analysis may be hampered by difficulties such as low-copy number (LCN) or degraded material. For these types of samples, standard PCR analysis may fail; therefore the use of enhanced PCR techniques for the amplification of nuclear DNA would be valuable. In this research a variety of compromised samples, including bone (nearly fresh to ancient), degraded blood, and touch-DNA, were examined using novel PCR techniques. Mini-STR primers were utilized as a means of amplifying smaller fragments of degraded DNA. Nested PCR was used with STRs and the sexing locus amelogenin, to determine if different primers and an increase in cycle number would amplify degraded DNA and to assist in anthropological sex determination. Amplification of the mini-STR loci was successful when using nested PCR on degraded blood and fresh bone, but not in other instances, such as with older skeletal material. The amelogenin nested PCR was successful to variable degrees with each of the sample sets, with the exception of 30 year-old bone, however allelic dropout due to stochastic effects was often observed. Overall, the enhanced PCR techniques were helpful with certain samples in amplifying degraded/LCN DNA and aiding in sex determination, and should be considered when dealing with compromised forensic DNA samples.