Evaluation of modified Yfiler^™ amplification strategy for compromised samples

Aim To characterize the data produced using a modified amplification protocol for the AmpFℓSTR^® Yfiler^™ PCR Amplifcation Kit (Applied Biosystems) and explore the potential of Y-chromosomal short tandem repeat (Y-STR) recovery from severely degraded skeletal remains encountered at the Armed Forces DNA Identification Laboratory Methods Experiments were performed using two sets of Yfiler^™ amplification parameters. One set of parameters reflected the manufacturer's recommendations. The second set of parameters included twice the recommended Taq concentration and 6 additional cycles. Recovery of authentic alleles and the incidence of drop-in alleles were assessed for 3 data sets: 8 different quantities of pristine DNA, 8 artificially-degraded samples, and 31 non-probative case samples. Results Samples tested with both protocols from all 3 data sets yielded twice as many authentic alleles under the modified parameters than under the standard parameters (62% vs 31%), with only a nominal associated increase in the occurrence of non-authentic alleles (1.36% of all alleles detected). When applied to a range of representative casework samples, the modified protocol leveraged 9 or more reproducible alleles from over half of the specimens tested. Conclusion Reproducible and informative Y-STR profiles can be recovered from a broad range of degraded and inhibited skeletal remains extracts when a commercially available kit is employed under modified amplification parameters.