Evaluation of Amp-FLP Markers and Summary of PCR-Based Forensic Casework

Abstract

Polymerase Chain Reaction (PCR) based testing in forensic casework has been validated in numerous courts with the use of HLA DQα testing for forensic specimens. HLA DQα has been used in thousands of cases throughout the world over the past several years, where the evidence yielded DNA of too limited quantity or too degraded for Restriction Fragment Length Polymorphism (RFLP) analysis. HLA DQα PCR based testing has enabled our laboratory to analyze hundreds of cases which previously would have proven unsuitable for RFLP DNA analysis. Items of evidence from these cases include specimens such as microscopic slides from sexual assault evidence, cigarette butts, fingernail scrapings, swabbings from gun barrels as well as a variety of evidentiary specimens where DNA recovered from the specimen was too highly degraded to produce results with RFLP analysis. HLA DQα, however, represented only a single genetic marker available for PCR based testing in forensic analysis. The purpose of this study was to characterize and validate several additional amplification fragment length polymorphism (AmpFLP) markers for potential use in forensic casework. The use of AmpFLPs with forensic specimens will extend the application of VNTR polymorphisms to specimens which were either too limited in quantity or too degraded for traditional RFLP analysis. Initially, we evaluated the following four AmpFLP markers for their potential use with forensic specimens: D1S80, YNZ22, Apolipoprotein-B, and Collagen 2A1. The results of evaluation with forensic specimens included the optimization of extraction, amplification, and gel resolution conditions for each genetic marker as well as standard methods for interpretation of results. Population distributions for allele frequencies were analyzed for each AmpFLP marker within major North American racial groups.