Validation of short tandem repeats (STRs) for forensic usage: Performance testing of fluorescent multiplex STR systems and analysis of authentic and simulated forensic samples

The amplification and typing conditions for the 13 core CODIS loci and thei r forensic applicability were evaluated. These loci are CSF1PO, FGA, TH01, TPOX, vWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11. Results were obtained using the multiplex STR systems AmpFlSTR((R)) Profiler Plus (TM) and AmpFlSTR COfiler (TM) (Applied Biosystems, Foster C ity, CA), GenePrint (TM) PowerPlex (TM) (Promega Corporation, Madison, WI), and subsets of these kits. For detection of fluorescently labeled amplifie d products, the ABI Prism((R)) 310 Genetic Analyzer, the ABI Prism 377 DNA Sequencer, the FMBIO(R) II Fluorescent Imaging Device, and the FluorImager (TM) were utilized. The following studies were conducted: (a) evaluation of PCR parameter ranges required for adequate performance in multiplex amplif ication of STR loci, (b) determination of the sensitivity of detection of t he systems, (c) characterization of non-allelic PCR products, (d) evaluatio n of heterozygous peak intensities, (e) determination of the relative level of stutter per locus, (f) determination of stochastic PCR thresholds, (g) analysis of previously typed case samples, environmentally insulted samples , and body fluid samples deposited on various substrates. and (h) detection of components of mixed DNA samples. The data demonstrate that the commerci ally available multiplex kits can be used to amplify and type STR loci succ essfully from DNA derived from human biological specimens. There was no evi dence of false positive or false negative results and no substantial eviden ce of preferential amplification within a locus. Although at times general balance among loci labeled with the same fluorophore was not observed, the results obtained were still valid and robust. Suggested criteria are provid ed for determining whether a sample is derived from a single source or from more than one contributor. These criteria entail the following: (a) the nu mber of peaks at a locus, (b) the relative height of stutter products, and (c) peak height ratios. Stochastic threshold levels and the efficiency of n on-templated nucleotide addition should be considered when evaluating the p resence of mixtures or low quantity DNA samples. Guidelines, not standards, for interpretation should be developed to interpret STR profiles in cases, because there will be instances in which the standards may not apply. Thes e instances include (a) a primer binding site variant for one allele at a g iven locus, (b) unusually high stutter product, (c)gene duplication, and (d ) translocation.