VWA STR genotyping: further inconsistencies between Perkin-Elmer and Promega kits

Abstract

We report a simultaneous study of the VWA STR locus by the Perkin-Elmer Profiler Plus kit and the Promega GenePrint CTTv kit in a population sample from North Portugal and in 418 meiosis from family material and paternity cases. PCR amplification and genotyping were performed according to the manufacturer's instructions using ABI 377 or ABI 310 automatic sequencers. Biological kinship in family material and paternity cases was validated by the use of the STR loci D3S1358, D5S818, D7S820, D8S1179, D13S317, D18S51, D21S11, FGA, CSF1PO, TH01 and TPOX. Out of 434 unrelated individuals we found 4 inconsistencies between the genotypes obtained using each kit. No exclusions were found in the meiotic analyses. In all cases, these inconsistencies were due to an annealing failure of the Perkin-Elmer forward primer resulting in false homozygotes. Sequencing analysis revealed an A-to-T substitution at position 1631 (GenBank sequence M25858), 52 bases upstream of the first TCTA motif of the repeat region. An estimate of the null allele frequency (s) in this study is thus obtainable from the expression s = 4/(2 x 434) = 0.46%. The relatively high frequency of these discrepancies in our population demonstrates the need for caution when comparing genotype or gene frequency estimates made from amplicons produced by different primers, when evaluating apparent exclusions in paternity testing and when searching for a match between individual genetic profiles in forensic databases. Our findings are also compared with those previously reported.