Sequence variation in humans and other primates at six short tandem repeatloci used in forensic identity testing

A large number of alleles from the six different short tandem repeat (STR) loci FGA, D3S1358, vWA, CSF1PO, TPOX and TH01, used in human identity testi ng were sequenced to provide support for the robustness of fluorescent STR DNA typing by allele size. Sequence information for some of these loci (FGA , vWA, TH01) is an extension of published work, whereas no extensive sequen ce information is available with respect to the D3S1358, CSF1PO, and TPOX l oci. Sequencing of alleles at each locus has provided quantitative data wit h respect to the true nucleotide length of common alleles, and of alleles t hat vary in length from the common alleles. All alleles that were identifie d as "off-ladder" alleles through fluorescent typing at these STR loci have proven to be true length variant alleles. Sequencing at the D3S1358 and CS F1PO loci allowed for the establishment of a common nomenclature for these loci. A correlation between percent stutter and the length of the core tand em repeat is demonstrated at the FGA locus. Alleles in which the core tande m repeat is interrupted by a repeat unit of different sequence have a reduc ed percent stutter. DNA samples from three non-human primates (chimpanzee, orangutan, and gorilla) were compared to the human sequences, and shown to differ markedly across loci with respect to their homology. The effects of primer binding site mutations on the amplification efficiency at a particul ar locus, and methods used to interpret amplification imbalance of heterozy gous alleles at a locus is also addressed. (C) 2001 Elsevier Science Irelan d Ltd. All rights reserved.