Enhancing resolution and statistical power by utilizing mass spectrometry for detection of SNPs within the short tandem repeats

Short tandem repeats (STRs) are used routinely for the analysis of DNA samples from evidentiary items, convicted offenders, relationship testing and other identity testing disciplines. The discriminatory power of the STRs is sufficient in most human identity testing comparisons to render an identification. However, STRs have some limitations in evaluations, such as parentage testing, identification of human remains, or pairwise evaluations of putative relatives by familial searching. A major assumption is that shared alleles in these associations stem from common ancestry, i.e. are Identical by Descent (IBD). However, STR alleles by definition are Identical by State (IBS). Using an electrospray ionization mass spectrometry (ESI-MS) system developed by Ibis Biosciences Inc., population databases were generated for the 13 core CODIS STRs from African Americans, Caucasians and Hispanics capturing both the length of the allele, aswell as SNP variation containedwithin repeatmotifs. SNPswere identified in 10 of the loci and some common alleles were subdivided with SNP typing. Inclusion of SNPs increases discrimination power significantly, whereby the seven most polymorphic SNP-containing STR loci have the discriminatory power of 10 traditionally typed loci. A system of nomenclature has been developed that facilitates the databasing, searching and analyses of these combined data forms. 2009 Elsevier Ireland Ltd. All rights reserved.