Development of a genotyping assay for the UK, European, and CODIS core STR loci identifying length and sequence variation in the target loci

Abstract

We have developed a highly automated assay covering twenty one markers spanning the UK, European, and CODIS core short tandem repeat (STR) loci. In this assay, sample DNA is amplified with an 8-well PCR panel, and the masses of the PCR products are determined on an electrospray ionization-mass spectrometry platform. The mass measurements are accurate enough to assign a base composition to the PCR products, specifying the number of their constituent dA, dG, dC, and dT residues. The base compositions in turn define the STR genotypes. Sequence variants have been observed in many of the STR loci, and the accuracy of the mass measurements supports their identification with this assay. Parameters in the initial evaluation of the assay included species specificity, sensitivity, reproducibility, accuracy, and concordance. Results indicate that the assay is concordant with existing assays while providing additional information by virtue of the detection of sequence variants of STR alleles.