Enhancement to the Discriminatory Power of STR Typing Through the use of Haplotypes

Abstract

Identification of remains in the past has been accomplished by using DNA analysis, specifically STR typing. However, there are times when the DNA results do not produce a compelling result for identification. Genetic marker systems of haplotypes are starting to be considered to enhance the STR test battery. The goal of this study was to use two markers, FESFPS and Penta E, that were physically linked and commercially available in STR typing kits to develop a haplotype database and determine the level of enhancement, if any, to the already used STR test batteries. A haplotype frequency database needed to be constructed and the rate of recombination determined. Frequencies for haplotypes consisting of FESFPS and Penta E markers were calculated using a conservative frequency estimate of the 95% upper confidence interval. The FESFPS-Penta E haplotype system was used to calculate parentage test cases and was found to enhance the likelihood ratio values by 2.43 fold in Blacks and 1.84 fold in Caucasians. In paternal mutation cases where the full STR test battery was available, the haplotype frequencies increased the LR values by an average of 7.05 fold. When a case of a questioned sibling relationship was analyzed, using the haplotype frequency instead of the allele frequency favored a non-relationship. The recombination rate of the FESFPS-Penta E haplotype was higher than the expected rate, indicating a recombination hotspot somewhere between the two markers.