Typing of 30 insertion/deletions in Danes using the first commercial indel kit—Mentype^® DIPplex

Abstract 

In this study, we tested the first commercial kit with insertion/deletion (indel) polymorphisms, the Mentype^® DIPplex PCR Amplification Kit (DIPplex kit). A total of 30 biallelic autosomal indels and Amelogenin were amplified with the DIPplex kit. All loci were amplified in one PCR multiplex and all amplicon lengths were shorter than 160bp. Full indel profiles were generated from as little as 100pg of DNA. A total of 117 individuals from Danish paternity cases were successfully typed. No deviation from Hardy–Weinberg equilibrium was observed for any of the indels. The combined mean match probability was 3.3×10⁻¹³, the mean paternity exclusion probability was 99.7% and the typical paternity indices for trios and duos were 2350 and 165, respectively. Furthermore, we typed five highly degraded DNA samples with the DIPplex kit, the AmpFlSTR^® SGM Plus kit and the AmpFlSTR^® SEfiler Plus kit. Full indel profiles were obtained with the DIPplex kit, whereas only partial profiles were obtained with the STR kits. In general, the DIPplex kit performed well and it would be a valuable assay for forensic genetic testing, especially in crime cases with partially degraded DNA or low amounts of template DNA. However, some difficulties with pull-ups were observed at DNA concentrations of 1000pg. Rearrangement of the allele windows by changing the lengths of some of the PCR primers would greatly improve the assay, and more robustness towards higher amounts of DNA would allow the use of the DIPplex kit without prior quantification of the samples.

Keywords: DIPplex PCR Amplification Kit, Autosomal indel multiplex, Forensic genetics, Insertion, Deletion