Evaluation of insertion-deletion polymorphisms with the kit Qiagen Investigator® DIPplex for forensic application in South Africa
Insertion-deletion polymorphisms (indels) have been underutilized in forensic identification of individuals in comparison with single nucleotide polymorphisms (SNPs) and short tandem repeat (STRs) systems. The use of indels for the purpose of human identification is more advantageous than previously used methods as it combines desirable characteristics of both the SNPs and STRs i.e. low costs and simplistic typing methods as well as indels having small amplicons size, making them suitable for genotyping highly degraded DNA. Currently there is only one commercial kit available for the forensic community, the Investigator® DIPlex kit (Qiagen), which cover a total of 30 indel loci distributed over 19 autosomal chromosomes. The objective of this study was to evaluate the Qiagen Investigator® DIPplex kit for forensic application in South Africa. The kit‘s performance was evaluated by comparing different extraction methods; sensitivity, robustness and reproducibility were evaluated and forensic parameters (match probability, power of discrimination, polymorphism information content, power of exclusion and typical paternity index) were estimated based on population data generated from five South African populations (Afrikaner, Mixed Ancestry, Indian-Asian, Xhosa and Zulu). Population comparisons were performed using Fst-analysis, factorial component analysis as well as phylogenetic tree construction. DNA was extracted from buccal swabs and whole blood collected from a total of 512 individuals from the five South African population groups and genotyped using the Qiagen Investigator® DIPplex kit. Sanger DNA sequencing and sequence alignments confirmed the presence of a null allele at locus HLD97 which was present in high frequency in the Xhosa and Zulu populations. This observation was made in 14 individuals belonging to the Xhosa and Zulu populations. Null allele frequencies in all five South African populations were also estimated. Null alleles were estimated for all loci using analytical methods i.e. Charkraborty null allele estimator, Brookfield null allele estimators 1 and 2 and ML-NullFreq software program. The kit performed well in the laboratory, not requiring any additional reagents or instrumentation and successfully generating profiles with input DNA amounts as low as 0.2 ng/μL. Although well suited for forensic application, the Qiagen Investigator® DIPplex kit showed some drawbacks with regards to application on South African populations. The presence of a null allele at the HLD97 locus as well as indication of population substructure affects allele frequency estimates for the South African populations. Correction for population substructure as present within the South African populations should be considered using FST analysis and it is recommended that the HLD97 locus should be excluded from any kinship analysis performed on South African populations.