Evaluation of the Investigator® 24plex GO! kit and associated allele frequency data for four South African population groups

Abstract

In this study, population data were generated from South Africans using the Investigator® 24plex GO! Kit (QIAGEN, Hilden, Germany). Participants represented the four major population groups in South Africa, with self-reported ancestral origin being African (n = 208), European (n = 213), Indian/Asian (n = 103) or Admixed (n = 209). Allele frequency data and forensic parameters were calculated for each population group using Arlequin (v.3.5.2.2) and FORSTAT (v1.0). TPOX had the lowest discrimination capacity for all population groups, except for the African population group where THO1 was the least informative. SE33 had the highest discrimination capacity for all population groups (>0.98), with 38 different alleles observed in the Admixed population group. Samples exhibiting novel alleles or anomalies underwent massively parallel sequencing using the ForenSeq™ DNA Signature Prep kit, which confirmed the following results: one null Y allele at Amelogenin, ten instances of TPOX tri-allelism and four novel micro-variant alleles. An additional four novel alleles in SE33 were observed but remain unconfirmed, due to SE33 not being included in the ForenSeq™ DNA Signature Prep kit. Moreover, nine individuals had an allele 8 or 9 at D1S1656, where the peaks for these alleles occur before the D1S1656 marker range on the electropherogram and showed as a peak within the DYS391 marker. Although this observation was rare overall (1.2%), these nine individuals were from three of the four population groups, which motivates for the adjustment of the Investigator® 24plex PCR chemistry to avoid allelic overlap of D1S1656 with DYS391. Overall, these findings highlight the diverse genetic makeup of the South Africa population and accentuate the importance of local population studies.