Observations and investigation of STR genotype inconsistencies due to mutations, silent alleles, and uniparental disomy in South African populations.

The fundamental concept of parentage and kinship testing is that a child inherits DNA in accordance with the principles of Mendelian inheritance. A child receives half of its DNA from each parent. However, sometimes the observed genotype patterns between a child and its purported parents do not fully align with Mendelian inheritance, which can result in a false conclusion regarding parentage. Mutations, silent alleles, and uniparental disomy (UPD) are examples of events that can produce non-Mendelian results. This study examines STR profiles from South African parentage testing data to assess the frequency of mutations, silent alleles, and UPD within the dataset. Mutations and population-specific silent allele rates are estimated for up to 26 STR loci. Results show the highest mutation rate was observed at SE33 (0.00657), whilst the lowest was at TH01 (0.000061). The paternal mutation rate was 5.6 times higher than the maternal rate. The overall silent allele rate was notably high at SE33 and vWA, especially within the South African Black and Coloured populations when tested with Promega's PowerPlex® chemistries. This suggests a potential underrepresentation of these groups in commercial kit research and development. Although the dataset was screened for UPD cases, no clear evidence of its occurrence was found. The data also present 'out of marker range' alleles and instances of partially amplified DNA template. The findings and frequencies provided by this study offer population-specific information for the South African population, enabling more appropriate likelihood ratios to be generated in forensic and kinship testing. Additionally, this paper offers practical guidance for analysts involved in kinship testing, facilitating the recognition and understanding of the potential impact of non-Mendelian events in specific cases.