Journal Article

Evaluating the effects of silent genes on pairwise kinship testing

Yang, Da, Wei, An Qi, Li, Mei Li

2024

Overview

Short tandem repeat (STR) loci are frequently utilized in kinship testing, and mutations of a single base occurring in the primer-binding region of the STR locus can result in the failure of allelic amplification and the emergence of silent genes. Silent genes are not observable and, therefore, are excluded from the genotypes assessed. Pedigree likelihood ratios (LRs) are often employed in kinship testing to determine the likelihood of different kinship scenarios. LR values are derived from various types of genotypes. LRexact values are based on the exact or actual genotypes, which may include silent genes. Conversely, LRobserve values are based on observed genotypes that exclude silent genes, while LRadjust values incorporate all potential genotypes, including both observed and those with silent genes. Initially, the formulae for LRs in 1st degree, 2nd degree, and 3rd degree kinship testing are presented according to different genotype forms of pairwise individuals. The correctness of these formulae is then verified using the Familias software, and the results are compared with those from the GeneVisa software (www.genevisa.net). Lastly, the simulation modules of GeneVisa are used to assess the impact of silent genes on pairwise kinship testing. The findings indicate that the overall impact of silent genes is minimal, although in some cases, the effects can be relatively significant. The influence of silent genes generally decreases as the kinship relationship becomes more distant. In specific kinship tests, the effect of silent genes is reduced when the individuals are unrelated compared to when there is a kinship relationship. Utilizing the LRadjust value for 1st degree and 2nd degree kinship testing can substantially mitigate the effects of silent genes. •Silent genes affect pedigree likelihood ratio used for kinship testing.•The effects of silent genes are evaluated by computer program.•The formulae for pedigree likelihood ratio involving silent gene are presented.•The overall impact of silent genes on pairwise kinship testing is minimal.•In some cases, the effects of silent genes can be relatively significant.

• Publisher: Elsevier B.V,Elsevier Limited
• Subject: computer software / DNA Fingerprinting / DNA testing / forensic sciences / Formula / Genes / Genotype / Genotype & phenotype / Genotypes / Humans / Hypotheses / Kinship / Likelihood Functions / Likelihood ratio / loci / Microsatellite Repeats / Models, Genetic / Mutation / Null gene / Paternity / Paternity testing / Pedigree / Pedigree likelihood / Silent gene / Simulation / Software