Evaluating the effects of silent genes on pairwise kinship testing

IF 2.2 3区 医学 Q1 MEDICINE, LEGAL Forensic science international Pub Date : 2024-11-05 DOI:10.1016/j.forsciint.2024.112290
Da Yang , Mei Li Li , An Qi Wei
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Abstract

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.
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评估沉默基因对配对亲缘关系测试的影响。
短串联重复(STR)基因座经常被用于亲缘关系检测,而 STR 基因座引物结合区发生的单碱基突变可导致等位基因扩增失败和沉默基因的出现。沉默基因是无法观察到的,因此被排除在评估的基因型之外。在亲缘关系检验中,通常会使用世系似然比(LR)来确定不同亲缘关系的可能性。LR 值来自不同类型的基因型。LRexact 值基于准确或实际的基因型,其中可能包括沉默基因。相反,LRobserve 值基于观察到的基因型,其中不包括沉默基因,而 LRadjust 值包含所有潜在的基因型,包括观察到的基因型和包含沉默基因的基因型。首先,根据成对个体的不同基因型形式,列出了一级、二级和三级亲缘关系检验中的 LR 计算公式。然后使用 Familias 软件验证这些公式的正确性,并将结果与 GeneVisa 软件(www.genevisa.net)的结果进行比较。最后,GeneVisa 的模拟模块用于评估沉默基因对配对亲缘关系检验的影响。研究结果表明,沉默基因的总体影响很小,但在某些情况下,其影响可能相对显著。沉默基因的影响一般会随着亲缘关系的疏远而减小。在特定的亲缘关系测试中,当个体之间没有亲缘关系时,沉默基因的影响比有亲缘关系时要小。在一级和二级亲缘关系检验中使用 LRadjust 值可以大大减轻沉默基因的影响。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Forensic science international
Forensic science international 医学-医学:法
CiteScore
5.00
自引率
9.10%
发文量
285
审稿时长
49 days
期刊介绍: Forensic Science International is the flagship journal in the prestigious Forensic Science International family, publishing the most innovative, cutting-edge, and influential contributions across the forensic sciences. Fields include: forensic pathology and histochemistry, chemistry, biochemistry and toxicology, biology, serology, odontology, psychiatry, anthropology, digital forensics, the physical sciences, firearms, and document examination, as well as investigations of value to public health in its broadest sense, and the important marginal area where science and medicine interact with the law. The journal publishes: Case Reports Commentaries Letters to the Editor Original Research Papers (Regular Papers) Rapid Communications Review Articles Technical Notes.
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