Evaluation of a Custom SNP Panel for Identifying and Rectifying of Misjudged Paternity in Deficiency Cases.

Liao Chang,Huiyun Yu,Siqi Wen,Bao Zhang,Xinyao Miao,Shengbin Li

doi:10.3389/fgene.2021.602429

Liao Chang, Huiyun Yu + Show 4 more

Open Access

https://doi.org/10.3389/fgene.2021.602429

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Abstract

Parentage testing is routinely performed by genotyping short tandem repeat (STR) through capillary electrophoresis in the present. However, ambiguous or even misjudged paternity based on STRs happens from time to time in cases where only one putative parent is available. We analyzed STR data of 7,818,969 unrelated pairs and 75 close-relative pairs and found that although the probability of a random false match between non-relatives was 4.22 × 10–6, the incidence of false or ambiguous paternity results between children and first-degree relatives of their true parent was as high as 18.67%. These results highlight the risk of false inclusion of a relative or even non-relatives in parentage testing with STRs. We then validated all ambiguous STR results by targeted sequencing with a custom panel containing 4,830 individual identification single nucleotide polymorphisms (IISNP), found that the ratio of mismatch loci to total SNPs was 1.78–6.95% in close relatives compared with 10.93–13.49% in unrelated pairs. Last, we reported three real cases with undetermined paternity by STRs and rectified them by dissecting with our IISNP panel. These results suggested that high-density IISNP panel can be used to identify and rectify misjudged cases effectively.

Highlights

Parentage testing plays a critical role in searching for missing persons (Yu and Fung, 2018), identifying disaster victims (Wright et al, 2018), solving inheritance disputes (Patidar et al, 2015), and immigration casework (Wenk and Shao, 2014)
Ambiguous short tandem repeat (STR) results are common in cases where only one putative parent is available (Borsting and Morling, 2011) or the alleged parent is a close relative to the real parent (Pinto et al, 2013), because it is difficult to distinguish the germline mutation from a real mismatch in the genetic inconsistency (Lindner et al, 2014)
In undetermined cases based on STRs, the most highly considered possibility is that the putative parent is a close relative to the real parent, especially in parentage testing for immigration purposes (Wenk and Shao, 2014)

Summary

INTRODUCTION

Parentage testing plays a critical role in searching for missing persons (Yu and Fung, 2018), identifying disaster victims (Wright et al, 2018), solving inheritance disputes (Patidar et al, 2015), and immigration casework (Wenk and Shao, 2014). STRs display mutation rate as high as 10−3–10−4 per generation (Legendre et al, 2007), so it is possible to observe more genetic incompatible loci in true parent–child pairs when adding STRs. In addition, compared with the ambiguous STR results between close relatives, a random but perfect false match (RPFM) between unrelated individuals may result in error. We first estimated the prevalence of ambiguous paternity in cases involving close relatives as well as the probability of random false match between non-relatives with STRs. we evaluated the performance of a custom panel with 4,830 individual identification SNPs (IISNP) in the above situations. 1 ng genome DNA was amplified using the HUMAN DNA Typing-YanHuang kit (FGI, China) on the thermal cycler (GeneAmp polymerase chain reaction 9700, Thermo Fisher Scientific, United States).

MATERIALS AND METHODS

RESULTS

DISCUSSION

ETHICS STATEMENT