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

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.

Identification of the Remains of an Adult Using DNA from Their Deciduous Teeth as a Reference Sample

“…The gain or loss of tandem repeats could lead to false maternal or paternal exclusions [30,32]. In addition, erroneous results can be produced by false matches with close family members or even with people who are completely unrelated to the victim, such that, in some cases, a probability of paternity greater than 99.99% does not necessarily indicate biological paternity [30,31,[38][39][40][41]. Poetsch et al [31] investigated how many wrong paternity inclusions could be detected when comparing [13][14][15] STRs between 336 children and 348 unrelated men.…”

“…They found that at least one and up to three "second father(s)" could be found for 23 children. In general, the false inclusion rate ranges between 19% and 23% [40]. These problems are being reported more frequently and are most common in cases where only one putative parent is available [31,40,42].…”

“…In general, the false inclusion rate ranges between 19% and 23% [40]. These problems are being reported more frequently and are most common in cases where only one putative parent is available [31,40,42]. The inclusion of additional autosomal STR loci may assist in clarifying some ambiguous cases.…”

“…Sometimes, however, the addition of more loci introduces additional mismatches. Furthermore, it has been observed that the inclusion of more loci does not compensate for the absence of genetic information from the mother or the father [35,40,[42][43][44]. The use of Y-chromosome STRs can help only when the victim is male, and the possibility that a close relative of the putative father is the biological father cannot be ruled out [45].…”

Evolution of single‐nucleotide polymorphism use in forensic genetics

“…MPS‐based iiSNP multiplexes lack extraneous artifacts such as stutter, which are routinely encountered when genotyping forensically relevant STRs on both MPS‐ and CE‐based platforms. Several iiSNP multiplexes have been developed with the primary goal of identity determination (Avent et al, 2019; Borsting et al, 2009; Chang et al, 2021; Churchill et al, 2016; Dixon et al, 2005; King et al, 2018; Pakstis et al, 2007; Sanchez et al, 2006; Vallone et al, 2005; Wei et al, 2014; Zhang et al, 2017).…”