The risk of false inclusion of a relative in parentage testing – an in silico population study

Lee, James Chun-I; Tsai, Li-Chin; Chu, Pao-Ching; Lin, Yen-Yang; Lin, Chun-Yen; Huang, Tsun-Ying; Yu, Yu-Jen; Linacre, Adrian; Hsieh, Hsing-Mei

doi:10.3325/cmj.2013.54.257

Cited by 10 publications

(7 citation statements)

References 15 publications

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“…The difficulty of rejecting close relatives as parents is a known problem in exclusion analysis (Lee et al . ). An additional challenge within our sample was that several horses were related in multiple branches of the family (for example, a half sibling pair sharing a sire but with dams that were also full siblings).…”

Section: Resultsmentioning

confidence: 97%

Single nucleotide polymorphisms for DNA typing in the domestic horse

et al. 2017

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Genetic markers are important resources for individual identification and parentage assessment. Although short tandem repeats (STRs) have been the traditional DNA marker, technological advances have led to single nucleotide polymorphisms (SNPs) becoming an attractive alternative. SNPs can be highly multiplexed and automatically scored, which allows for easier standardization and sharing among laboratories. Equine parentage is currently assessed using STRs. We obtained a publicly available SNP dataset of 729 horses representing 32 diverse breeds. A proposed set of 101 SNPs was analyzed for DNA typing suitability. The overall minor allele frequency of the panel was 0.376 (range 0.304-0.419), with per breed probability of identities ranging from 5.6 × 10 to 1.86 × 10 . When one parent was available, exclusion probabilities ranged from 0.9998 to 0.999996, although when both parents were available, all breeds had exclusion probabilities greater than 0.9999999. A set of 388 horses from 35 breeds was genotyped to evaluate marker performance on known families. The set included 107 parent-offspring pairs and 101 full trios. No horses shared identical genotypes across all markers, indicating that the selected set was sufficient for individual identification. All pairwise comparisons were classified using ISAG rules, with one or two excluding markers considered an accepted parent-offspring pair, two or three excluding markers considered doubtful and four or more excluding markers rejecting parentage. The panel had an overall accuracy of 99.9% for identifying true parent-offspring pairs. Our developed marker set is both present on current generation SNP chips and can be highly multiplexed in standalone panels and thus is a promising resource for SNP-based DNA typing.

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Section: Resultsmentioning

confidence: 97%

Single nucleotide polymorphisms for DNA typing in the domestic horse

et al. 2017

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“…With the GlobalFiler TM system, Ochiai predicted that the probability of matches with only 1 mismatch in 21 STRs for full siblings was 23.5% ( Ochiai et al, 2016 ). Lee simulated families with 15 STRs in silico; the false inclusion rate was 19.0% when considering a sibling as the parent ( Lee et al, 2013 ). These data suggested that the current STR systems are insufficient to distinguish a close relative from the true parent in deficiency cases, and supplementary investigations need to be performed.…”

Section: Discussionmentioning

confidence: 99%

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

Chang

Miao

et al. 2021

Front. Genet.

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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.

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“…Therefore, the use of strict guidelines to conduct motherless cases were sufficient to avoid false inclusions between unrelated children and alleged fathers in our data set of more than 20 000 cases. The single inclusion found highlights that relatedness is a concern in motherless cases 1,7,10 and calls attention to the importance of obtaining information on family circumstances before the analysis and especially to the importance of testing the mother in all situations, even if maternity is not disputed.…”

Section: Discussionmentioning

confidence: 99%

“…The motherʼs absence increases the probability of false paternity inclusion, 1 and several studies have reported that in some circumstances motherless analysis can result in incorrect paternity calls and have advised precaution in such cases. [2][3][4][5][6][7][8][9][10][11][12] Despite the challenges, motherless testing continues to be used, for example, (a) when the mother is unavailable or (b) in some countries, motherʼs participation is not mandatory for tests that are for personal (nonlegal) purposes.…”

Section: Introductionmentioning

confidence: 99%

Assessing false paternity risk in simulated motherless cases from more than 20 000 real exclusion trios

Aguiar

Castro²,

Pinto³

et al. 2020

Transfusion

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Background: When the motherʼs DNA profile is not available for paternity testing, there is a smaller probability that a locus will exclude an alleged father. This study aims to evaluate the risk of potential false paternity inclusions in motherless cases. Study Design and Methods: More than 20 000 duos were generated by removing the maternal genotypes from exclusion trios. After recalculating paternity in these duos, any found inclusions would be false. Results: The use of an appropriate number of loci, mutation model, and mutation rates to analyze motherless paternity cases was robust against false inclusions. A single potential false inclusion was observed in a case wherein kinship plays a role. This result highlights the importance of testing the mother when available and of obtaining information on family circumstances for the proper handling of cases involving related individuals. Conclusion: The guidelines we used here were sufficient to avoid false inclusions in a data set of more than 20 000 motherless cases.

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The risk of false inclusion of a relative in parentage testing – an in silico population study

Cited by 10 publications

References 15 publications

Single nucleotide polymorphisms for DNA typing in the domestic horse

Single nucleotide polymorphisms for DNA typing in the domestic horse

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

Assessing false paternity risk in simulated motherless cases from more than 20 000 real exclusion trios

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