Systematic evaluation of sensitivity and specificity of sibship determination by using 15 STR loci

Pu, Chang En; Linacre, Adrian

doi:10.1016/j.jflm.2007.12.018

Cited by 20 publications

(18 citation statements)

References 9 publications

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“…Only 3 % of the calculations led to values lower than 10 % (Table 5). These data also fit to a former simulation study: In a simulation of 355,620 pairs of half siblings (15 STRs, three populations), about 12 % of obtained combined half sibling index (CHSI) values were found to be less than 1 [9].…”

Section: Scenario 2: Half Siblings/unrelatedsupporting

confidence: 55%

“…The difference to our results might be due to the rather low number of individuals investigated by Reid et al [8]. Pu and Linacre, for example, generated 357,630 full sibling pairs from DNA profiles of random populations (Chinese, Caucasian, and African Americans) using the 15 STRs provided with the Identifiler Kit (Applied Biosystems) [9]. They found in about 1.5 % of their cases CSI values less than 1 which corresponds to our findings of 1.8 % of pairs with LR<1/99.…”

Section: Resultsmentioning

confidence: 56%

“…In sibship analysis, several authors recommend to investigate as many STRs as possible, since the significance of the analysis would benefit greatly by including more than 15 STRs or additional genetic markers such as mitochondrial DNA or gonosomal STRs [9]. In an attempt to verify these assertions, we investigated 88 of our twin pairs (including the cases with lowest probabilities) and additionally using the Powerplex® 21 kit which comprises altogether 20 STR markers.…”

Section: Investigation Of 20 Instead Of 15 Strsmentioning

confidence: 99%

“…For many years, several STR multiplex PCRs of different companies are routinely used in kinship analysis such as the AmpFlSTR Identifiler kit (Applied Biosystems) or the Powerplex® 16 (Promega) both amplifying 15 STR loci in parallel [8][9][10][11][12]. Recently, multiplex PCRs were developed comprising even more loci, such as the GlobalFiler® with 24 loci (Applied Biosystems) or the Powerplex® 21 providing 20 STR loci (Promega).…”

Section: Introductionmentioning

confidence: 99%

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About the power of biostatistics in sibling analysis—comparison of empirical and simulated data

et al. 2015

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The determination of potential sibship is a common task in routine kinship analysis, but often the putative parents are not available for analysis anymore. Then, a sibling analysis has to be conducted investigating only the potential siblings, thus reducing the power of the conclusion. In an attempt to determine meaningfulness of biostatistical calculations, 346 dizygotic twin pairs, 30 confirmed half siblings, and 112 unrelated people (to generate 6216 pair comparisons) were studied, all genetically typed using at least the Powerplex® 16 STRs. From every pair, the probabilities for a full sibship (identical parents) and half sibship (different fathers) were calculated using a commercially available computer program. Additionally, we simulated marker data for one million pairs of full sibs, half sibs, and unrelated persons each. Ninety-five percent of full sibling pairs demonstrated a likelihood ratio (LR) > 9 (W-value > 90 %) and less than 4% of these showed a LR < 3 (W-value < 75%) for full sibship after analysis of 15 STRs. The results for half siblings are less unambiguous. Here, only 57% achieved a LR > 9 and 23% a LR < 3. Regarding the unrelated pairs, more than 90% had a LR < 1/9 and only 2% reached a LR > 9. All in all, our results show that 15 to 20 STRs have sufficient power for analyses in kinship. Moreover, our data provide a statistical basis for the determination of the information content of a LR/W-value in a sibship case. Investigating an identical number of full siblings and unrelated pairs, it could be shown that 92% of pairs with a LR > 9 for full sibship probability really are full siblings. So, setting a cutoff level for full sibship at LR > 9, less than 10% of pairs will be wrongly assumed as full siblings even though they are unrelated.

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Section: Scenario 2: Half Siblings/unrelatedsupporting

confidence: 55%

Section: Resultsmentioning

confidence: 56%

Section: Investigation Of 20 Instead Of 15 Strsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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About the power of biostatistics in sibling analysis—comparison of empirical and simulated data

et al. 2015

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“…To attain this goal, researchers have developed several genetic marker panels, the most notable of which was developed by the ISAG cattle parentage testing committee. Evaluation of marker sets and genotyping platforms to be used as a parentage panel should include measures of both sensitivity and specificity when the true pedigree is known (Pu and Linacre 2008). When the number of allowed mismatching calls is increased, there is a risk of qualifying an incorrect sire, thereby reducing the sensitivity of the platform (Weller et al 2004;Hong et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Analysis of validated and population-specific single nucleotide polymorphism parentage panels in pedigreed and commercial beef cattle populations

Buchanan

Woronuk²,

Marquess³

et al. 2016

Can. J. Anim. Sci.

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A pedigreed population containing 71 calves and 8 sires was used to compare sire qualification using three genotyping platforms [14 microsatellite, real-time quantitative PCR, and 100, 200, 500, and 1000 single nucleotide polymorphism (SNP) arrays]. Parentage was also qualified in an unknown-pedigree population containing 8480 calves with 460 sires using SNP arrays. The three platforms qualified the true sire in the known-pedigree population with zero mismatches. The 100 and 200 SNP arrays yielded specificities of 0.92 and 0.99 with a 1% mismatch rate in the knownpedigree population, respectively. In the larger population, SNP panels of the 500 and 1000 highest minor allele frequency SNPs were also evaluated. The 1000 SNP panel qualified paternity to a single sire for 82.1% of calves with 1% or 2% mismatches. Not all commercial sires were genotyped, which accounts for missing paternity for some calves. In this larger population, the 100 SNP array qualified multiple sires to 0.42% of calves and single sires to 80.84% of calves without mismatches. The 200 SNP array assigned unique paternity, and 79.8% of calves were qualified to a sire without mismatches. With a 2% mismatch rate, sire qualifications agreed with the 1000 SNP array. This study highlights the interplay among population size, genotyping error rates, and the specificity and sensitivity of parentage platforms.Key words: SNP parentage panel, sensitivity (parentage), specificity (parentage), Charolais, cattle (beef).Résumé : Une population à pedigree contenant 71 veaux et 8 géniteurs mâles a été utilisée pour comparer la qualification des géniteurs mâles au moyen de trois plateformes de génotypage (14 microsatellites, PCR quantitative en temps réel, ainsi que des réseaux de 100, 200, 500, et 1000 SNPs). La parenté a aussi été qualifiée dans une population de pedigree inconnu contenant 8480 veaux et 460 géniteurs mâles au moyen des réseaux de SNPs. Les trois plateformes ont qualifié le véritable géniteur dans la population à pedigree connu avec aucun écart. Les réseaux à 100 et 200 SNPs ont rendu des spécificités de 0,92 et 0,99 avec un taux d'écart de 1 % dans la population à pedigree connu, respectivement. Dans la plus grande population, les panels de SNPs de 500 et 1000 SNPs de fréquence d'allèles mineurs les plus élevés ont aussi été évalués. Le panel de 1000 SNPs a qualifié la paternité à un seul géniteur pour 82,1 % des veaux avec seulement 1 % à 2 % d'écarts. Tous les géniteurs mâles commerciaux n'ont pas été génotypés ce qui explique la paternité manquante pour certains veaux. Dans cette population plus grande, le réseau à 100 SNPs a qualifié de multiples géniteurs à 0,42 % des veaux et un seul géniteur à 80,84 % des veaux sans écarts. Le réseau à 200 SNPs a assigné une paternité unique et 79,8 % des veaux ont été qualifiés à un géniteur sans écart. Avec un taux d'écart de 2 %, la qualification des géniteurs était en accord avec le réseau de 1000 SNPs. Cette étude souligne l'interdépendance entre la taille de la population, les taux d'éca...

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Three mutations at a Y-STR haplotype defy a paternal half-brothers kinship case analysis

2023

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Systematic evaluation of sensitivity and specificity of sibship determination by using 15 STR loci

Cited by 20 publications

References 9 publications

About the power of biostatistics in sibling analysis—comparison of empirical and simulated data

About the power of biostatistics in sibling analysis—comparison of empirical and simulated data

Analysis of validated and population-specific single nucleotide polymorphism parentage panels in pedigreed and commercial beef cattle populations

Three mutations at a Y-STR haplotype defy a paternal half-brothers kinship case analysis

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