An overall limited effect on the weight-of-evidence when taking STR DNA sequence polymorphism into account in kinship analysis

Staadig, Adam; Tillmar, Andreas

doi:10.1016/j.fsigen.2018.11.020

Cited by 14 publications

(4 citation statements)

References 22 publications

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“…In this work, we used STR allele frequencies from PCR-CE analyses for the simulations and it may be speculated that sequenced STR alleles may provide more information. However, data from STR sequencing would only have marginal effects on the evidential weights [43].…”

Section: Discussionmentioning

confidence: 99%

Performance of a 74-Microhaplotype Assay in Kinship Analyses

Tomas,

Rodrigues,

Jønck

et al. 2024

Genes

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Microhaplotypes (MHs) consisting of multiple SNPs and indels on short stretches of DNA are new and interesting loci for forensic genetic investigations. In this study, we analysed 74 previously defined MHs in two of the populations that our laboratory provides with forensic genetic services, Danes and Greenlanders. In addition to the 229 SNPs that originally made up the 74 MHs, 66 SNPs and 3 indels were identified in the two populations, and 45 of these variants were included in new definitions of the MHs, whereas 24 SNPs were considered rare and of little value for case work. The average effective number of alleles (Ae) was 3.2, 3.0, and 2.6 in Danes, West Greenlanders, and East Greenlanders, respectively. High levels of linkage disequilibrium were observed in East Greenlanders, which reflects the characteristics of this population that has a small size, and signs of admixture and substructure. Pairwise kinship simulations of full siblings, half-siblings, first cousins, and unrelated individuals were performed using allele frequencies from MHs, STRs and SNPs from Danish and Greenlandic populations. The MH panel outperformed the currently used STR and SNP marker sets and was able to differentiate siblings from unrelated individuals with a 0% false positive rate and a 1.1% false negative rate using an LR threshold of 10,000 in the Danish population. However, the panel was not able to differentiate half-siblings or first cousins from unrelated individuals. The results generated in this study will be used to implement MHs as investigative markers for relationship testing in our laboratory.

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Section: Discussionmentioning

confidence: 99%

Performance of a 74-Microhaplotype Assay in Kinship Analyses

Tomas,

Rodrigues,

Jønck

et al. 2024

Genes

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“…The effectiveness of 40 STRs plus 91 SNPs was shown to be better than 27 STRs and 91 SNPs or 40 STRs alone [ 588 ]. Only a minor increase in LRs was observed when taking NGS-generated allele sequence variation rather than fragment length allele variation [ 589 ]. The statistical power of exclusion and inclusion can be used to prioritize family members selected for testing in resolving missing person cases [ 590 ].…”

Section: Emerging Technologies Research Studies and Other Topicsmentioning

confidence: 99%

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

Butler

2023

Forensic Science International: Synergy

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“…A recent paper by Hwa et al [33] used EuroForMix to resolve related contributors in mixtures, and further estimated their corresponding relatedness using the relMix R-package [34]. When Staadig and Tillmar [35] carried out a comparison of LRs with/without sequence information on simulated kinships they observed that "the overall impact of STR sequence polymorphism in kinship testing was rather limited" but for indidividuals that have low frequency alleles, the differentiation could be more significant.…”

Section: Relatednessmentioning

confidence: 99%

An examination of STR nomenclatures, filters and models for MPS mixture interpretation

Bleka

Just

et al. 2020

Forensic Science International: Genetics

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The increased interest in the use of Massively Parallel Sequencing (MPS) technologies to type traditional autosomal STR markers raises multiple questions regarding interpretation of the results via probabilistic genotyping. To begin to address some of those questions, we examined the effects of using differing degrees of sequence information, pre-filtering, and data modeling to interpret complex MPS-STR mixtures in a probabilistic genotyping software. Sixty ForenSeq typing results for mixtures of from two to four contributors were: 1) represented using three separate formats that captured different degrees of sequence information, and 2) were analyzed using three different filtering approaches prior to probabilistic interpretation. All mixtures for the different format and filtering variants were subsequently interpreted with respect to ten reference profiles, using both qualitative (LRmix) and quantitative (EuroForMix) models to calculate the likelihood ratio (LR). The LR results indicated moderate information gain when the STR nomenclature was based upon the longest uninterrupted stretch (LUS) compared with conventional capillary electrophoresis repeat units (RU), whereas additional gains were very small when the complete sequence information was utilised. Use of a static analytical threshold for data pre-filtering improved LRs compared to a dynamic (percentage-based) threshold, as the static threshold prevented excessive filtering of alleles originating from minor contributors. For interpretations performed using a quantitative model, a small improvement in performance was observed if a stutter model was employed instead of using stutter thresholds to pre-filter the data, whereasas expectedperformance worsened considerably under the qualitative model when stutter was not pre-filtered. Given the empirical and theoretical findings in this study we discuss the value of utilizing sequence-level information and potential paths forward to increase information gain using MPS systems.

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An overall limited effect on the weight-of-evidence when taking STR DNA sequence polymorphism into account in kinship analysis

Cited by 14 publications

References 22 publications

Performance of a 74-Microhaplotype Assay in Kinship Analyses

Performance of a 74-Microhaplotype Assay in Kinship Analyses

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

An examination of STR nomenclatures, filters and models for MPS mixture interpretation

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