Extended population genetic analysis of 12 X-STRs – Exemplified using a Norwegian population sample

Bergseth, Erik Francisco; Tillmar, Andreas; Haddeland, P. Jørgen T.; Kling, Daniel

doi:10.1016/j.fsigen.2022.102745

Cited by 4 publications

(4 citation statements)

References 43 publications

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“…Routine kinship analyses rely almost exclusively on commercial kits, such as the commonly used Argus X-12 QS which consists of 12 X-STRs [3,[26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][42][43][44]. However, current implementations of state-of-the-art statistical framework for estimation from pedigrees, besides being quite onerous to use, are already very slow for 12 markers and so unsuitable for larger panels without the availability of large computational resources [48,49].…”

Section: Discussionmentioning

confidence: 99%

“…For this reason, traditional analyses of highly polymorphic haplotypes, consisting of X-STR markers organised into "linkage groups" or "clusters", were devised in order to increase the evidential weight, which would be otherwise statistically inconclusive [6]. Nowadays four different X-STR linkage groups are routinely used for forensic applications [3,[26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43][44]. However, it has been shown that, while well spaced along the X chromosome, some of these linkage groups cannot be considered truly independent from each other [45][46][47].…”

Section: Introductionmentioning

confidence: 99%

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Recombulator-X: a fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics

Aneli

Fariselli

Chierto

et al. 2023

Preprint

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Background and Objective: Genetic markers (especially short tandem repeats or STRs) located on the X chromosome are a valuable resource to solve complex kinship cases in forensic genetics in addition or alternatively to autosomal STRs. Groups of tightly linked markers are combined into haplotypes, thus increasing the discriminating power of tests. However, this approach requires precise knowledge of the recombination rates between adjacent markers. Recombination rates vary across the human genome and cannot be automatically derived from linkage physical maps. The International Society of Forensic Genetics recommends that recombination rate estimation on the X chromosome is performed from pedigree genetic data while taking into account the confounding effect of mutations. However, the only existing implementations that satisfy these requirements have several drawbacks: they were never publicly released, they are very slow and/or need cluster-level hardware and strong computational expertise to use. In order to address these key concerns, we developed Recombulator-X, a new open-source Python tool. Methods: The most challenging issue, namely the running time, was addressed with dynamic programming techniques to greatly reduce the computational complexity of the algorithm, coupled with JIT compilation to further increase performance. We also extended the statistical framework from STR to any polymorphic marker. Results: Compared to the previous methods, Recombulator-X reduces the estimation times from weeks or months to less than one hour for typical datasets. Moreover, the estimation process, including preprocessing, has been streamlined and packaged into a simple command-line tool that can be run on a normal PC. Where previous approaches were limited to small panels of STR markers (up to 15), our tool can handle greater numbers (up to 100) of mixed STR and non-STR markers. Conclusions: In the genetic forensic community, state-of-the-art estimation methods for X chromosome recombination rates have seen limited usage due to the technical hurdles posed by previous implementations. Recombulator-X makes the process much simpler, faster and accessible to researchers without a computational background, hopefully spurring increased adoption of best practices. Moreover, it extends the estimation framework to larger panels of genetic markers (not only STRs), allowing analyses of sequencing-based data.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Recombulator-X: a fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics

Aneli

Fariselli

Chierto

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Routine kinship analyses rely almost exclusively on commercial kits, such as the commonly used Argus X-12 QS which consists of 12 X-STRs [3,[26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43][44]. However, current implementations of state-of-the-art statistical framework for estimation from pedigrees, besides being quite onerous to use, are already very slow for 12 markers and so unsuitable for larger panels without the availability of large computational resources [48,49].…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics

Aneli,

Fariselli,

Chierto

et al. 2023

PLoS Comput Biol

View full text Add to dashboard Cite

Genetic markers (especially short tandem repeats or STRs) located on the X chromosome are a valuable resource to solve complex kinship cases in forensic genetics in addition or alternatively to autosomal STRs. Groups of tightly linked markers are combined into haplotypes, thus increasing the discriminating power of tests. However, this approach requires precise knowledge of the recombination rates between adjacent markers. The International Society of Forensic Genetics recommends that recombination rate estimation on the X chromosome is performed from pedigree genetic data while taking into account the confounding effect of mutations. However, implementations that satisfy these requirements have several drawbacks: they were never publicly released, they are very slow and/or need cluster-level hardware and strong computational expertise to use. In order to address these key concerns we developed Recombulator-X, a new open-source Python tool. The most challenging issue, namely the running time, was addressed with dynamic programming techniques to greatly reduce the computational complexity of the algorithm. Compared to the previous methods, Recombulator-X reduces the estimation times from weeks or months to less than one hour for typical datasets. Moreover, the estimation process, including preprocessing, has been streamlined and packaged into a simple command-line tool that can be run on a normal PC. Where previous approaches were limited to small panels of STR markers (up to 15), our tool can handle greater numbers (up to 100) of mixed STR and non-STR markers. In conclusion, Recombulator-X makes the estimation process much simpler, faster and accessible to researchers without a computational background, hopefully spurring increased adoption of best practices.

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An overview of autosomal STRs and identity SNPs in a Norwegian population using massively parallel sequencing

Agudo,

Aanes,

Albert

et al. 2024

Forensic Science International: Genetics

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Extended population genetic analysis of 12 X-STRs – Exemplified using a Norwegian population sample

Cited by 4 publications

References 43 publications

Recombulator-X: a fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics

Recombulator-X: a fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics

Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics

An overview of autosomal STRs and identity SNPs in a Norwegian population using massively parallel sequencing

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