Allele and haplotype frequencies of 12 X-STRs in Mexican population

Cortés-Trujillo, Irán; Zuñiga-Chiquette, F.; Ramos-González, Benito; Chávez-Briones, Maria de Loures; Islas-González, Karely Liliana; Betancourt-Guerra, David Adrián; Peralta-Coria, Rocío; Martínez-Cortés, Gabriela; Rangel-Villalobos, Héctor

doi:10.1016/j.fsigen.2018.10.012

Cited by 9 publications

(7 citation statements)

References 13 publications

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“…17 In the Mexican population, the allele frequency of the X-STR marker ranged between 0.00107 and 0.53162, and allele 15 of the DXS423 locus also showed the greatest frequency. 35 In a comparison of different population groups among the US population, the frequency of allele 10 on the DXS8378 locus in US Asians was higher than that in other populations (African American, US Caucasian and US Hispanic). 36 A previous study of the X-STRs in the Thai population was inconsistent with our studied population.…”

Section: Discussionmentioning

confidence: 96%

Genetic analysis of 12 X-short tandem repeats loci in a northern Thai population

Khacha-ananda

Mahawong

2020

Med Sci Law

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Short tandem repeats (STRs) are widely used as DNA markers in paternity testing and criminal investigations because of their high genetic polymorphism among individuals in population. However, many factors influence genetic variations of STRs. Therefore, understanding STR information within individual populations could provide database and scientifically reliable STR genotyping for forensic genetic purposes. We aimed to examine allele frequencies of X-STRs, including some forensic parameters, in a northern Thai population. A retrospective descriptive study was conducted by collecting X-STR data from unrelated individuals living in a northern region of Thailand. The allele frequency and forensic parameters – for example polymorphism information content (PIC), power of discrimination in females and males (PDf and PDm), mean exclusion chance (MEC) and haplotype frequency – were calculated. The Hardy–Weinberg equilibrium was analysed. A total of 132 alleles were observed, with corresponding allele frequency ranging from 0.0064 to 0.4904. The PIC of all loci was >0.6, representing high genetic polymorphism, except DXS8378 and DXS7423. Notably, DXS10135 was the most diverse loci with the highest PD and MEC, while DXS7423 was the least polymorphic marker with the lowest PD and MEC. The highest haplotype diversity in male data was on linkage group III (DXS10101-DXS10103-HPRTB) by 0.9895. The genetic distance analysis demonstrated that the northern Thai population had a close relationship with Taiwanese (DA = 0.023). There are no significant deviations among the Hardy–Weinberg equilibrium except DXS10148. This study has established a northern Thai X-STRs reference database to be used as a tool for forensic genetic purposes.

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Section: Discussionmentioning

confidence: 96%

Genetic analysis of 12 X-short tandem repeats loci in a northern Thai population

Khacha-ananda

Mahawong

2020

Med Sci Law

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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%

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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“…A part from the U.S., Argentina and Brazil, the X-STRs popu-lation data reported within the North America (including Central America and Caribbean) are limited to Mexico (e.g. [149]) and Costa Rica [150]. As for the South America, similar studies are limited to Colombia (e.g.…”

Section: Worldwide Populationsmentioning

confidence: 99%

Applications of X-Chromosome Short Tandem Repeats for Human Identification: A Review

Mahat

Alwi²,

Salleh³

et al. 2023

J.Trop.Life.Science

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The forensic DNA profiling technique has tremendously contributed to forensic human identification, an important aspect in forensic investigations. In instances whereby comparison samples are unavailable, utilization of short tandem repeats of X chromosome (X-STRs) may prove useful to resolve complex kinship investigations involving missing persons and mass disasters. Despite such evidential values, the use of X-STRs during investigations remains scarce in many Southeast Asian countries including Malaysia, requiring concerted efforts for establishing forensic statistical support for its diverse populations (especially the admixture populations), standardizing core loci and procedure, improving the knowledge among practitioners as well as developing suitable standard operating procedure for incorporating X-STRs analysis in the overall DNA profiling framework. Hence, this review paper aims to highlight the developments, applications and population data of X-STRs, as well as its challenges and future insights for forensic casework.

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Allele and haplotype frequencies of 12 X-STRs in Mexican population

Cited by 9 publications

References 13 publications

Genetic analysis of 12 X-short tandem repeats loci in a northern Thai population

Genetic analysis of 12 X-short tandem repeats loci in a northern Thai population

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

Applications of X-Chromosome Short Tandem Repeats for Human Identification: A Review

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