Population data and genetic characteristics of 12 X-STR loci using the Investigator® Argus X-12 Quality Sensor kit for the Kedayan population of Borneo in Malaysia

Hakim, Hashom Mohd; Khan, Hussein Omar; Ismail, Siti Afifah; Lalung, Japareng; Kofi, Abban Edward; Aziz, Mohd Yusmaidie; Pati, Siddhartha; Nelson, Bryan Raveen; Chambers, Geoffrey K.; Edinur, Hisham Atan

doi:10.1007/s00414-021-02577-0

Cited by 9 publications

(8 citation statements)

References 8 publications

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“…For example, the heterogenous population of Malaysia consists of the Malays and Bumiputera (69.8%), Chinese (22.4%), Indians (6.8%) and others minorities/ indigenous populations (1%) [168]. Being a classic example, X-STRs population data for Malaysia are limited to the Malays in Kuala Lumpur alone [110], the sub-ethnicities of indigenous people (Senoi, Proto-Malay and Negrito) in Peninsular Malaysia [169] and one minor ethnicity in Borneo (Kedayan) [111]. Not only the available population data do not represent the diverse population of Malaysia, the one particular study for the indigenous people only utilized 164 participants for representing the three sub-ethnic populations which may not be adequately representative.…”

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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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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“…In many circumstances, DNA profiling of autosomal STR loci can be reliably used for solving criminal and paternity cases focused on males [ 66 ]. Nonetheless, in those cases involving close blood-relatives as putative fathers, the exclusion power of autosomal STRs is considerably reduced, and ChrX (Chromosome X) STRs may be most appropriate [ 16 ].…”

Section: Forensic Applicationsmentioning

confidence: 99%

“…It is important to underline the significance of larger databases to enhance the estimation of haplotype frequencies, more software packages for kinship evaluations of ChrX transmission [ 2 ], and new, tested, and optimized X-STRs markers for kinship analysis. To support further development of X-STRs, the studies conducted presented the discovery of novel X-STRs markers and multiplex systems which are highly promising for forensic use [ 49 , 66 , 77 , 78 ] and the extension of local haplotype data through studies of the viability and discriminatory power of X-STRs [ 9 , 40 , 79 , 80 , 81 ]. Despite more than 20 years of usage and X-STR research in forensic genetics, there is still a continuous demand for high-quality genetic data to support new studies and expand the application of these gonosomal markers.…”

Section: Forensic Applicationsmentioning

confidence: 99%

Forensic Applications of Markers Present on the X Chromosome

García

Bessa

Santos

et al. 2022

Genes

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Microsatellite genetic markers are the gold standard for human genetic identification. Forensic analyses around the world are carried out through protocols using the analysis of STR markers in autosomal chromosomes and in the Y chromosome to solve crimes. However, these analyses do not allow for the resolution of all cases, such as rape situations with suspicion of incest, paternity without a maternal sample for comparison, and biological traces with DNA mixture where the profile sought is female, among other situations. In these complex cases, the study of X-chromosome STR markers significantly increases the probability of identification by complementing the data obtained for autosomal and Y-chromosome markers, due to the unique structure of the X chromosome and its exclusive method of inheritance. However, there are currently no validated Brazilian protocols for this purpose, nor are there any population data necessary for statistical analyses that must be included in the issuance of expert reports. Thus, the aim of this article is to provide a literary review of the applications of X-chromosomal markers in population genetics.

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“…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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Population data and genetic characteristics of 12 X-STR loci using the Investigator® Argus X-12 Quality Sensor kit for the Kedayan population of Borneo in Malaysia

Cited by 9 publications

References 8 publications

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

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

Forensic Applications of Markers Present on the X Chromosome

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

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