Analysis of mutation rates and haplotypes of 23 Y-chromosomal STRs in Korean father–son pairs

Lee, Dong Gyu; Kim, Su Jin; Cho, Woo-Cheol; Cho, YoonJung; Park, Ji Hwan; Lee, Jinmyung; Jung, Ju Yeon

doi:10.1016/j.fsigen.2023.102875

Cited by 4 publications

(1 citation statement)

References 31 publications

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“…Many studies on determining Y-STR mutation rates focused on father-son pairs [12][13][14][15], as this is considered the best approach for obtaining accurate mutation rate estimates for Y-STRs, as long as the number of pairs is large enough. However, large father-son pair studies are labor and resource intensive, as for every genetic transfer (meiosis) tested, two DNA samples need to be analyzed.…”

Section: Introductionmentioning

confidence: 99%

Male Pedigree Toolbox: A Versatile Software for Y-STR Data Analyses

Ralf,

van Wersch,

Montiel González

et al. 2024

Genes

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Y-chromosomal short tandem repeats (Y-STRs) are widely used in forensic, genealogical, and population genetics. With the recent increase in the number of rapidly mutating (RM) Y-STRs, an unprecedented level of male differentiation can be achieved, widening and improving the applications of Y-STRs in various fields, including forensics. The growing complexity of Y-STR data increases the need for automated data analyses, but dedicated software tools are scarce. To address this, we present the Male Pedigree Toolbox (MPT), a software tool for the automated analysis of Y-STR data in the context of patrilineal genealogical relationships. The MPT can estimate mutation rates and male relative differentiation rates from input Y-STR pedigree data. It can aid in determining ancestral haplotypes within a pedigree and visualize the genetic variation within pedigrees in all branches of family trees. Additionally, it can provide probabilistic classifications using machine learning, helping to establish or prove the structure of the pedigree and the level of relatedness between males, even for closely related individuals with highly similar haplotypes. The tool is flexible and easy to use and can be adjusted to any set of Y-STR markers by modifying the intuitive input file formats. We introduce the MPT software tool v1.0 and make it publicly available with the goal of encouraging and supporting forensic, genealogical, and other geneticists in utilizing the full potential of Y-STRs for both research purposes and practical applications, including criminal casework.

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Section: Introductionmentioning

confidence: 99%

Male Pedigree Toolbox: A Versatile Software for Y-STR Data Analyses

Ralf,

van Wersch,

Montiel González

et al. 2024

Genes

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Y-chromosomal STRs Mutation Rates in the Yakut Population

Adamov,

Fedorova

2024

Russ J Genet

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Improvement of the Discrimination Capacity through the Expansion of Y Chromosomal STR Markers

Lee,

Park

et al. 2023

Biomed Sci Letters

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Y chromosomal short tandem repeat (Y-STR) markers have been developed continuously to complement forensic DNA analyses and population genetic studies. Initially, we collected data from previously reported Korean population Y-STR haplotype studies on 1133 individuals. We then conducted a marker expansion analysis using a dataset from the Y-STR Haplotype Reference Database (YHRD), covering up to 29 Y-STRs, referred to as Ymax. Additionally, we examined the impact of rapidly mutating (RM) Y-STRs included in this expanded marker set on the discrimination capacity. We observed that marker expansions both with (0.9896), and without (0.9510), RM Y-STR improved the discrimination capacity. Subsequently, we focused on 16 individuals belonging to seven distinct groups sharing identical haplotypes. These particular haplotypes had been previously identified among 476 unrelated males using 23 Y-STR markers from the PowerPlex ® Y23 System. We expanded the marker panel up to Ymax to explore how discrimination improved with an expansion of Y-STR markers for these 16 individuals. Among the expanded markers, DYS627, which had high discriminatory power, had a high mutation rate (1.10 × 10 -2 ) and high gene diversity (0.83). In contrast, DYF387S1 displayed high gene diversity (0.95) but a relatively low mutation rate (2.80 × 10 -3 ). We propose that these findings will be valuable in the selection of suitable Y-STR markers, depending on the objectives of forensic analyses. Additionally, the presence of frequently observed Y-haplotypes in Korean population will facilitate statistical interpretation in Y-STR DNA profiling.

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Analysis of mutation rates and haplotypes of 23 Y-chromosomal STRs in Korean father–son pairs

Cited by 4 publications

References 31 publications

Male Pedigree Toolbox: A Versatile Software for Y-STR Data Analyses

Male Pedigree Toolbox: A Versatile Software for Y-STR Data Analyses

Y-chromosomal STRs Mutation Rates in the Yakut Population

Improvement of the Discrimination Capacity through the Expansion of Y Chromosomal STR Markers

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