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Evaluation of RMplex system for differentiating father-son pairs using Y-STRs in a Korean population.
Forensic Sci Int Genet
January 2025
Forensic DNA Division, National Forensic Service, Wonju, South Korea. Electronic address:
Y-chromosomal short tandem repeats (Y-STRs) at rapidly mutating (RM) loci have been suggested as tools for differentiating paternally related males. RMplex is a recently developed system that incorporates 26 RM loci and four fast-mutating (FM) loci, targeting 44 male-specific loci. Here, we evaluated the RMplex by estimating Y-STR mutation rates and the overall differentiation rates for 542 Korean father-son pairs, as well as the genetic population values for 409 unrelated males.
View Article and Find Full Text PDFSmall variant benchmark from a complete assembly of X and Y chromosomes.
Nat Commun
January 2025
Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, USA.
The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To enable technology developers along with research and clinical laboratories to evaluate variant detection on male sex chromosomes X and Y, we create a small variant benchmark set with 111,725 variants for the Genome in a Bottle HG002 reference material. We develop an active evaluation approach to demonstrate the benchmark set reliably identifies errors in challenging genomic regions and across short and long read callsets.
View Article and Find Full Text PDFA machine learning approach for estimating Eastern Asian origins from massive screening of Y chromosomal short tandem repeats polymorphisms.
Int J Legal Med
January 2025
Institute of Forensic and Anthropological Science, Seoul National University Medical Research Center, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
Inferring the ancestral origin of DNA evidence recovered from crime scenes is crucial in forensic investigations, especially in the absence of a direct suspect match. Ancestry informative markers (AIMs) have been widely researched and commercially developed into panels targeting multiple continental regions. However, existing forensic ancestry inference panels typically group East Asian individuals into a homogenous category without further differentiation.
View Article and Find Full Text PDFGenetic Polymorphism of Y-Chromosome in Turkmen Population from Turkmenistan.
Genes (Basel)
November 2024
Kh. Dosmukhamedov Atyrau University, Atyrau 060000, Kazakhstan.
This study investigates the Y-chromosome genetic diversity of the Turkmen population in Turkmenistan, analyzing 23 Y-STR loci for the first time in a sample of 100 individuals. Combined with comparative data from Turkmen populations in Afghanistan, Iran, Iraq, Russia, and Uzbekistan, this analysis offers insights into the genetic structure and relationships among Turkmen populations across regions across Central Asia and the Near East. High haplotype diversity in the Turkmen of Turkmenistan is shaped by founder effects (lineage expansions) from distinct haplogroups, with haplogroups Q and R1a predominating.
View Article and Find Full Text PDFA Genetic Make Up of Italian Lipizzan Horse Through Uniparental Markers to Preserve Historical Pedigrees.
Biology (Basel)
December 2024
Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Research Centre for Animal Production and Aquaculture, Via Salaria 31, 00015 Monterotondo, Italy.
Lipizzan is a famous horse breed dating back to 1580 when the original stud of Lipica was established by the Hasburg Archduke Charles II. Currently, the Italian State Stud of Lipizzan Horses (ASCAL) is a conservation nucleus managed through strict mating rules where mitochondrial DNA sequences are used to verify the correct assignment of mares to a historical pedigree maternal lineage. Here, we analyzed the D-loop sequences of Lipizzan horses from the ASCAL in Monterotondo (Rome, Italy) in order to confirm their pedigree assignment to known female founder families.
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