Characterization of the highly discriminatory loci DYS449, DYS481, DYS518, DYS612, DYS626, DYS644 and DYS710

D’Amato, María Eugenia; Ehrenreich, Liezle; Cloete, Kevin Wesley; Benjeddou, Mongi; Davison, Sean

doi:10.1016/j.fsigen.2009.06.011

Cited by 37 publications

(22 citation statements)

References 24 publications

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“…The emergence of massively parallel sequencing (MPS) technologies improved upon this principle by allowing for the detection of a substantially-larger amount of genetic sequence information with a higher throughput, lower cost, and greater ease-of-use than previous methods. Studies involving each of these approaches have resulted in the detection of intra-repeat single nucleotide polymorphisms (SNPs) and novel repeat motif variants, which allow for a greater level of distinction than that of traditional CE methods [5–10] . For instance, two individuals with the same nominal allele(s) (based on length) at a certain locus potentially may be distinguished by MPS if the nucleotide sequence of the allele differs between them.…”

Section: Introductionmentioning

confidence: 99%

Novel Y-Chromosome Short Tandem Repeat Variants Detected through the use of Massively Parallel Sequencing

Warshauer

Churchill

Novroski

et al. 2015

Genomics, Proteomics &Amp; Bioinformatics

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Massively parallel sequencing (MPS) technology is capable of determining the sizes of short tandem repeat (STR) alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs) within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics). The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles.

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Section: Introductionmentioning

confidence: 99%

Novel Y-Chromosome Short Tandem Repeat Variants Detected through the use of Massively Parallel Sequencing

Warshauer

Churchill

Novroski

et al. 2015

Genomics, Proteomics &Amp; Bioinformatics

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“…Indeed, the DYS710 marker exhibited the highest allele number of 21 distinct alleles. This marker was one of the highest discriminatory markers in many populations’ particularly in three South African groups .…”

Section: Discussionmentioning

confidence: 99%

“…Three Y‐STRs primers for DYS456, DYS458, and DYS710 loci were chosen from published studies . We designed primers for the remaining Y‐STRs using Genome Browser, Primer3, and OligoExplorer softwares (primers sequences are available upon request).…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity and haplotype structure of 21 Y‐STRs, including nine noncore loci, in South Tunisian Population: Forensic relevance

et al. 2015

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Y chromosome STRs (Y-STRs) are being used frequently in forensic laboratories. Previous studies of Y-STR polymorphisms in different groups of the Tunisian population identified low levels of diversity and discrimination capacity (DC) using various commercial marker sets. This definitely limits the use of such systems for Y-STRs genotyping in Tunisia. In our investigation on South Tunisia, 200 unrelated males were typed for the 12 conventional Y-STRs included in the PowerPlex® Y System. Additional set of nine noncore Y-STRs including DYS446, DYS456, DYS458, DYS388, DYS444, DYS445, DYS449, DYS710, and DYS464 markers were genotyped and evaluated for their potential in improving DC. Allele frequency, gene diversity, haplotype diversity (HD), and DC calculation revealed that DYS464 was the most diverse marker followed by DYS710 and DYS449 markers. The standard panel of 12 Y-STRs (DC = 80.5%) and the nine markers were combined to obtain DC of 99%. Among the 198 different haplotypes observed, 196 haplotypes were unique (HD = 99.999). Out of the nine noncore set, six Y-STRs (DYS458, DYS456, DYS449, DYS710, DYS444, and DYS464) had the greatest impact on enhancing DC. Our data provided putative Y-STRs combination to be used for genetic and forensic applications.

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“…Both of these kits contain the core Y-STR loci advocated by the Scientific Working Group on DNA Analysis Methods (SWGDAM) and the European minimal haplotype [33]. A considerable amount of effort has since been dedicated to identifying additional Y-STR loci that may increase the discriminatory power of Yhaplotype data, as well as be more effective for amplification of challenged samples [34][35][36][37][38][39]. Both PowerPlex® Y23 (Promega) and Yfiler™ Plus (Thermo Fisher Scientific) are enhanced Y-STR multiplex kits that may increase the typing capability of Y-STRs in bone samples.…”

Section: Introductionmentioning

confidence: 99%

Improved Y-STR typing for disaster victim identification, missing persons investigations, and historical human skeletal remains

et al. 2018

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Bones are a valuable source of DNA in forensic, anthropological, and archaeological investigations. There are a number of scenarios in which the only samples available for testing are highly degraded and/or skeletonized. Often it is necessary to perform more than one type of marker analysis on such samples in order to compile sufficient data for identification. Lineage markers, such as Y-STRs and mitochondrial DNA (mtDNA), represent important systems to complement autosomal DNA markers and anthropological metadata in making associations between unidentified remains and living relatives or for characterization of the remains for historical and archaeological studies. In this comparative study, Y-STR typing with both Yfiler™ and Yfiler™ Plus (Thermo Fisher Scientific, Waltham, MA, USA) was performed on a variety of human skeletal remains, including samples from the American Civil War (1861-1865), the late nineteenth century gold rush era in Deadwood, SD, USA (1874-1877), the Seven Years' War (1756-1763), a seventeenth-century archaeological site in Raspenava, Bohemia (Czech Republic), and World War II (1939-1945). The skeletal remains used for this study were recovered from a wide range of environmental conditions and were extracted using several common methods. Regardless of the DNA extraction method used and the age/condition of the remains, 22 out of 24 bone samples yielded a greater number of alleles using the Yfiler™ Plus kit compared to the Yfiler™ kit using the same quantity of input DNA. There was no discernable correlation with the degradation index values for these samples. Overall, the efficacy of the Yfiler™ Plus assay was demonstrated on degraded DNA from skeletal remains. Yfiler™ Plus increases the discriminatory power over the previous generation multiplex due to the larger set of Y-STR markers available for analysis and buffer modifications with the newer version kit. Increased haplotype resolution is provided to infer or refute putative genetic relationships.

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Characterization of the highly discriminatory loci DYS449, DYS481, DYS518, DYS612, DYS626, DYS644 and DYS710

Cited by 37 publications

References 24 publications

Novel Y-Chromosome Short Tandem Repeat Variants Detected through the use of Massively Parallel Sequencing

Novel Y-Chromosome Short Tandem Repeat Variants Detected through the use of Massively Parallel Sequencing

Genetic diversity and haplotype structure of 21 Y‐STRs, including nine noncore loci, in South Tunisian Population: Forensic relevance

Improved Y-STR typing for disaster victim identification, missing persons investigations, and historical human skeletal remains

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