Next Generation Sequencing of Y-STRs in Father-Son Pairs and Comparison with Traditional Capillary Electrophoresis

Bredemeyer, Steffi; Roewer, Lutz; Willuweit, Sascha

doi:10.1080/20961790.2021.1898078

Cited by 6 publications

(10 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Sequence diversity could detect variations within alleles and distinguish iso-alleles, rather than just length. 7 Therefore, analyzing the highly polymorphic loci with complex/compound repeat structures having various combinations would be important in research on human genetic identification. 7 18 23 …”

Section: Discussionmentioning

confidence: 99%

“… 7 Therefore, analyzing the highly polymorphic loci with complex/compound repeat structures having various combinations would be important in research on human genetic identification. 7 18 23 …”

Section: Discussionmentioning

confidence: 99%

“…Recently, rapidly mutating Y-STRs (RM Y-STRs; average mutation rate per locus per generation > 10 −2 ) 4 with higher mutation rates (over 10-fold) than existing Y-STRs, have been demonstrated to be suitable for identifying male relatives in many studies. 4 5 6 7 8 9 All 13 known RM Y-STRs have shown the possibility of differentiating between closely related males, i.e., between father and son, as well as unrelated men. In 2010, Ballantyne et al 4 5 6 discovered these 13 RM Y-STRs, 4 and reported their superior performance in differentiating between closely and distantly related males compared to traditional Y-STR kits 5 ; a subsequent multi-center study showed the possibility of male individualization and male relative differentiation.…”

Section: Introductionmentioning

confidence: 99%

“…In 2010, Ballantyne et al 4 5 6 discovered these 13 RM Y-STRs, 4 and reported their superior performance in differentiating between closely and distantly related males compared to traditional Y-STR kits 5 ; a subsequent multi-center study showed the possibility of male individualization and male relative differentiation. 6 Bredemeyer et al 7 had also tested the 13 RM Y-STRs using a modified RM-Yplex 8 in 64 father-son pairs and identified possible mutations. Furthermore, the value of RM Y-STR set to distinguish paternal lineages had been demonstrated even from endogamous populations with low Y-STR diversity.…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, scrutinizing STRs using the MPS method would be more useful in cases of challenging samples, such as degraded DNA, 10 11 12 while increases in the number of alleles due to sequence variances have also been reported in many STR studies using MPS. 7 13 14 15 16 17 18 19 …”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Sequence Variations of 31 γ-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population

2022

View full text Add to dashboard Cite

Background Rapidly mutating (RM) Y-chromosomal short tandem repeats (Y-STRs) have been demonstrated to increase the possibility of distinguishing between male relatives due to a higher mutation rate than conventional Y-STRs. Massively parallel sequencing (MPS) can be useful for forensic DNA typing as it allows the detection of sequence variants of many forensic markers. Here, we present sequence variations of 31 Y-STRs including nine RM Y-STRs (DYF387S1, DYF399S1, DYF404S1, DYS449, DYS518, DYS570, DYS576, DYS612, and DYS627), their frequencies, distribution, and the gain in the number of alleles using MPS. Methods We constructed a multiplex MPS assay capable of simultaneously amplifying 32 Y-chromosomal markers, producing amplicons ranging from 85–274 bp. Barcoded libraries from 220 unrelated males from four populations—African Americans, Caucasians, Hispanics, and Koreans—were generated via two-step polymerase chain reaction and sequenced on a MiSeq system. Genotype concordance between the capillary electrophoresis (CE) and MPS method and sequence variation of Y-STRs were investigated. Results In total, 195 alleles were increased by MPS compared to CE-based alleles (261 to 456). The DYS518 marker showed the largest increase due to repeat region variation (a 3.69-fold increase). The highest increase in the number of alleles due to single nucleotide polymorphisms in the flanking region was found in DYF399S1. RM Y-STRs had more diverse sequences than conventional Y-STRs. Furthermore, null alleles were observed in DYS576 due to primer-binding site mutation, and allele drop-outs in DYS449 resulted from low marker coverage of less than the threshold. Conclusion The results suggest that the expanded and discriminative MPS assay could provide more genetic information for Y-STRs, especially for RM Y-STRs, and could advance male individualization. Compiling sequence-based Y-STR data for worldwide populations would facilitate the application of MPS in the field of forensic genetics and could be applicable in solving male-related forensic cases.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Sequence Variations of 31 γ-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population

2022

View full text Add to dashboard Cite

show abstract

Next generation sequencing: Forensic applications and policy considerations

Browne,

Freeman

2024

WIREs Forensic Science

View full text Add to dashboard Cite

Next generation sequencing (NGS) or massively parallel sequencing (MPS) is a high‐throughput technology that can be used to analyze DNA and RNA molecules with greater sensitivity, scalability, and speed than traditional Sanger sequencing. NGS systems are slowly gaining popularity in forensic science and may eventually become the future of forensic DNA analysis. The data generated can be utilized to conduct an array of forensic biology analyses such as short tandem repeats (STR) profiling, forensic genetic genealogy, predictive DNA phenotyping, and more. However, the adoption of NGS for forensic casework is associated with a lot of ethical, social, and legal concerns. This article provides a comprehensive review of NGS systems, data analysis, and forensic applications. It also provides policy considerations that aim to reduce harm and bias, while promoting informed consent, standardization, transparency, and accountability.This article is categorized under: Forensic Biology > Interpretation of Biological Evidence Forensic Biology > Ethical and Social Implications Forensic Biology > Forensic DNA Technologies

show abstract

Concordance study on Y-STRs typing between SeqStudio™ genetic analyzer for HID and MiSeq™ FGx forensic genomics system

Soldati,

Turrina,

Treccani

et al. 2023

Mol Biol Rep

View full text Add to dashboard Cite

Background Massively Parallel Sequencing (MPS) allowed an increased number of information to be retrieved from short tandem repeat (STR) analysis, expanding them not only to the size, as already performed in Capillary Electrophoresis (CE), but also to the sequence. MPS requires constant development and validation of the analytical parameters to ensure that the genotyping results of STRs correspond to those obtained by CE. Given the increased frequency of usage of Y-STRs as supplementary markers to the autosomal STRs analysis, it is urgent to validate the concordance of the typing results between CE and MPS analyses. Methods and results DNA extracted from 125 saliva samples of unrelated males was genotyped using Yfiler™ Plus PCR Amplification Kit and ForenSeq™ DNA Signature Prep Kit, which were analyzed by SeqStudio™ Genetic Analyzer for HID and MiSeq™ FGx Forensic Genomics System, respectively. For each shared Y-STR, allele designation, number of length- and sequence-based alleles per locus, stutter percentage, and the intra-locus balance of multicopy Y-STRs were screened. Conclusions Although the number of forensic genetics laboratories that are applying the MPS technique in routine analysis is small and does not allow a global assessment of MPS limitations, this comparative study highlights the ability of MPS to produce reliable profiles despite the generation of large amounts of raw data.

show abstract

Next Generation Sequencing of Y-STRs in Father-Son Pairs and Comparison with Traditional Capillary Electrophoresis

Cited by 6 publications

References 46 publications

Sequence Variations of 31 γ-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population

Sequence Variations of 31 γ-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population

Next generation sequencing: Forensic applications and policy considerations

Concordance study on Y-STRs typing between SeqStudio™ genetic analyzer for HID and MiSeq™ FGx forensic genomics system

Contact Info

Product

Resources

About