The Y chromosomal haplogroup determined from single nucleotide polymorphism (SNP) combinations is a valuable genetic marker to study ancestral male lineage and ethical distribution. Next-generation sequencing has been developed for widely diverse genetics fields. For this study, we demonstrate 34 Y-SNP typing employing the Ion PGM™ system to perform haplogrouping. DNA libraries were constructed using the HID-Ion AmpliSeq™ Identity Panel. Emulsion PCR was performed, then DNA sequences were analyzed on the Ion 314 and 316 Chip Kit v2. Some difficulties became apparent during the analytic processes. No-call was reported at rs2032599 and M479 in six samples, in which the least coverage was observed at M479. A minor misreading occurred at rs2032631 and M479. A real time PCR experiment using other pairs of oligonucleotide primers showed that these events might result from the flanking sequence. Finally, Y haplogroup was determined completely for 81 unrelated males including Japanese (n=59) and Malay (n=22) subjects. The allelic divergence differed between the two populations. In comparison with the conventional Sanger method, next-generation sequencing provides a comprehensive SNP analysis with convenient procedures, but further system improvement is necessary.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.legalmed.2016.08.001 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Testing the informativeness of Y-STR and mitochondrial DNA control region markers in an attempt to predict ancestry of World War II victims from Slovenian mass grave.
Int J Legal Med
November 2024
Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, Ljubljana, 1000, Slovenia.
Identification of human remains is a challenge in forensic genetics without relatives or personal items available. In Slovenia, a Konfin II mass grave from the Second World War (WWII) was found, containing skeletal remains of 65 victims. The archival documents detailing victims' information describe 45 persons of which 33 could be considered Germanic and 12 Slavic.
View Article and Find Full Text PDFApplications and Performance of Precision ID GlobalFiler NGS STR, Identity, and Ancestry Panels in Forensic Genetics.
Genes (Basel)
August 2024
School of Natural Sciences, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, UK.
Short Tandem Repeat (STR) testing via capillary electrophoresis is undoubtedly the most popular forensic genetic testing method. However, its low multiplexing capabilities and limited performance with challenging samples are among the factors pushing scientists towards new technologies. Next-generation sequencing (NGS) methods overcome some of these limitations while also enabling the testing of Single-Nucleotide Polymorphisms (SNPs).
View Article and Find Full Text PDFComparison of the optimal and suboptimal quantity of mitotype libraries using next-generation sequencing.
Int J Legal Med
March 2024
Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
Optimizing analysis parameters and sample input is crucial in forensic genetics methods to generate reliable results, and even more so when working with muti-copy mitochondrial DNA (mtDNA) and low-quality samples. This study compared mitotypes based on next-generation sequencing (NGS) results derived from the same samples at two different sequencing library concentrations-30 pM and 0.3 pM.
View Article and Find Full Text PDFA Multisample Approach in Forensic Phenotyping of Chronological Old Skeletal Remains Using Massive Parallel Sequencing (MPS) Technology.
Genes (Basel)
July 2023
Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
Article Synopsis
- Reliable phenotypic results are crucial for identifying missing persons from old skeletal remains, especially in WWII cases.
- Three bones from each of the eight analyzed skeletons were used to create a consensus profile for accurate pigmentation predictions.
- Advanced techniques like the PowerQuant System and customized HIrisPlex panel led to consistent predictions of eye and hair color across the samples, demonstrating the effectiveness of multisample analysis.
Eye and hair color prediction of an early medieval adult and subadult skeleton using massive parallel sequencing technology.
Int J Legal Med
September 2023
Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia.
Phenotypic trait prediction in ancient DNA analysis can provide information about the external appearance of individuals from past human populations. Some studies predicting eye and hair color in ancient adult skeletons have been published, but not for ancient subadult skeletons, which are more prone to decay. In this study, eye and hair color were predicted for an early medieval adult skeleton and a subadult skeleton that was anthropologically characterized as a middle-aged man and a subadult of unknown sex about 6 years old.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!