Evaluation of Y chromosomal SNP haplogrouping in the HID-Ion AmpliSeq™ Identity Panel
| Autor: | Keiko Miyashita, Yu Kakimoto, Masato Nakatome, Kiyoshi Minaguchi, Motoki Osawa, Phrabhakaran Nambiar, Fumiko Satoh, Eriko Ochiai |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Forensic Genetics Male Sequence analysis Human Y-chromosome DNA haplogroup Population Single-nucleotide polymorphism Biology Polymorphism Single Nucleotide DNA sequencing Haplogroup Pathology and Forensic Medicine 03 medical and health sciences symbols.namesake 0302 clinical medicine Genes Y-Linked Japan Humans 030216 legal & forensic medicine education Sanger sequencing Genetics education.field_of_study High-Throughput Nucleotide Sequencing Sequence Analysis DNA DNA Fingerprinting Issues ethics and legal aspects 030104 developmental biology Genetics Population symbols SNP array |
| Zdroj: | Legal medicine (Tokyo, Japan). 22 |
| ISSN: | 1873-4162 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full Text from ScienceDirect