title: Evaluation of Y chromosomal SNP haplogrouping in the HID-Ion AmpliSeq™ Identity Panel.
abstract: 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.
authors: Department of Forensic Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan.
authors: Eriko
authors: E
authors: Ochiai
authors: Department of Forensic Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan.
authors: Kiyoshi
authors: K
authors: Minaguchi
authors: Department of Diagnostic and Integrated Dental Practice, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.
authors: Phrabhakaran
authors: P
authors: Nambiar
authors: Department of Forensic Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan.
authors: Yu
authors: Y
authors: Kakimoto
authors: Department of Legal Medicine, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan.
authors: Fumiko
authors: F
authors: Satoh
authors: Department of Forensic Dental Science, Unit of Social Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
authors: Masato
authors: M
authors: Nakatome
authors: Department of Forensic Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan.
authors: Keiko
authors: K
authors: Miyashita
authors: Department of Forensic Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan. Electronic address: osawa@is.icc.u-tokai.ac.jp.
authors: Motoki
authors: M
authors: Osawa
mesh_terms: D016172:DNA Fingerprinting / Q000379:methods; D053803:Forensic Genetics / Q000379:methods*; D050173:Genes, Y-Linked / Q000235:genetics*; D005828:Genetics, Population; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D007564:Japan; D008297:Male; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: Ethnic distribution; Ion PGM™; Japanese; Malay; Next-generation sequencing; Y-SNPs