- •Multiplex STR genotyping of 10 autosomal STRs is feasible by Ion PGM™ system.
- •Sequence variations of 10 autosomal STR loci in 165 Chinese individuals were presented, and 8 new alleles of STR loci were observed.
- •D3S1358, D2S441, D19S433 and D7S820 demonstrated an increased allele number obtained by MPS typing compared to CE typing.
- •D13S317, D5S818 and D7S820 displayed variants adjacent to the core repeats and caused discordances between MPS and CE typing results.
- •D13S317, D16S539, D2S441, D5S818, D7S820 and TPOX displayed significant variations in the flanking regions.
Massively parallel sequencing (MPS) technology is gaining interest in the forensic community. The capabilities of high throughput and simultaneously analyses of many markers enable MPS as an attractive method for human forensics. Recent studies have demonstrated the successful application of the MPS system to short tandem repeat (STR) typing. However, not only DNA sequence variations in the repeat regions of STR but also in flanking regions are required to facilitate profiles sharing with capillary electrophoresis (CE)-based typing method. In this study, we constructed a multiplex PCR system for the MPS analysis of 10 autosomal STR loci (D13S317, D16S539, D19S433, D2S441, D3S1358, D5S818, D6S1043, D7S820, TH01, TPOX) by designing amplicons in the size range of 168–273 base pairs. Sequencing results from 165 Chinese unrelated individuals demonstrated 11 variations in the flanking regions between amplification primer binding sites and core repeat motifs. In addition, three loci, D13S317, D5S818, and D7S820, displayed variants adjacent to the core repeats and caused discordances between sequence-based and length-based typing results. Four loci (D3S1358, D2S441, D19S433 and D7S820) demonstrated an increased allele number using MPS-based typing. This study demonstrated that STR typing by MPS could provide more genetic information from both repeat and flanking regions of STR loci, thus improving the diversity and discrimination power of the system in forensic detection.
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- New turns from old STaRs: enhancing the capabilities of forensic short tandem repeat analysis.Electrophoresis. 2014; 35: 3173-3187
- STR allele sequence variation: current knowledge and future issues.Forensic Sci. Int. Genet. 2015; 18: 118-130
- Sequence variation of 22 autosomal STR loci detected by next generation sequencing.Forensic Sci. Int. Genet. 2015; 21: 15-21
- Automated analysis of sequence polymorphism in STR alleles by PCR and direct electrospray ionization mass spectrometry.Forensic Sci. Int. Genet. 2012; 6: 594-606
- Evaluation of the Illumina® beta version ForenSeq™ DNA signature prep kit for use in genetic profiling.Forensic Sci. Int. Genet. 2016; 20: 20-29
- Characterization of mutations and sequence variants in the D21S11 locus by next generation sequencing.Forensic Sci. Int. Genet. 2014; 8: 68-72
- High sensitivity multiplex short tandem repeat loci analyses with massively parallel sequencing.Forensic Sci. Int. Genet. 2015; 16: 38-47
- An evaluation of the PowerSeq™ Auto System: a multiplex short tandem repeat marker kit compatible with massively parallel sequencing.Forensic Sci. Int. Genet. 2015; 19: 172-179
- Second-generation sequencing of forensic STRs using the ion torrent™ HID STR 10-plex and the ion PGM™.Forensic Sci. Int. Genet. 2015; 14: 132-140
- Next generation sequencing and its applications in forensic genetics.Forensic Sci. Int. Genet. 2015; 18: 78-89
- Short tandem repeat typing on the 454 platform: strategies and considerations for targeted sequencing of common forensic markers.Forensic Sci. Int. Genet. 2014; 12: 107-119
- Second generation sequencing of three STRs D3S1358: D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR alleles.Forensic Sci. Int. Genet. 2014; 12: 38-41
- The next dimension in STR sequencing: polymorphisms in flanking regions and their allelic associations.Forensic Sci. Int. Genet. 2015; https://doi.org/10.1016/j.fsigss.2015.09.049
- Primer3Plus, an enhanced web interface to Primer3.Nucleic Acids Res. 2007; 35: W71-W74
- Y-STRs analysis using the ion torrent personal genome machine (PGM).Forensic Sci. Int. Genet. 2015; 19: 192-196
- Massively parallel sequencing of forensic STRs: considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements.Forensic Sci. Int. Genet. 2016; 22: 54-63
- Evaluation of the Ion Torrent™ HID SNP 169-plex: a SNP typing assay developed for human identification by second generation sequencing.Forensic Sci. Int. Genet. 2014; 12: 144-154
- Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons.Forensic Sci. Int. Genet. 2016; 22: 1-7
- Forensic Loci Allele Database (FLAD): Automatically generated: permanent identifiers for sequenced forensic alleles.Forensic Sci. Int. Genet. 2016; 20: 1-3
- Evaluation of next generation mtGenome sequencing using the ion torrent personal genome machine (PGM).Forensic Sci. Int. Genet. 2013; 7: 632-639
- Performance comparison of benchtop high-throughput sequencing platforms.Nat. Biotechnol. 2012; 30: 434-439
Published online: July 30, 2016
Accepted: July 27, 2016
Received in revised form: July 13, 2016
Received: March 3, 2016
© 2016 Elsevier Ireland Ltd. All rights reserved.