- •STR typing on the Ion PGM™ using the Ion Torrent™ HID STR 10-plex resulted in full concordance for 10 control samples typed in duplicate.
- •Sensitivity: >50 pg.
- •Allele and locus balance was below the current standard for PCR-CE assays.
- •Detection was possible for 20:1 mixtures.
- •This panel was able to produce full profiles for crime case samples from real crime cases where only partial profiles were obtained with the PCR-CE assays.
Second-generation sequencing (SGS) using Roche/454 and Illumina platforms has proved capable of sequencing the majority of the key forensic genetic STR systems. Given that Roche has announced that the 454 platforms will no longer be supported from 2015, focus should now be shifted to competing SGS platforms, such as the MiSeq (Illumina) and the Ion Personal Genome Machine (Ion PGM™; Thermo Fisher). There are currently several challenges faced with amplicon-based SGS STR typing in forensic genetics, including current lengths of amplicons for CE-typing and lack of uniform data analysis between laboratories.
Thermo Fisher has designed a human identification (HID) short tandem repeat (STR) 10-plex panel including amelogenin, CSF1PO, D16S539, D3S1358, D5S818, D7S820, D8S1179, TH01, TPOX and vWA, where the primers have been designed specifically for the purpose of SGS and the data analysis is supported by Ion Torrent™ software. Hence, the combination of the STR 10-plex and the Ion PGM™ represents the first fully integrated SGS STR typing solution from PCR to data analysis.
In this study, four experiments were performed to evaluate the alpha-version of the STR 10-plex: (1) typing of control samples; (2) analysis of sensitivity; (3) typing of mixtures; and (4) typing of biological crime case samples. Full profiles and concordant results between replicate SGS runs and CE-typing were observed for all control samples. Full profiles were seen with DNA input down to 50 pg, with the exception of a single locus drop-out in one of the 100 pg dilutions. Mixtures were easily deconvoluted down to 20:1, although alleles from the minor contributor had to be identified manually as some signals were not called by the Ion Torrent™ software. Interestingly, full profiles were obtained for all biological samples from real crime and identification cases, in which only partial profiles were obtained with PCR-CE assays. In conclusion, the Ion Torrent™ HID STR 10-plex panel offers an all-in-one solution from amplification of STRs and amelogenin, and sequencing to data analysis.
To read this article in full you will need to make a payment
Purchase one-time access:Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
One-time access price info
- For academic or personal research use, select 'Academic and Personal'
- For corporate R&D use, select 'Corporate R&D Professionals'
Subscribe:Subscribe to Forensic Science International: Genetics
Already a print subscriber? Claim online access
Already an online subscriber? Sign in
Register: Create an account
Institutional Access: Sign in to ScienceDirect
- Non-uniform phenotyping of D12S391 resolved by second generation sequencing.Forensic Sci. Int. Genet. 2014; 8: 195-199
- Characterization of mutations and sequence variants in the D21S11 locus by next generation sequencing.Forensic Sci. Int. Genet. 2014; 8: 68-72
- My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing.Forensic Sci. Int. Genet. 2014; 9: 1-8
- Comparing six commercial autosomal STR kits in a large Dutch population sample.Forensic Sci. Int. Genet. 2014; 10: 55-63
- Short tandem repeat typing on the 454 platform: strategies and considerations for targeted sequencing of common forensic markers.Forensic Sci. Int. Genet. 2014; 12: 107-109
- Second generation sequencing of three complex STRs D3S1358, D21S11 and D12S391 in Danes and a proposal for nomenclature of sequenced STR alleles.Forensic Sci. Int. Genet. 2014; 12: 38-41
- Concordance study and population frequencies for 16 autosomal STRs analyzed with Powerplex® ESI 17 and AmpFLSTR® NGMSelect™ in Somalis, Danes and Greenlanders.Forensic Sci. Int. Genet. 2014; 11: e18-e21
- STRait razor: a length-based forensic STR allele-calling tool for use with second generation sequencing data.Forensic Sci. Int. Genet. 2013; 7: 409-417
- Short-read, high-throughput sequencing technology for STR genotyping.Biotechniques. 2012; : 1-6https://doi.org/10.2144/000113857
- Forensic STR analysis using massive parallel sequencing.Forensic Sci. Int. Genet. 2012; 6: 810-818
- Second generation sequencing allows for mtDNA mixture deconvolution and high resolution detection of heteroplasmy.Croat. Med. J. 2011; 52: 299-313
- High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform.Biotechniques. 2011; 51: 127-133
- An integrated semiconductor device enabling non-optical genome sequencing.Nature. 2011; 475: 348-352
- Single nucleotide polymorphism typing with massively parallel sequencing for human identification.Int. J. Legal Med. 2013; 127: 1079-1086
- 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
- Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing.Mol. Ecol. Resour. 2014; 14: 554-568
- Rapid development of microsatellite markers for the endangered fish Schizothorax biddulphi (Gunther) using next generation sequencing and cross-species amplification.Int. J. Mol. Sci. 2012; 13: 14946-14955
- Examination of the variability in mixed DNA profile parameters for the Identifiler™ multiplex.Forensic Sci. Int. Genet. 2010; 4: 111-114
- Performance of two 17 locus forensic identification STR kits – Applied Biosystems's AmpFlSTR® NGMSElect™ and Promega's PowerPlex® ESI17 kits.Forensic Sci. Int. Genet. 2012; 6: 523-531
- Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PMG).Forensic Sci. Int. Genet. 2013; 7: 543-549
Published online: October 03, 2014
Accepted: September 23, 2014
Received in revised form: August 20, 2014
Received: June 16, 2014
© 2014 Elsevier Ireland Ltd. Published by Elsevier Inc. All rights reserved.