Highlights
- •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.
Abstract
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.
Keywords
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Article info
Publication history
Published online: October 03, 2014
Accepted:
September 23,
2014
Received in revised form:
August 20,
2014
Received:
June 16,
2014
Identification
Copyright
© 2014 Elsevier Ireland Ltd. Published by Elsevier Inc. All rights reserved.
