Original scientific paper
https://doi.org/10.3325/cmj.2015.56.218
Blind study evaluation illustrates utility of the Ion PGM™ system for use in human identity DNA typing
Jennifer D. Churchill
; Institute of Applied Genetics Department of Molecular and Medical Genetics, University of North Texas Health Science Center Fort Worth, TX, USA
Joseph Chang
; Human Identification, Thermo Fisher Scientific, South San Francisco, CA, USA
Jianye Ge
; Human Identification, Thermo Fisher Scientific, South San Francisco, CA, USA
Narasimhan Rajagopalan
; Human Identification, Thermo Fisher Scientific, South San Francisco, CA, USA
Sharon C. Wootton
; Human Identification, Thermo Fisher Scientific, South San Francisco, CA, USA
Chien-Wei Chang
; Human Identification, Thermo Fisher Scientific, South San Francisco, CA, USA
Robert Lagacé
; Human Identification, Thermo Fisher Scientific, South San Francisco, CA, USA
Jonathan L. King
; Institute of Applied Genetics Department of Molecular and Medical Genetics, University of North Texas Health Science Center Fort Worth, TX, USA
Bruce Budowle
; Institute of Applied Genetics Department of Molecular and Medical Genetics, University of North Texas Health Science Center Fort Worth, TX, USA
Abstract
Aim To perform a blind study to assess the capability of
the Ion Personal Genome Machine® (PGM™) system to sequence
forensically relevant genetic marker panels and to
characterize unknown individuals for ancestry and possible
relatedness.
Methods Twelve genomic samples were provided by a
third party for blinded genetic analysis. For these 12 samples,
the mitochondrial genome and three PGM™ panels
containing human identity single nucleotide polymorphisms
(SNPs), ancestry informative SNPs, and short tandem
repeats (STRs) were sequenced on the PGM™ system
and analyzed.
Results All four genetic systems were run and analyzed on
the PGM™ system in a reasonably quick time frame. Completeness
of genetic profiles, depth of coverage, strand
balance, and allele balance were informative metrics that
illustrated the quality and reliability of the data produced.
SNP genotypes allowed for identification of sex, paternal
lineage, and population ancestry. STR genotypes were
shown to be in complete concordance with genotypes
generated by standard capillary electrophoresis-based
technologies. Variants in the mitochondrial genome data
provided information on population background and maternal
relationships.
Conclusion All results from analysis of the 12 genomic
samples were consistent with sample information provided
by the sample providers at the end of the blinded study.
The relatively easy identification of intra-STR allele SNPs offered
the potential for increased discrimination power. The
promising nature of these results warrants full validation
studies of this massively parallel sequencing technology
and its further development for forensic data analysis.
Keywords
Hrčak ID:
144067
URI
Publication date:
15.6.2015.
Visits: 1.591 *