title: Reprint of: Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM).
abstract: Insights into the human mitochondrial phylogeny have been primarily achieved by sequencing full mitochondrial genomes (mtGenomes). In forensic genetics (partial) mtGenome information can be used to assign haplotypes to their phylogenetic backgrounds, which may, in turn, have characteristic geographic distributions that would offer useful information in a forensic case. In addition and perhaps even more relevant in the forensic context, haplogroup-specific patterns of mutations form the basis for quality control of mtDNA sequences. The current method for establishing (partial) mtDNA haplotypes is Sanger-type sequencing (STS), which is laborious, time-consuming, and expensive. With the emergence of Next Generation Sequencing (NGS) technologies, the body of available mtDNA data can potentially be extended much more quickly and cost-efficiently. Customized chemistries, laboratory workflows and data analysis packages could support the community and increase the utility of mtDNA analysis in forensics. We have evaluated the performance of mtGenome sequencing using the Personal Genome Machine (PGM) and compared the resulting haplotypes directly with conventional Sanger-type sequencing. A total of 64mtGenomes (>1 million bases) were established that yielded high concordance with the corresponding STS haplotypes (<0.02% differences). About two-thirds of the differences were observed in or around homopolymeric sequence stretches. In addition, the sequence alignment algorithm employed to align NGS reads played a significant role in the analysis of the data and the resulting mtDNA haplotypes. Further development of alignment software would be desirable to facilitate the application of NGS in mtDNA forensic genetics.
authors.affiliation: Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA. Electronic address: walther.parson@i-med.ac.at.
authors.forename: Walther
authors.initials: W
authors.lastname: Parson
authors.affiliation: Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
authors.forename: Christina
authors.initials: C
authors.lastname: Strobl
authors.affiliation: Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Huber
authors.affiliation: Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
authors.forename: Bettina
authors.initials: B
authors.lastname: Zimmermann
authors.affiliation: Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
authors.forename: Sibylle M
authors.initials: SM
authors.lastname: Gomes
authors.affiliation: Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
authors.forename: Luis
authors.initials: L
authors.lastname: Souto
authors.affiliation: Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Division of Human Genetics, Innsbruck Medical University, Innsbruck, Austria.
authors.forename: Liane
authors.initials: L
authors.lastname: Fendt
authors.affiliation: Department of Chemical Pathology, School of Medicine, University of Pretoria, South Africa.
authors.forename: Rhena
authors.initials: R
authors.lastname: Delport
authors.affiliation: Life Technologies, Foster City, CA, USA.
authors.forename: Reina
authors.initials: R
authors.lastname: Langit
authors.affiliation: Life Technologies, Foster City, CA, USA.
authors.forename: Sharon
authors.initials: S
authors.lastname: Wootton
authors.affiliation: Life Technologies, Foster City, CA, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Lagacé
authors.affiliation: FBI Laboratory, Quantico, VA, USA.
authors.forename: Jodi
authors.initials: J
authors.lastname: Irwin
keywords: Forensic science; Heteroplasmy; Next Generation Sequencing; PGM; Sanger-type sequencing; mtDNA genomes