Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM)
Forensic Science International: Genetics
Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, United States; Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal; Division of Human Genetics, Innsbruck Medical University, Innsbruck, Austria; Department of Chemical Pathology, School of Medicine, University of Pretoria, South Africa; Life Technologies, Foster City, CA, United States; FBI Laboratory, Quantico, VA, United States
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 64 mtGenomes (>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. © 2013 Elsevier Ireland Ltd. All rights reserved.
mitochondrial DNA; article; comparative study; gene sequence; haplotype; heteroplasmy; human; human genome; priority journal; sequence alignment; Forensic science; Heteroplasmy; mtDNA genomes; Next Generation Sequencing; PGM; Sanger-type sequencing; Algorithms; DNA, Mitochondrial; Forensic Genetics; Genome, Human; Genome, Mitochondrial; Haplotypes; High-Throughput Nucleotide Sequencing; Humans; Sequence Alignment; Sequence Analysis, DNA
2011-MU-MU-K402, NIJ, National Institute of Justice