Evaluation of Next Generation mtGenome Sequencing Using the Ion Torrent Personal Genome Machine PGM

• NCJ Number: 246423
• Journal: Forensic Science International: Genetics Volume: 7 Issue: 5 Dated: September 2013 Pages: 543-549
• Author(s): Walther Parson; Christina Strobl; Gabriela Huber; Bettina Zimmermann; Sibylle M. Gomes; Luis Souto; Liane Fendt; Rhena Delport; Reina Langit; Sharon Woott; Robert Lagace; Jodi Irwin
• Date Published: September 2013
• Length: 8 pages
• Grant Number(s): 2011-MU-MU-K402
• Sponsoring Agency: National Institute of Justice (NIJ)
• Publication Format: Article
• Publication Type: Report (Study/Research)
• Language: English
• Country: United States of America

Annotation

Insights into the human mitochondrial phylogeny have been primarily achieved by sequencing full mitochondrial genomes mtGenomes.

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 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.