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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Reprint of: Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM)
Forensic Science International: Genetics, Volume 7, No. 6, Year 2013
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Description
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 The authors.
Authors & Co-Authors
Parson, Walther
Austria, Innsbruck
Medizinische Universitat Innsbruck
United States, University Park
Eberly College of Science
Strobl, Christina
Austria, Innsbruck
Medizinische Universitat Innsbruck
Huber, Gabriela
Austria, Innsbruck
Medizinische Universitat Innsbruck
Zimmermann, Bettina
Austria, Innsbruck
Medizinische Universitat Innsbruck
Gomes, Sibylle M.
Portugal, Aveiro
Universidade de Aveiro
Souto, Luis
Portugal, Aveiro
Universidade de Aveiro
Fendt, Liane
Austria, Innsbruck
Medizinische Universitat Innsbruck
Delport, Rhena
South Africa, Pretoria
University of Pretoria
Langit, Reina
United States, Foster City
Life Technologies
Wootton, Sharon
United States, Foster City
Life Technologies
Lagacé, Robert
United States, Foster City
Life Technologies
Irwin, Jodi A.
United States, Quantico
Fbi Laboratory
Statistics
Citations: 15
Authors: 12
Affiliations: 6
Identifiers
Doi:
10.1016/j.fsigen.2013.09.007
ISSN:
18724973
e-ISSN:
18780326
Research Areas
Genetics And Genomics