Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel

Strobl C 1 , Churchill Cihlar J 2 , Lagacé R 3 , Wootton S 3 , Roth C 3 , Huber N 1 Show all authors , Schnaller L 1 , Zimmermann B 1 , Huber G 1 , Lay Hong S 4 , Moura-Neto R 5 , Silva R 6 , Alshamali F 7 , Souto L 8 , Anslinger K 9 , Egyed B 10 , Jankova-Ajanovska R 11 , Casas-Vargas A 12 , Usaquén W 12 , Silva D 13 , Barletta-Carrillo C 14 , Tineo DH 15 , Vullo C 16 , Würzner R 17 , Xavier C 1 , Gusmão L 13 , Niederstätter H 1 , Bodner M 1 , Budowle B 2 , Parson W 18

Affiliations 

  • 1 Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
  • 2 Center for Human Identification, University of North Texas Health Science Center, TX, USA
  • 3 Human Identification Group, ThermoFisher Scientific, San Francisco, CA, USA
  • 4 School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
  • 5 Laboratório de Biologia Molecular Forense, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
  • 6 Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
  • 7 Dubai Police, Gen. Dept. Forensic Science & Criminology, Dubai, United Arab Emirates
  • 8 Laboratorio de Genética Aplicada, Departamento de Biologia, Universidade de Aveiro, Portugal
  • 9 Institute of Legal Medicine, University of Munich, Germany
  • 10 Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
  • 11 Institute of Forensic Medicine, Criminalistic and Medical Deontology, Medical Faculty, University "St. Cyril and Methodius", Skopje, Macedonia
  • 12 Group of Population Genetics and Identification, Genetics Institute, National University of Colombia, Bogotá, Colombia
  • 13 DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
  • 14 Laboratorio de Genética Humana, Universidad Nacional Mayor de San Marcos, Lima, Peru
  • 15 Universidad Nacional Mayor de San Marcos, Instituto de Medicina Legal del Perú, Lima, Peru
  • 16 DNA Forensic Laboratory, Argentinean Forensic Anthropology team (EAAF), Córdoba, Argentina
  • 17 Division of Hygiene & Med. Microbiology, Medical University of Innsbruck, Austria
  • 18 Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA. Electronic address: [email protected]
Forensic Sci Int Genet, 2019 09;42:244-251.
PMID: 31382159 DOI: 10.1016/j.fsigen.2019.07.013

Abstract

The emergence of Massively Parallel Sequencing technologies enabled the analysis of full mitochondrial (mt)DNA sequences from forensically relevant samples that have, so far, only been typed in the control region or its hypervariable segments. In this study, we evaluated the performance of a commercially available multiplex-PCR-based assay, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific), for the amplification and sequencing of the entire mitochondrial genome (mitogenome) from even degraded forensic specimens. For this purpose, more than 500 samples from 24 different populations were selected to cover the vast majority of established superhaplogroups. These are known to harbor different signature sequence motifs corresponding to their phylogenetic background that could have an effect on primer binding and, thus, could limit a broad application of this molecular genetic tool. The selected samples derived from various forensically relevant tissue sources and were DNA extracted using different methods. We evaluated sequence concordance and heteroplasmy detection and compared the findings to conventional Sanger sequencing as well as an orthogonal MPS platform. We discuss advantages and limitations of this approach with respect to forensic genetic workflow and analytical requirements.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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