Massive parallel sequencing of human whole mitochondrial genomes with Ion Torrent technology: an optimized workflow for Anthropological and Population Genetics studies

Sara De Fanti, Dario Vianello, Cristina Giuliani, Andrea Quagliariello, Anna Cherubini, Federica Sevini, Nicoletta Iaquilano, Claudio Franceschi, Marco Sazzini, Donata Luiselli

Research output: Contribution to journalArticle

Abstract

Investigation of human mitochondrial DNA variation patterns and phylogeny has been extensively used in Anthropological and Population Genetics studies and sequencing the whole mitochondrial genome is progressively becoming the gold standard. Among the currently available massive parallel sequencing technologies, Ion Torrent™ semiconductor sequencing represents a promising approach for such studies. Nevertheless, an experimental protocol conceived to enable the achievement of both as high as possible yield and of the most homogeneous sequence coverage through the whole mitochondrial genome is still not available. The present work was thus aimed at improving the overall performance of whole mitochondrial genomes Ion Torrent™ sequencing, with special focus on the capability to obtain robust coverage and highly reliable variants calling. For this purpose, a series of cost-effective modifications in standard laboratory workflows was fine-tuned to optimize them for medium- and large-scale population studies. A total of 54 human samples were thus subjected to sequencing of the whole mitochondrial genome with the Ion Personal Genome Machine™ System in four distinct experiments and using Ion 314 chips. Seven of the selected samples were also characterized by means of conventional Sanger sequencing for the sake of comparison. Obtained results demonstrated that the implemented optimizations had definitely improved sequencing outputs in terms of both variants calling efficiency and coverage uniformity, enabling to setup an effective and accurate protocol for whole mitochondrial genome sequencing and a considerable reduction in experimental time consumption and sequencing costs.

Original languageEnglish
Pages (from-to)1-8
Number of pages8
JournalMitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis
DOIs
Publication statusAccepted/In press - Oct 31 2016

Keywords

  • Anthropological genetics
  • human whole mitochondrial genomes
  • ion torrent sequencing
  • massive parallel sequencing
  • population genetics

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

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