Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/97339
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Type: Journal article
Title: From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes
Author: Clarke, A.
Prost, S.
Stanton, J.
White, W.
Kaplan, M.
Matisoo-Smith, E.
Genographic Consortium
Citation: BMC Genomics, 2014; 15(1):68-1-68-12
Publisher: BioMed Central
Issue Date: 2014
ISSN: 1471-2164
1471-2164
Statement of
Responsibility: 
Andrew C Clarke, Stefan Prost, Jo-Ann L Stanton, W Timothy J White, Matthew E Kaplan, Elizabeth A Matisoo-Smith, and The Genographic Consortium
Abstract: BACKGROUND: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users. RESULTS: Here we present an 'A to Z' protocol for obtaining complete human mitochondrial (mtDNA) genomes - from DNA extraction to consensus sequence. Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling). CONCLUSIONS: All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. The molecular steps are scalable to large numbers (hundreds) of individuals and all steps post-DNA extraction can be carried out in 96-well plate format. Also, the protocol has been assembled so that individual 'modules' can be swapped out to suit available resources.
Keywords: Genographic Consortium; Mitochondria; Humans; DNA, Mitochondrial; Specimen Handling; Polymerase Chain Reaction; Computational Biology; Genome, Mitochondrial; High-Throughput Nucleotide Sequencing
Description: Genographic Consortium Contributors: Alan Cooper and Wolfgang Haak for the University of Adelaide
Rights: © 2014 Clarke et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
RMID: 0030017720
DOI: 10.1186/1471-2164-15-68
Appears in Collections:Genetics publications

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