Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/83202
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Type: Journal article
Title: DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification
Author: Templeton, J.
Brotherton, P.
Llamas, B.
Soubrier, J.
Haak, W.
Cooper, A.
Austin, J.
Citation: Investigative Genetics, 2013; 4(26):1-13
Publisher: BioMed Central Ltd
Issue Date: 2013
ISSN: 2041-2223
2041-2223
Statement of
Responsibility: 
Jennifer E L Templeton, Paul M Brotherton, Bastien Llamas, Julien Soubrier, Wolfgang Haak, Alan Cooper and Jeremy J Austin
Abstract: BACKGROUND Mitochondrial DNA (mtDNA) typing can be a useful aid for identifying people from compromised samples when nuclear DNA is too damaged, degraded or below detection thresholds for routine short tandem repeat (STR)-based analysis. Standard mtDNA typing, focused on PCR amplicon sequencing of the control region (HVS I and HVS II), is limited by the resolving power of this short sequence, which misses up to 70% of the variation present in the mtDNA genome. METHODS We used in-solution hybridisation-based DNA capture (using DNA capture probes prepared from modern human mtDNA) to recover mtDNA from post-mortem human remains in which the majority of DNA is both highly fragmented (<100 base pairs in length) and chemically damaged. The method ‘immortalises’ the finite quantities of DNA in valuable extracts as DNA libraries, which is followed by the targeted enrichment of endogenous mtDNA sequences and characterisation by next-generation sequencing (NGS). RESULTS We sequenced whole mitochondrial genomes for human identification from samples where standard nuclear STR typing produced only partial profiles or demonstrably failed and/or where standard mtDNA hypervariable region sequences lacked resolving power. Multiple rounds of enrichment can substantially improve coverage and sequencing depth of mtDNA genomes from highly degraded samples. The application of this method has led to the reliable mitochondrial sequencing of human skeletal remains from unidentified World War Two (WWII) casualties approximately 70 years old and from archaeological remains (up to 2,500 years old). CONCLUSIONS This approach has potential applications in forensic science, historical human identification cases, archived medical samples, kinship analysis and population studies. In particular the methodology can be applied to any case, involving human or non-human species, where whole mitochondrial genome sequences are required to provide the highest level of maternal lineage discrimination. Multiple rounds of in-solution hybridisation-based DNA capture can retrieve whole mitochondrial genome sequences from even the most challenging samples.
Keywords: Mitochondrial DNA; Degraded DNA; Ancient DNA; DNA hybridisation; DNA enrichment; Forensic science; Next-generation sequencing
Rights: © 2013 Templeton 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.
RMID: 0020137144
DOI: 10.1186/2041-2223-4-26
Appears in Collections:Earth and Environmental Sciences publications

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