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Type: Journal article
Title: Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions
Author: Brotherton, P.
Endicott, P.
Sanchez, J.
Beaumont, M.
Barnett, R.
Austin, J.
Cooper, A.
Citation: Nucleic Acids Research, 2007; 35(17):5717-5728
Publisher: Oxford Univ Press
Issue Date: 2007
ISSN: 0305-1048
Statement of
Paul Brotherton, Phillip Endicott, Juan J. Sanchez, Mark Beaumont, Ross Barnett, Jeremy Austin and Alan Cooper
Abstract: Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C > U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy.
Keywords: Animals; Humans; DNA Damage; Cytosine; Uracil; Guanine; Taq Polymerase; DNA; Adenosine; DNA Primers; Nucleic Acid Amplification Techniques; Polymerase Chain Reaction; Sequence Analysis, DNA; DNA Fragmentation; Templates, Genetic; Fossils
Description: Copyright © 2007 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
RMID: 0020073622
DOI: 10.1093/nar/gkm588
Appears in Collections:Australian Centre for Ancient DNA publications
Earth and Environmental Sciences publications
Environment Institute Leaders publications

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