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Nucleic Acids Research Advance Access published online on October 27, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp897
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX

Paul Brotherton1,2,*, Juan J. Sanchez3, Alan Cooper1 and Phillip Endicott2,4

1Australian Centre for Ancient DNA, Darling Building, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, Adelaide, South Australia 5005, Australia, 2Department of Zoology, University of Oxford, South Parks Rd, Oxford, OX1 3PS, UK, 3National Institute of Toxicology and Forensic Sciences, Canary Islands Delegation, Tenerife, Spain and 4Musée de l'H;omme, 17 Place du Trocadero, 75116 Paris, France

*To whom correspondence should be addressed. Tel: +61 8 8303 8242; Fax: +61 8 8303 4364; Email: paul_m_brotherton{at}yahoo.co.uk

Received June 1, 2009. Revised September 9, 2009. Accepted October 6, 2009.

The analysis of targeted genetic loci from ancient, forensic and clinical samples is usually built upon polymerase chain reaction (PCR)-generated sequence data. However, many studies have shown that PCR amplification from poor-quality DNA templates can create sequence artefacts at significant levels. With hominin (human and other hominid) samples, the pervasive presence of highly PCR-amplifiable human DNA contaminants in the vast majority of samples can lead to the creation of recombinant hybrids and other non-authentic artefacts. The resulting PCR-generated sequences can then be difficult, if not impossible, to authenticate. In contrast, single primer extension (SPEX)-based approaches can genotype single nucleotide polymorphisms from ancient fragments of DNA as accurately as modern DNA. A single SPEX-type assay can amplify just one of the duplex DNA strands at target loci and generate a multi-fold depth-of-coverage, with non-authentic recombinant hybrids reduced to undetectable levels. Crucially, SPEX-type approaches can preferentially access genetic information from damaged and degraded endogenous ancient DNA templates over modern human DNA contaminants. The development of SPEX-type assays offers the potential for highly accurate, quantitative genotyping from ancient hominin samples.


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