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Type: Journal article
Title: Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX
Author: Brotherton, P.
Sanchez, J.
Cooper, A.
Endicott, P.
Citation: Nucleic Acids Research, 2010; 38(2):E7-1-E7-12
Publisher: Oxford Univ Press
Issue Date: 2010
ISSN: 0305-1048
Statement of
Paul Brotherton, Juan J. Sanchez, Alan Cooper and Phillip Endicott
Abstract: 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.
Keywords: Animals; Hominidae; Humans; Reproducibility of Results; Nucleic Acid Amplification Techniques; Polymerase Chain Reaction; Sequence Analysis, DNA; Base Sequence; Genotype; Polymorphism, Single Nucleotide; Museums; Molecular Sequence Data
Rights: © The Author(s) 2009. Published by Oxford University Press.
RMID: 0020100229
DOI: 10.1093/nar/gkp897
Appears in Collections:Australian Centre for Ancient DNA publications
Earth and Environmental Sciences publications
Environment Institute Leaders publications

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