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https://hdl.handle.net/2440/59941
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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 1362-4962 |
Statement of Responsibility: | 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. |
DOI: | 10.1093/nar/gkp897 |
Published version: | http://dx.doi.org/10.1093/nar/gkp897 |
Appears in Collections: | Aurora harvest 5 Australian Centre for Ancient DNA publications Earth and Environmental Sciences publications Environment Institute Leaders publications |
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