Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX
Date
2010
Authors
Brotherton, P.
Sanchez, J.
Cooper, A.
Endicott, P.
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Journal article
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Nucleic Acids Research, 2010; 38(2):E7-1-E7-12
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Paul Brotherton, Juan J. Sanchez, Alan Cooper and Phillip Endicott
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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.
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© The Author(s) 2009. Published by Oxford University Press.