Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX.
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.
Brotherton
Paul
P
Australian Centre for Ancient DNA, Darling Building, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, Adelaide, South Australia 5005, Australia.
Sanchez
Juan J
JJ
Cooper
Alan
A
Endicott
Phillip
P
D000818:Animals; D001483:Base Sequence; D005838:Genotype; D015186:Hominidae / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009144:Museums; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA