ArticleNucleic acids research2007
Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers.
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Who cites it
110 citing papers in PubMed.
- A depositional taphonomy model for sedaDNA based on biotic profiles of contrasting sedimentation regimes.PNAS nexus · 2026Article
- Molecular Clock Dating of Ancient Environmental DNA Reveals Damage Beyond Deamination.bioRxiv : the preprint server for biology · 2026Article
- Recovery and analysis of ancient DNA: challenges, methods, and applications in forensic and archaeological science.Journal, genetic engineering & biotechnology · 2026Article
- Robust imputation-based method for eye, hair, and skin colour prediction from low-coverage ancient DNA.Scientific reports · 2026Article
- Optimizing ancient DNA recovery from archaeological plant seeds.Scientific reports · 2025Article
- Article
- An ancient influenza genome from Switzerland allows deeper insights into host adaptation during the 1918 flu pandemic in Europe.BMC biology · 2025Article
- AncientScience (New York, N.Y.) · 2025Article
- A Post-Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA.Molecular ecology resources · 2025Article
- Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach.Scientific reports · 2024Article
- Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.Cell · 2024Article
- Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections.Biodiversity data journal · 2023Article
- Whole-genome sequencing of artificial single-nucleotide variants induced by DNA degradation in biological crime scene traces.International journal of legal medicine · 2023Article
- Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in southern Armenia.Scientific reports · 2022Article
- The untapped potential of macrofossils in ancient plant DNA research.The New phytologist · 2022Article
- An empirical evaluation of genotype imputation of ancient DNA.G3 (Bethesda, Md.) · 2022Article
- Imputation of Ancient Whole GenomeFrontiers in genetics · 2022Article
- Article
- Article
- Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction.Ecology and evolution · 2020Article
50 more citing papers are in PubMed but not listed here.
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7 authors.
Funding
Abstract
Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C > U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy.
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