DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA
Open accessAbstract
We show that DNA molecules amplified by PCR from DNA extracted from animal bones and teeth that vary in age between 25 000 and over 50 000 years carry C-->T and G-->A substitutions. These substitutions can reach high proportions among the molecules amplified and are due to the occurrence of modified deoxycytidine residues in the template DNA. If the template DNA is treated with uracil N-glycosylase, these substitutions are dramatically reduced. They are thus likely to result from deamination of deoxycytidine residues. In addition, 'jumping PCR', i.e. the occurrence of template switching during PCR, may contribute to these substitutions. When DNA sequences are amplified from ancient DNA extracts where few template molecules initiate the PCR, precautions such as DNA sequence determination of multiple clones derived from more than one independent amplification are necessary in order to reduce the risk of determination of incorrect DNA sequences. When such precautionary measures are taken, errors induced by damage to the DNA template are unlikely to be more frequent than approximately 0.1% even under the unlikely scenario where each amplification starts from a single template molecule.
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aDNA damage results in C-to-T and G-to-A substitutions.
“This therefore results in a pattern of C-to-T substitutions. When a double-stranded library preparation is used, these substitutions can occur on the opposite strand thus resulting in G-to-A substitutions due to base complementarity.”
From <tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings (2025) · cites this paper as [6]
The Introduction states that cytosine deamination in ancient DNA can produce C→T and G→A transitions in sequences recovered by PCR, and the Patterns of nucleotide substitutions section reports both types. The paper does not address the citing sentence’s specific condition of double-stranded library preparation; its experiments concern PCR amplification. (LLM, conf=0.86)
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A Fast and Efficient Single-stranded Genomic Library Preparation Method Optimized for Ancient DNA
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The Human Condition—A Molecular Approach
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Nuclear Gene Indicates Coat-Color Polymorphism in Mammoths
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“First, DNA sequences from ancient DNA often contain misincorporations stemming from base damage [12,19-21].”
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Nuclear Gene Sequences from a Late Pleistocene Sloth Coprolite
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- Authors
- Hofreiter, M.
- Affiliations
- Max Planck Institute for Evolutionary Anthropology (DE)
- Corresponding author
- Hofreiter, M.
- ORCID
- Hofreiter, M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2001-12-01
- Volume
- 29
- Issue
- 23
- Pages
- 4793-4799
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC96698
- OpenAlex
- W2013367562
- Cited by
- 684
- References
- 29
- Citations by year
- 2026: 13 · 2025: 17 · 2024: 14 · 2023: 24 · 2022: 24 · 2021: 23 · 2020: 37 · 2019: 27 · 2018: 52 · 2017: 26 · 2016: 26 · 2015: 28 · 2014: 37 · 2013: 31 · 2012: 27
- FWCI
- 7.30
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Funders
- Deutsche Forschungsgemeinschaft
- Max-Planck-Gesellschaft
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- ancient DNA, cytosine deamination, PCR artifacts, uracil-DNA glycosylase, template switching, sequencing error rate
- MeSH terms
- Animals, Base Sequence, Bone and Bones, Cloning, Molecular, Cytosine, Deamination, DNA, Models, Genetic, Molecular Sequence Data, N-Glycosyl Hydrolases, Paleontology, Polymerase Chain Reaction, Mutagenesis, Artifacts, Sequence Analysis, DNA, DNA Glycosylases, History, Ancient, Uracil-DNA Glycosidase
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