Cited by 685Forensic and Genetic ResearchMolecular Biology Techniques and ApplicationsGenomics and Phylogenetic Studies

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DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA

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Hofreiter, M.·2001·Nucleic Acids Research

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Abstract

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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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
DOI: 10.1093/nar/29.23.4793
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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DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA

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