mapDamage: testing for damage patterns in ancient DNA sequences
Open accessAbstract
Summary: Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequencing reads that could be advantageously used to argue for sequence validity. mapDamage is a Perl script that computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome. The Perl script outputs are further automatically processed in embedded R script in order to detect typical patterns of genuine ancient DNA sequences. Availability and implementation: The Perl script mapDamage is freely available with documentation and example files at http://geogenetics.ku.dk/all_literature/mapdamage/. The script requires prior installation of the SAMtools suite and R environment and has been validated on both GNU/Linux and MacOSX operating systems. Contact: aginolhac@snm.ku.dk Supplementary information: Supplementary data available at Bioinformatics online
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Previous studies have reported lower error rates and higher extension termination rates for Pfu-based polymerases (such as Phusion) compared to Taq-based and other uracil-tolerant polymerases.
“Previous studies have reported lower error rates and higher extension termination rates for Pfu‐based polymerases (such as Phusion) compared to Taq‐based and other uracil‐tolerant polymerases (Heyn et al., 2010; Ginolhac et al., 2011; Wales et al., 2014).”
From Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus (2016) · cites this paper as Ginolhac et al., 2011
In the 'mapDamage options' section (page not supplied), the paper reports fewer cytosine-to-thymine misincorporations in a Phusion-amplified ancient-DNA library than in one amplified with high-fidelity Taq. That supports a narrower claim about damage-related misincorporations, not general polymerase error rates. Our copy does not report extension-termination rates or comparisons with other uracil-tolerant polymerases. (LLM, conf=0.87)
Experimental — accuracy not yet measuredThe authenticity of the human reads obtained from archaeological dental calculus and dentine was assessed by examining damage patterns typical of ancient DNA.
“The authenticity of the human reads obtained from archaeological dental calculus and dentine was assessed by examining damage patterns typical of ancient DNA (Briggs et al., 2007; Ginolhac et al., 2011; Jonsson et al., 2013).”
From Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus (2016) · cites this paper as Ginolhac et al., 2011
Authentic ancient DNA exhibits characteristic damage including short DNA fragment lengths, a high rate of cytosine deamination at the termini of DNA fragments, and an enrichment of purine bases at DNA breakage sites.
“Briefly, authentic ancient DNA is known to exhibit characteristic damage that includes short DNA fragment lengths, a high rate of cytosine deamination at the termini of DNA fragments, and an enrichment of purine bases at DNA breakage sites.”
From Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus (2016) · cites this paper as Ginolhac et al., 2011
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- Authors
- Ginolhac, A., Rasmussen, M., Gilbert, M. T. P., Willerslev, E., & Orlando, L.
- Affiliations
- Centre for Geogenetics, Natural History Museum of Denmark, Copenhagen University, 1350 København K, Denmark
- University of Copenhagen (DK)
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-06-09
- Volume
- 27
- Issue
- 15
- Pages
- 2153-2155
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2103283541
- Cited by
- 363
- References
- 15
- Citations by year
- 2026: 25 · 2025: 25 · 2024: 37 · 2023: 30 · 2022: 23 · 2021: 34 · 2020: 33 · 2019: 19 · 2018: 16 · 2017: 28 · 2016: 29 · 2015: 11 · 2014: 22 · 2013: 19 · 2012: 8
- FWCI
- 10.57
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Open Repository and Bibliography (University of Luxembourg) (submittedVersion, cc-by-nc-sa)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Funders
- National Research Foundation
- Danmarks Grundforskningsfond
- Lundbeckfonden (R70-2010-6286, R24-2008-2527)
- Danmarks Frie Forskningsfond
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- ancient DNA, DNA damage, nucleotide misincorporation, DNA fragmentation, sequencing reads, contamination detection, reference genome mapping, endogenous DNA
- MeSH terms
- Base Sequence, DNA Damage, DNA Restriction Enzymes, Humans, Paleontology, Reference Standards, Software, Genome, Human, Sequence Analysis, DNA, Computational Biology, DNA Contamination
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