ArticleNucleic acids research2010
Road blocks on paleogenomes--polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- Improving STR typing for low template DNA by abasic-site-mediated semi-linear preamplification.Scientific reports · 2025Article
- DEEPOMICS FFPE, a deep neural network model, identifies DNA sequencing artifacts from formalin fixed paraffin embedded tissue with high accuracy.Scientific reports · 2024Article
- Engineered viral DNA polymerase with enhanced DNA amplification capacity: a proof-of-concept of isothermal amplification of damaged DNA.Scientific reports · 2020Article
- Why Formalin-fixed, Paraffin-embedded Biospecimens Must Be Used in Genomic Medicine: An Evidence-based Review and Conclusion.The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society · 2020Article
- Article
- An Internal Control for Evaluating Bisulfite Conversion in the Analysis of Short Stature Homeobox 2 Methylation in Lung Cancer.Asian Pacific journal of cancer prevention : APJCP · 2019Article
- A Robust Framework for Microbial Archaeology.Annual review of genomics and human genetics · 2017Review
- Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus.American journal of physical anthropology · 2016Article
- Reconstructing ancient genomes and epigenomes.Nature reviews. Genetics · 2015Review
- Ancient genomics.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Review
- Article
- Unlocking the vault: next-generation museum population genomics.Molecular ecology · 2013Article
- Ancient DNA damage.Cold Spring Harbor perspectives in biology · 2013Review
- Article
- Dramatic reduction of sequence artefacts from DNA isolated from formalin-fixed cancer biopsies by treatment with uracil- DNA glycosylase.Oncotarget · 2012Article
- Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.PloS one · 2012Article
- Evaluating the impact of post-mortem damage in ancient DNA: a theoretical approach.Journal of molecular evolution · 2011Article
- DNA damage in plant herbarium tissue.PloS one · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although the last few years have seen great progress in DNA sequence retrieval from fossil specimens, some of the characteristics of ancient DNA remain poorly understood. This is particularly true for blocking lesions, i.e. chemical alterations that cannot be bypassed by DNA polymerases and thus prevent amplification and subsequent sequencing of affected molecules. Some studies have concluded that the vast majority of ancient DNA molecules carry blocking lesions, suggesting that the removal, repair or bypass of blocking lesions might dramatically increase both the time depth and geographical range of specimens available for ancient DNA analysis. However, previous studies used very indirect detection methods that did not provide conclusive estimates on the frequency of blocking lesions in endogenous ancient DNA. We developed a new method, polymerase extension profiling (PEP), that directly reveals occurrences of polymerase stalling on DNA templates. By sequencing thousands of single primer extension products using PEP methodology, we have for the first time directly identified blocking lesions in ancient DNA on a single molecule level. Although we found clear evidence for blocking lesions in three out of four ancient samples, no more than 40% of the molecules were affected in any of the samples, indicating that such modifications are far less frequent in ancient DNA than previously thought.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.