Abstract
DNA damage is a threat to genome integrity and can be a cause of many human diseases, owing to either changes in the chemical structure of DNA or conversion of the damage into a mutation, that is, a permanent change in DNA sequence. Determining the exact positions of DNA damage and ensuing mutations in the genome are important for identifying mechanisms of disease aetiology when characteristic mutations are prevalent and probably causative in a particular disease. However, this approach is challenging particularly when levels of DNA damage are low, for example, as a result of chronic exposure to environmental agents or certain endogenous processes, such as the generation of reactive oxygen species. Over the past few years, a comprehensive toolbox of genome-wide methods has been developed for the detection of DNA damage and rare mutations at single-nucleotide resolution in mammalian cells. Here, we review and compare these methods, describe their current applications and discuss future research questions that can now be addressed.
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The work of the authors is supported by National Institutes of Health grant R01CA276031 to G.P.P.
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Glossary
- Base excision repair
-
(BER). A DNA repair pathway that removes DNA bases with small chemical modifications and replaces them with the correct, unmodified bases.
- Concatemerized DNA
-
A long DNA molecule consisting of linked, multiple copies of the same sequence.
- Homologous recombination repair
-
A DNA repair pathway that corrects DNA double-strand breaks by using alignment and recombination of the broken DNA with an intact copy of the same sequence.
- Mismatch repair
-
(MMR). A DNA repair pathway that excises mismatched DNA bases.
- Nonhomologous end joining
-
(NHEJ). A DNA repair pathway that corrects DNA double-strand breaks by joining two broken ends.
- Nucleotide excision repair
-
(NER). A DNA repair pathway that removes DNA bases with large chemical modifications and replaces them with the correct, unmodified bases.
- Okazaki fragments
-
Short, 100–200-bp DNA fragments formed by lagging strand synthesis during DNA replication.
- Unique molecular identifier
-
(UMI). A short DNA sequence that is added as a molecular barcode before PCR amplification to tag each molecule in a sequencing library.
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Pfeifer, G.P., Jin, SG. Methods and applications of genome-wide profiling of DNA damage and rare mutations. Nat Rev Genet (2024). https://doi.org/10.1038/s41576-024-00748-4
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DOI: https://doi.org/10.1038/s41576-024-00748-4
