ArticleGenome research2017
Short template switch events explain mutation clusters in the human genome.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 35 citations in OpenAlex.
- Highly Recurrent Multinucleotide Mutations in SARS-CoV-2.Molecular biology and evolution · 2025Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Generation of de novo miRNAs from template switching during DNA replication.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Mutation bias and adaptation in bacteria.Microbiology (Reading, England) · 2023Review
- Revisiting mutagenesis at non-B DNA motifs in the human genome.Nature structural & molecular biology · 2023Article
- How to optimally sample a sequence for rapid analysis.Bioinformatics (Oxford, England) · 2023Article
- Finding Rearrangements in Nanopore DNA Reads with LAST and dnarrange.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Hrq1/RECQL4 regulation is critical for preventing aberrant recombination during DNA intrastrand crosslink repair and is upregulated in breast cancer.PLoS genetics · 2022Article
- Template switching in DNA replication can create and maintain RNA hairpins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Characteristics and possible mechanisms of formation of microinversions distinguishing human and chimpanzee genomes.Scientific reports · 2022Article
- Protein innovation through template switching in the Saccharomyces cerevisiae lineage.Scientific reports · 2021Article
- The origin of human mutation in light of genomic data.Nature reviews. Genetics · 2021Review
- Short-range template switching in great ape genomes explored using pair hidden Markov models.PLoS genetics · 2021Article
- Systematic Nucleotide Exchange Analysis of ESTs From the Human Cancer Genome Project Report: Origins of 347 Unknown ESTs Indicate Putative Transcription of Non-Coding Genomic Regions.Frontiers in genetics · 2020Article
- DNA damage tolerance in stem cells, ageing, mutagenesis, disease and cancer therapy.Nucleic acids research · 2019Review
- CRISPR/Cas9-mediated homology-directed repair by ssODNs in zebrafish induces complex mutational patterns resulting from genomic integration of repair-template fragments.Disease models & mechanisms · 2018Article
- The Prevalence and Evolutionary Conservation of Inverted Repeats in Proteobacteria.Genome biology and evolution · 2018Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Resequencing efforts are uncovering the extent of genetic variation in humans and provide data to study the evolutionary processes shaping our genome. One recurring puzzle in both intra- and inter-species studies is the high frequency of complex mutations comprising multiple nearby base substitutions or insertion-deletions. We devised a generalized mutation model of template switching during replication that extends existing models of genome rearrangement and used this to study the role of template switch events in the origin of short mutation clusters. Applied to the human genome, our model detects thousands of template switch events during the evolution of human and chimp from their common ancestor and hundreds of events between two independently sequenced human genomes. Although many of these are consistent with a template switch mechanism previously proposed for bacteria, our model also identifies new types of mutations that create short inversions, some flanked by paired inverted repeats. The local template switch process can create numerous complex mutation patterns, including hairpin loop structures, and explains multinucleotide mutations and compensatory substitutions without invoking positive selection, speculative mechanisms, or implausible coincidence. Clustered sequence differences are challenging for current mapping and variant calling methods, and we show that many erroneous variant annotations exist in human reference data. Local template switch events may have been neglected as an explanation for complex mutations because of biases in commonly used analyses. Incorporation of our model into reference-based analysis pipelines and comparisons of de novo assembled genomes will lead to improved understanding of genome variation and evolution.
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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.