Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms
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Investigating genomic structural variants at basepair resolution is crucial for understanding their formation mechanisms. We identify and analyse 8,943 deletion breakpoints in 1,092 samples from the 1000 Genomes Project. We find breakpoints have more nearby SNPs and indels than the genomic average, likely a consequence of relaxed selection. By investigating the correlation of breakpoints with DNA methylation, Hi–C interactions, and histone marks and the substitution patterns of nucleotides near them, we find that breakpoints with the signature of non-allelic homologous recombination (NAHR) are associated with open chromatin. We hypothesize that some NAHR deletions occur without DNA replication and cell division, in embryonic and germline cells. In contrast, breakpoints associated with non-homologous (NH) mechanisms often have sequence microinsertions, templated from later replicating genomic sites, spaced at two characteristic distances from the breakpoint. These microinsertions are consistent with template-switching events and suggest a particular spatiotemporal configuration for DNA during the events. Structural variation is a major source of complexity in the human genome. Here Abyzov et al.present the identification, classification and analysis of a large database of variants giving an insight into mechanisms generating them.
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TAD boundaries are significantly less likely (P < 0.02) to be affected by known deletion and duplication polymorphisms derived from genomes of healthy human populations.
“Interestingly, TAD boundaries are significantly less likely (P < 0.02) to be affected by known deletion and duplication polymorphisms derived from genomes of healthy human populations25–27 (Extended Data Fig. 2d).”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [26]
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- Authors
- Abyzov, A., Li, S., Kim, D. R., Mohiyuddin, M., Stütz, A. M., Parrish, N. F., Mu, X. J., Clark, W., Chen, K., Hurles, M., Korbel, J. O., Lam, H. Y. K., Lee, C., & Gerstein, M. B.
- Affiliations
- Mayo Clinic (US)
- Yale University (US)
- European Molecular Biology Laboratory (DE)
- Kyoto University (JP)
- The University of Texas MD Anderson Cancer Center (US)
- Wellcome Sanger Institute (GB)
- European Bioinformatics Institute (GB)
- The Jackson Laboratory for Genomic Medicine (US)
- Corresponding author
- Abyzov, Alexej
- Gerstein, Mark B.
- ORCID
- Venue
- Nature Communications
- Published
- 2015-06-01
- Volume
- 6
- Issue
- 1
- Pages
- 7256-7256
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC4451611
- OpenAlex
- W1595360086
- Cited by
- 91
- References
- 68
- Citations by year
- 2026: 4 · 2025: 10 · 2024: 3 · 2023: 4 · 2022: 7 · 2021: 7 · 2020: 10 · 2019: 14 · 2018: 7 · 2017: 6 · 2016: 13 · 2015: 6
- FWCI
- 7.29
- Type
- journal article
- Language
- en
- Update notices
- erratum (2015-09-08)
- Open access
- gold
- doi.org
- Licence
- Locations
- Nature Communications (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- Funders
- Deutsche Forschungsgemeinschaft
- Japan Society for the Promotion of Science
- National Human Genome Research Institute (U41HG007497)
- National Cancer Institute (R01CA172652, P30CA016672, P30CA034196)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- deletion breakpoints, structural variants, non-allelic homologous recombination, non-homologous end joining, template switching, DNA methylation, open chromatin, histone modifications, relaxed selection, 1000 Genomes Project, human genome
- MeSH terms
- Chromatin, DNA, DNA Replication, Humans, Mutation, Nucleotides, Genome, Human, Gene Deletion, Sequence Deletion, Chromosome Breakpoints, Homologous Recombination
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