ArticlePloS one2014
Tandem repeats and G-rich sequences are enriched at human CNV breakpoints.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 57 citations in OpenAlex.
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- DNA replication initiation drives focal mutagenesis and rearrangements in human cancers.Nature communications · 2024Article
- Optical genome mapping of structural variants in Parkinson's disease-related induced pluripotent stem cells.BMC genomics · 2024Article
- Diversity of ribosomes at the level of rRNA variation associated with human health and disease.Cell genomics · 2024Article
- Whole genome and reverse protein phase array landscapes of patient derived osteosarcoma xenograft models.Scientific reports · 2024Article
- Genome-wide repeat landscapes in cancer and cell-free DNA.Science translational medicine · 2024Article
- Chromosomal Abnormalities of Interest in Turner Syndrome: An Update.Journal of pediatric genetics · 2023Review
- Whole-genome sequencing of 1029 Indian individuals reveals unique and rare structural variants.Journal of human genetics · 2023Article
- Stepwise use of genomics and transcriptomics technologies increases diagnostic yield in Mendelian disorders.Frontiers in cell and developmental biology · 2023Article
- Cytogenomic Characterization of a Novel de novo Balanced Reciprocal Translocation t(1;12) by Genome Sequencing Leading to Fusion Gene Formation ofMolecular syndromology · 2022Article
- DNA sequence features underlying large-scale duplications and deletions in human.Journal of applied genetics · 2022Article
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- Variations of wheat (Frontiers in plant science · 2022Article
- Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in cancer.BMC cancer · 2020Article
- From R-Loops to G-Quadruplexes: Emerging New Threats for the Replication Fork.International journal of molecular sciences · 2020Review
- ERCC1/XPF Is Important for Repair of DNA Double-Strand Breaks Containing Secondary Structures.iScience · 2019Article
- Insight into the mechanisms and consequences of recurrent telomere capture associated with a sub-telomeric deletion.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2018Article
- Extreme clustering of type-1 NF1 deletion breakpoints co-locating with G-quadruplex forming sequences.Human genetics · 2018Article
- Insights about genome function from spatial organization of the genome.Human genomics · 2018Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Chromosome breakage in germline and somatic genomes gives rise to copy number variation (CNV) responsible for genomic disorders and tumorigenesis. DNA sequence is known to play an important role in breakage at chromosome fragile sites; however, the sequences susceptible to double-strand breaks (DSBs) underlying CNV formation are largely unknown. Here we analyze 140 germline CNV breakpoints from 116 individuals to identify DNA sequences enriched at breakpoint loci compared to 2800 simulated control regions. We find that, overall, CNV breakpoints are enriched in tandem repeats and sequences predicted to form G-quadruplexes. G-rich repeats are overrepresented at terminal deletion breakpoints, which may be important for the addition of a new telomere. Interstitial deletions and duplication breakpoints are enriched in Alu repeats that in some cases mediate non-allelic homologous recombination (NAHR) between the two sides of the rearrangement. CNV breakpoints are enriched in certain classes of repeats that may play a role in DNA secondary structure, DSB susceptibility and/or DNA replication errors.
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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.