ArticleGenome biology2014
SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed, 85 citations in OpenAlex.
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- Jumping in the human brain: A review on somatic transposition.Fundamental research · 2026Review
- Image-based DNA sequencing encoding for detecting low-mosaicism somatic mobile element insertions.Nature communications · 2025Article
- Long-read genome and RNA sequencing resolve a pathogenic intronic germline LINE-1 insertion in APC.NPJ genomic medicine · 2025Article
- Mini-heterochromatin domains constrain the cis-regulatory impact of SVA transposons in human brain development and disease.Nature structural & molecular biology · 2024Article
- ZNF91 is an endogenous repressor of the molecular phenotype associated with X-linked dystonia-parkinsonism (XDP).Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Retrotransposons in embryogenesis and neurodevelopment.Biochemical Society transactions · 2024Review
- Genetic/epigenetic effects in NF1 microdeletion syndrome: beyond the haploinsufficiency, looking at the contribution of not deleted genes.Human genetics · 2024Article
- Contribution ofmedRxiv : the preprint server for health sciences · 2024Article
- Correlation between large rearrangements and patient phenotypes in NF1 deletion syndrome: an update and review.BMC medical genomics · 2024Article
- Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement.Genome research · 2024Article
- Exome sequencing identified rare recurrent copy number variants and hereditary breast cancer susceptibility.PLoS genetics · 2023Article
- Small allelic variants are a source of ancestral bias in structural variant breakpoint placement.bioRxiv : the preprint server for biology · 2023Article
- Hominoid SVA-lncRNA AK057321 targets human-specific SVA retrotransposons in SCN8A and CDK5RAP2 to initiate neuronal maturation.Communications biology · 2023Article
- Transposable element insertions in 1000 Swedish individuals.PloS one · 2023Article
- The landscape of aging.Science China. Life sciences · 2022Review
- Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency.Thrombosis and haemostasis · 2022Article
- Mechanisms of disease-associated SINE-VNTR-Alus.Experimental biology and medicine (Maywood, N.J.) · 2022Review
- Distinct sequence features underlie microdeletions and gross deletions in the human genome.Human mutation · 2022Article
- An ancestral genomic sequence that serves as a nucleation site for de novo gene birth.PloS one · 2022Article
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Authors and funding
16 authors at 10 institutions in 7 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenomic disorders are caused by copy number changes that may exhibit recurrent breakpoints processed by nonallelic homologous recombination. However, region-specific disease-associated copy number changes have also been observed which exhibit non-recurrent breakpoints. The mechanisms underlying these non-recurrent copy number changes have not yet been fully elucidated.
resultsWe analyze large NF1 deletions with non-recurrent breakpoints as a model to investigate the full spectrum of causative mechanisms, and observe that they are mediated by various DNA double strand break repair mechanisms, as well as aberrant replication. Further, two of the 17 NF1 deletions with non-recurrent breakpoints, identified in unrelated patients, occur in association with the concomitant insertion of SINE/variable number of tandem repeats/Alu (SVA) retrotransposons at the deletion breakpoints. The respective breakpoints are refractory to analysis by standard breakpoint-spanning PCRs and are only identified by means of optimized PCR protocols designed to amplify across GC-rich sequences. The SVA elements are integrated within SUZ12P intron 8 in both patients, and were mediated by target-primed reverse transcription of SVA mRNA intermediates derived from retrotranspositionally active source elements. Both SVA insertions occurred during early postzygotic development and are uniquely associated with large deletions of 1 Mb and 867 kb, respectively, at the insertion sites.
conclusionsSince active SVA elements are abundant in the human genome and the retrotranspositional activity of many SVA source elements is high, SVA insertion-associated large genomic deletions encompassing many hundreds of kilobases could constitute a novel and as yet under-appreciated mechanism underlying large-scale copy number changes in the human genome.
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