ArticleNature communications2022
Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 1 of them a synthesis that pooled it.
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40 citing papers in PubMed, 1 synthesis or guideline pooled it, 47 citations in OpenAlex.
- Correlation between 22q11.2 deletion syndrome phenotype and deletion location: a meta-analysis.Archives of gynecology and obstetrics · 2025Pooled it
- dicast: a machine learning method for accurate structural variant detection from short-read sequencing data.Genome biology · 2026Article
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- ZBP1 in Neuroinflammation and Neurodegeneration: Z-Nucleic-Acid Sensing, RHIM Signalling and Therapeutic Targeting.International journal of molecular sciences · 2026Review
- Hi-C technology for detection of chromosomal rearrangements in families with adverse pregnancy outcomes: a preliminary exploratory study.BMC pregnancy and childbirth · 2026Article
- HaploC-tools reveal haplotype-specific chromosome conformation and chromatin states.Nature communications · 2026Article
- Haplotype-resolved reconstruction and functional interrogation of cancer karyotypes.Cell systems · 2026Article
- Genomic structural variations contribute to inform prognosis in patients with cytogenetically normal acute myeloid leukemia.Blood cancer journal · 2026Article
- A method for structural variant detection using Hi-C contact matrix and neural networks.Scientific reports · 2026Article
- SLUR(M)-py: a SLURM powered Pythonic pipeline for parallel processing of 3D (Epi)genomic profiles.Epigenomics · 2025Article
- Exploring the size limits of Bionano optical genome mapping to resolve alternative structures of linked interspersed chromosomal duplications.Genome medicine · 2025Article
- Structural variants in the 3D genome as drivers of disease.Nature reviews. Genetics · 2025Review
- Generating three-dimensional genome structures with a variational quantum algorithm.Briefings in bioinformatics · 2025Article
- Enhancer activation from transposable elements in extrachromosomal DNA.Nature cell biology · 2025Article
- Enhancer activation from transposable elements in extrachromosomal DNA.bioRxiv : the preprint server for biology · 2025Article
- Changes in 3D Chromatin Organization Drive Topologically Determined Gene Expression in the Poststroke Mouse Cortex.Stroke · 2025Article
- DNA and Histone Modifications Identify a Putative Controlling Element (CE) on the X Chromosome ofCells · 2025Article
- Chromoanagenesis in Osteosarcoma.Biomolecules · 2025Review
- Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.Nature genetics · 2025Article
- Parental Phasing Study Identified Lineage-Specific Variants Associated with Gene Expression and Epigenetic Modifications in European-Chinese Hybrid Pigs.Animals : an open access journal from MDPI · 2025Article
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Authors and funding
31 authors at 15 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structural variants are a common cause of disease and contribute to a large extent to inter-individual variability, but their detection and interpretation remain a challenge. Here, we investigate 11 individuals with complex genomic rearrangements including germline chromothripsis by combining short- and long-read genome sequencing (GS) with Hi-C. Large-scale genomic rearrangements are identified in Hi-C interaction maps, allowing for an independent assessment of breakpoint calls derived from the GS methods, resulting in >300 genomic junctions. Based on a comprehensive breakpoint detection and Hi-C, we achieve a reconstruction of whole rearranged chromosomes. Integrating information on the three-dimensional organization of chromatin, we observe that breakpoints occur more frequently than expected in lamina-associated domains (LADs) and that a majority reshuffle topologically associating domains (TADs). By applying phased RNA-seq, we observe an enrichment of genes showing allelic imbalanced expression (AIG) within 100 kb around the breakpoints. Interestingly, the AIGs hit by a breakpoint (19/22) display both up- and downregulation, thereby suggesting different mechanisms at play, such as gene disruption and rearrangements of regulatory information. However, the majority of interpretable genes located 200 kb around a breakpoint do not show significant expression changes. Thus, there is an overall robustness in the genome towards large-scale chromosome rearrangements.
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