ArticleCell genomics2022
Unscrambling cancer genomes via integrated analysis of structural variation and copy number.
Article in Cell genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Multi-omics analysis reveals the attenuation of the interferon pathway as a driver of chemo-refractory ovarian cancer.Cell reports. Medicine · 2025Trial
- A Living Multi-Omics PDX Biobank of High-Risk Sarcomas Reveals ecDNA-Driven Oncogene Amplification in Osteosarcoma and Enables Preclinical Precision Oncology.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Unraveling the lexicon of complex mutational phenomena in human cancers.Nature cancer · 2026Review
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- A single chromosome 3p break initiates clear cell renal cell carcinoma evolution.bioRxiv : the preprint server for biology · 2026Article
- Beyond chromosomes: exploring the diverse functions of extrachromosomal circular DNA.Journal of advanced research · 2026Review
- Therapy-associated mutagenesis at CTCF binding sites is shaped by chromatin context and DNA repair capacity.bioRxiv : the preprint server for biology · 2026Article
- Convergent evolution of complex structural variants drives therapy resistance in metastatic prostate cancer.Genome biology · 2026Article
- Proof-of-concept study for the detection of somatic structural variant driver alterations using HiFi long-read sequencing in a pediatric leukemia cohort.NPJ genomic medicine · 2026Article
- Integrative molecular analyses of lineage identity and morphology in aggressive variant prostate cancer.NPJ precision oncology · 2026Article
- Deep Learning-Enabled Multi-Omics Integration: A New Frontier in Precise Drug Target Discovery.Biology · 2026Review
- Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.Nature biotechnology · 2026Article
- Molecular decoupling of lineage identity and morphology in aggressive variant prostate cancer.medRxiv : the preprint server for health sciences · 2026Article
- A breakage-replication/fusion process explains complex rearrangements and segmental DNA amplification.Nature genetics · 2026Article
- High-quality phased genome assemblies of line-bred Korean Hanwoo cattle.Scientific data · 2025Article
- Decoding the Genomic and Functional Landscape of Emerging Subtypes in Ovarian Cancer.Cancer discovery · 2025Article
- Complex structural variant visualization with SVTopo.BMC genomics · 2025Article
- SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read sequencing.Nature methods · 2025Article
- Divergent trajectories to structural diversity impact patient survival in high grade serous ovarian cancer.Nature communications · 2025Article
6 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Complex somatic genomic rearrangements and copy number alterations are hallmarks of nearly all cancers. We have developed an algorithm, LINX, to aid interpretation of structural variant and copy number data derived from short-read, whole-genome sequencing. LINX classifies raw structural variant calls into distinct events and predicts their effect on the local structure of the derivative chromosome and the functional impact on affected genes. Visualizations facilitate further investigation of complex rearrangements. LINX allows insights into a diverse range of structural variation events and can reliably detect pathogenic rearrangements, including gene fusions, immunoglobulin enhancer rearrangements, intragenic deletions, and duplications. Uniquely, LINX also predicts chained fusions that we demonstrate account for 13% of clinically relevant oncogenic fusions. LINX also reports a class of inactivation events that we term homozygous disruptions that may be a driver mutation in up to 9% of tumors and may frequently affect
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