ArticleCell systems2022
Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer.
Article in Cell systems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 41 citations in OpenAlex.
- Nivolumab plus ipilimumab in advanced salivary gland cancer: a phase 2 trial.Nature medicine · 2023Trial
- The RNA cargo of plasma-derived extracellular vesicles in mCRPC patients captures cancer cells and tumor microenvironment signals.bioRxiv : the preprint server for biology · 2026Article
- Gene mutant dosage is associated with prognosis and metastatic tropism in 60,000 clinical cancer samples.Nature genetics · 2026Article
- CNVeil resolves haplotype-specific copy number and uncovers subclonal architecture hidden from total copy number profiling in single-cell cancer genomes.bioRxiv : the preprint server for biology · 2026Article
- Integrated high-resolution copy number and histomolecular analysis of diffuse hemispheric glioma, H3 G34-mutant reveals universal TP53 abnormalities.Brain pathology (Zurich, Switzerland) · 2026Article
- Landscape of Allele-Specific Expression in Prostate Cancer Reveals Recurrent, Stage-Specific Events in AR Signaling and Resistance Pathways.Molecular cancer research : MCR · 2026Article
- TET2 germline mutation in a patient with sequential lymphoid malignancies: a novel case report.Annals of hematology · 2026Article
- Widespread Epistasis between Cancer Driver Mutations and Allele-Specific Copy Number Variations.bioRxiv : the preprint server for biology · 2025Article
- Interferon Epsilon Loss Is Elusive 9p21 Link to Immune-Cold Tumors, Resistant to Immune Checkpoint Therapy, and Endogenous CXCL9/10 Induction.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2025Review
- Drosophila and human cell studies reveal a conserved role for CEBPZ, NOC2L and NOC3L in rRNA processing and tumorigenesis.Journal of cell science · 2025Article
- Somatic Uniparental Disomy of PTEN in Endothelial Cells Causes Vascular Malformations in Patients with PTEN Hamartoma Tumor Syndrome.Cancer discovery · 2025Article
- Article
- Tumor ploidy determination in low-pass whole genome sequencing and allelic copy number visualization using the Constellation Plot.Genome biology · 2025Article
- Integrative Computational Analysis of Common EXO5 Haplotypes: Impact on Protein Dynamics, Genome Stability, and Cancer Progression.Journal of chemical information and modeling · 2025Article
- CINner: Modeling and simulation of chromosomal instability in cancer at single-cell resolution.PLoS computational biology · 2025Article
- Diploidy confers genomic instability inbioRxiv : the preprint server for biology · 2025Article
- Benchmarking copy number aberrations inference tools using single-cell multi-omics datasets.Briefings in bioinformatics · 2025Article
- Double Heterozygous Pathogenic Variants inInternational journal of molecular sciences · 2024Article
- Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver mutations.Nature communications · 2024Article
- CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 3 countries.
Funding
Abstract
Pan-cancer studies sketched the genomic landscape of the tumor types spectrum. We delineated the purity- and ploidy-adjusted allele-specific profiles of 4,950 patients across 27 tumor types from the Cancer Genome Atlas (TCGA). Leveraging allele-specific data, we reclassified as loss of heterozygosity (LOH) 9% and 7% of apparent copy-number wild-type and gain calls, respectively, and overall observed more than 18 million allelic imbalance somatic events at the gene level. Reclassification of copy-number events revealed associations between driver mutations and LOH, pointing out the timings between the occurrence of point mutations and copy-number events. Integrating allele-specific genomics and matched transcriptomics, we observed that allele-specific gene status is relevant in the regulation of TP53 and its targets. Further, we disclosed the role of copy-neutral LOH in the impairment of tumor suppressor genes and in disease progression. Our results highlight the role of LOH in cancer and contribute to the understanding of tumor progression.
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