ReviewNPJ precision oncology2021
Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology.
Review in NPJ precision oncology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
65 citing papers in PubMed.
- Invas: an inversion-aware method for transcriptome assembly.Nature communications · 2026Article
- SAP18 drives vasculogenic mimicry in esophageal squamous cell carcinoma: a machine learning and multi-omics investigation.NPJ precision oncology · 2026Article
- Genomic Variability of the HCT116 Cell Line Identified Using Oxford Nanopore Sequencing.International journal of molecular sciences · 2026Article
- Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies.Cell genomics · 2026Article
- Article
- Long-Read Haplotype Phasing Resolves Allelic Configuration as a Missing Layer of Precision Oncology.medRxiv : the preprint server for health sciences · 2026Article
- Exploring the Molecular and Genomic Landscape of the Dark Agouti Rat Mammary Adenocarcinoma: Preliminary Insights for Triple-Negative Breast Cancer Modeling.Journal of mammary gland biology and neoplasia · 2026Article
- Machine learning-predicted chromatin organization landscape across pediatric tumors.Scientific reports · 2026Article
- SVNeoPP: A Workflow for Structural-Variant-Derived Neoantigen Prediction and Prioritization Using Multi-Omics Data.Biology · 2026Article
- Cross-Species Exome Sequencing Reveals Recurrent Genomic Alterations in California Sea Lion (Genes · 2026Article
- Molecular residual disease assessment in colorectal and bladder cancer by somatic structural variant analysis of cell-free DNA whole-genome sequencing data.Journal of translational medicine · 2026Article
- DNA and RNA-based next-generation sequencing for companion diagnostic rearrangement detection in solid tumors.The oncologist · 2026Article
- Multiplatform comparisons and annotation of structural variants highlight the utility of the T2T reference genome in human diagnostics.GigaScience · 2026Article
- Evaluation of quantitative polymerase chain reaction for detecting BRCA1 or BRCA2 copy number loss in high-grade serous ovarian cancer.Scientific reports · 2026Article
- Whole-Genome Landscape of Retinal Hemangioblastomas.Translational vision science & technology · 2026Article
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
- Biomarkers for predicting and monitoring the efficacy of cancer vaccines.Frontiers in oncology · 2026Review
- Article
- Tumor-informed liquid biopsy detection of structural variants in high grade serous ovarian cancer.Oncoscience · 2026Article
- Genomic characterization of host gene alterations in Theileria annulata-transformed leukocytes.Communications biology · 2025Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cancer is generally characterized by acquired genomic aberrations in a broad spectrum of types and sizes, ranging from single nucleotide variants to structural variants (SVs). At least 30% of cancers have a known pathogenic SV used in diagnosis or treatment stratification. However, research into the role of SVs in cancer has been limited due to difficulties in detection. Biological and computational challenges confound SV detection in cancer samples, including intratumor heterogeneity, polyploidy, and distinguishing tumor-specific SVs from germline and somatic variants present in healthy cells. Classification of tumor-specific SVs is challenging due to inconsistencies in detected breakpoints, derived variant types and biological complexity of some rearrangements. Full-spectrum SV detection with high recall and precision requires integration of multiple algorithms and sequencing technologies to rescue variants that are difficult to resolve through individual methods. Here, we explore current strategies for integrating SV callsets and to enable the use of tumor-specific SVs in precision oncology.
Identifiers
What OpenQuestion holds
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.