ArticleBMC bioinformatics2020
CNV Radar: an improved method for somatic copy number alteration characterization in oncology.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 18 citations in OpenAlex.
- An enhanced genetic model of relapsed IGH-translocated multiple myeloma evolutionary dynamics.Blood cancer journal · 2020Trial
- Haplotype-aware segmentation with HapASeg increases accuracy of detecting homolog-specific somatic copy number alterations.Genome biology · 2026Article
- Methylation profiling in neuropathological tumors diagnosis: a comprehensive review.Frontiers in oncology · 2025Review
- Establishment and characterization of 18 Sarcoma Cell Lines: Unraveling the Molecular Mechanisms of Doxorubicin Resistance in Sarcoma Cell Lines.Journal of translational medicine · 2024Article
- Clinical Value of Liquid Biopsy in Patients with FGFR2 Fusion-Positive Cholangiocarcinoma During Targeted Therapy.Clinical cancer research : an official journal of the American Association for Cancer Research · 2024Article
- Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia.Nature communications · 2024Article
- Copy number variations at theFrontiers in plant science · 2024Article
- Technological and computational approaches to detect somatic mosaicism in epilepsy.Neurobiology of disease · 2023Review
- Article
- Immunohistochemical staining patterns of p53 predict the mutational status of TP53 in oral epithelial dysplasia.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2022Article
- Article
- Identification of Three Prognosis-Related Differentially Expressed lncRNAs Driven by Copy Number Variation in Thyroid Cancer.Journal of immunology research · 2022Article
- Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine.Non-coding RNA · 2021Review
- A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency.Genome biology · 2021Article
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Authors and funding
16 authors at 9 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCancer associated copy number variation (CNV) events provide important information for identifying patient subgroups and suggesting treatment strategies. Technical and logistical issues, however, make it challenging to accurately detect abnormal copy number events in a cost-effective manner in clinical studies.
resultsHere we present CNV Radar, a software tool that utilizes next-generation sequencing read depth information and variant allele frequency patterns, to infer the true copy number status of genes and genomic regions from whole exome sequencing data. Evaluation of CNV Radar in a public multiple myeloma dataset demonstrated that CNV Radar was able to detect a variety of CNVs associated with risk of progression, and we observed > 70% concordance with fluorescence in situ hybridization (FISH) results. Compared to other CNV callers, CNV Radar showed high sensitivity and specificity. Similar results were observed when comparing CNV Radar calls to single nucleotide polymorphism array results from acute myeloid leukemia and prostate cancer datasets available on TCGA. More importantly, CNV Radar demonstrated its utility in the clinical trial setting: in POLLUX and CASTOR, two phase 3 studies in patients with relapsed or refractory multiple myeloma, we observed a high concordance rate with FISH for del17p, a risk defining CNV event (88% in POLLUX and 90% in CASTOR), therefore allowing for efficacy assessments in clinically relevant disease subgroups. Our case studies also showed that CNV Radar is capable of detecting abnormalities such as copy-neutral loss of heterozygosity that elude other approaches.
conclusionsWe demonstrated that CNV Radar is more sensitive than other CNV detection methods, accurately detects clinically important cytogenetic events, and allows for further interrogation of novel disease biology. Overall, CNV Radar exhibited high concordance with standard methods such as FISH, and its success in the POLLUX and CASTOR clinical trials demonstrated its potential utility for informing clinical and therapeutic decisions.
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