ArticleBioinformatics (Oxford, England)2024
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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Who cites it
112 citing papers in PubMed, 102 citations in OpenAlex.
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- Nivolumab and ipilimumab in recurrent or refractory cancer of unknown primary: a phase II trial.Nature communications · 2023Trial
- Apc-deficient pituitary stem cells drive adamantinomatous craniopharyngioma through senescence-associated inflammation.EMBO molecular medicine · 2026Article
- High-grade astrocytoma with piloid features: A clinical and genomic analysis of prognostic factors using a large cohort.Neuro-oncology · 2026Article
- Gliomas with pleomorphic and pseudopapillary features (GPAP) are circumscribed tumors with targetable mutations, prolonged survival, and frequent tumor predisposition.Brain pathology (Zurich, Switzerland) · 2026Article
- CpG hypermethylation and WNT/AP-1 cooperativity define the epigenetic landscape and a clinical subgroup of high-risk pediatric adrenocortical carcinoma.Nature communications · 2026Article
- DNA methylation profiling identifies long-range epigenetic silencing of clustered protocadherins as a key determinant of meningioma progression.Nature communications · 2026Article
- DNA methylation profiling enables subclassification of mucinous ovarian carcinoma and distinguishes it from extraovarian mucinous metastases.Cell reports. Medicine · 2026Article
- Sex-linked placental DNA methylation associated with early-onset preeclampsia.Research square · 2026Article
- Molecular heterogeneity and prognostic biomarkers in primary meningeal melanocytic tumors.Brain pathology (Zurich, Switzerland) · 2026Article
- Integrated multiomic profiling reveals 2 distinct splenic marginal zone lymphoma subgroups with prognostic relevance.Blood advances · 2026Article
- Time-dependent prognostic value of automated Ki67 assessment and its integration with molecular risk profiling in WHO grade 2 meningioma.Acta neuropathologica communications · 2026Article
- Circulating tumor DNA precision oncology enables effective and sensitive molecular diagnostics and actionable target detection in pediatric solid tumors - the INFORM experience.Genome medicine · 2026Article
- Sarcomatous transformation of an astrocytoma IDH-mutant following radiotherapy.Virchows Archiv : an international journal of pathology · 2026Article
- Improved prognostic survival models for pediatric medulloblastoma using high dimensional gene expression data.BMC medical genomics · 2026Article
- Exploring epigenome-proteome interactions underlying post-surgical progression of non-functioning pituitary adenomas using hypernetwork modelling.Journal of translational medicine · 2026Article
- Spatially resolved single-cell analyses of human meningioma identify novel cell states influencing tumor microenvironment and progression.Nature genetics · 2026Article
- Radiotherapy Response Prediction in Myxofibrosarcomas and Undifferentiated Soft Tissue Sarcomas Using DNA Methylation and Copy Number Profiling.International journal of surgical pathology · 2026Article
- Spatially resolved ex vivo drug response profiling in SMARCB1-deficient sinonasal carcinoma.EMBO molecular medicine · 2026Article
- DNA methylation biomarkers-based pan-cancer classifier: predictive modeling for cancer classification.Genome medicine · 2026Article
52 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
Abstract
motivationCopy-number variations (CNVs) are common genetic alterations in cancer and their detection may impact tumor classification and therapeutic decisions. However, detection of clinically relevant large and focal CNVs remains challenging when sample material or resources are limited. This has motivated us to create a software tool to infer CNVs from DNA methylation arrays which are often generated as part of clinical routines and in research settings.
resultsWe present our R package, conumee 2.0, that combines tangent normalization, an adjustable genomic binning heuristic, and weighted circular binary segmentation to utilize DNA methylation arrays for CNV analysis and mitigate technical biases and batch effects. Segmentation results were validated in a lung squamous cell carcinoma dataset from TCGA (n = 367 samples) by comparison to segmentations derived from genotyping arrays (Pearson's correlation coefficient of 0.91). We further introduce a segmented block bootstrapping approach to detect focal alternations that achieved 60.9% sensitivity and 98.6% specificity for deletions affecting CDKN2A/B (60.0% and 96.9% for RB1, respectively) in a low-grade glioma cohort from TCGA (n = 239 samples). Finally, our tool provides functionality to detect and summarize CNVs across large sample cohorts. AVAILABILITY AND IMPLEMENTATION: Conumee 2.0 is available under open-source license at: https://github.com/hovestadtlab/conumee2.
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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.