ArticleJournal of computational biology : a journal of computational molecular cell biology2019
Measuring DNA Copy Number Variation Using High-Density Methylation Microarrays.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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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
10 citing papers in PubMed, 18 citations in OpenAlex.
- Development, validation, and utility of a clinically applicable methylation classifier for recurrence risk prediction in meningiomas.Acta neuropathologica communications · 2025Article
- Methods in DNA methylation array dataset analysis: A review.Computational and structural biotechnology journal · 2024Review
- Navigating Illumina DNA methylation data: biology versus technical artefacts.NAR genomics and bioinformatics · 2024Article
- Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice.Bioinformatics (Oxford, England) · 2024Article
- DNA Methylation Episignatures in Neurodevelopmental Disorders Associated with Large Structural Copy Number Variants: Clinical Implications.International journal of molecular sciences · 2022Review
- DNA methylation as a diagnostic tool.Acta neuropathologica communications · 2022Review
- Editorial: Computational Methods for Analysis of DNA Methylation Data.Frontiers in bioinformatics · 2022Article
- MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions.Frontiers in bioinformatics · 2022Article
- DNA Copy Number Variation Associated with Anti-tumour Necrosis Factor Drug Response and Paradoxical Psoriasiform Reactions in Patients with Moderate-to-severe Psoriasis.Acta dermato-venereologica · 2021Article
- DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome.Clinical epigenetics · 2021Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Genetic and epigenetic changes drive carcinogenesis, and their integrated analysis provides insights into mechanisms of cancer development. Computational methods have been developed to measure copy number variation (CNV) from methylation array data, including ChAMP-CNV, CN450K, and, introduced here, Epicopy. Using paired single nucleotide polymorphism (SNP) and methylation array data from the public The Cancer Genome Atlas repository, we optimized CNV calling and benchmarked the performance of these methods. We optimized the thresholds of all three methods and showed comparable performance across methods. Using Epicopy as a representative analysis of Illumina450K array, we show that Illumina450K-derived CNV methods achieve a sensitivity of 0.7 and a positive predictive value of 0.75 in identifying CNVs, which is similar to results achieved when comparing competing SNP microarray platforms with each other.
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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.