ArticleGenetic epidemiology2020
Critical evaluation of copy number variant calling methods using DNA methylation.
Article in Genetic epidemiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Epigenome-wide association studies identify novel DNA methylation sites associated with PTSD: a meta-analysis of 23 military and civilian cohorts.Genome medicine · 2024Pooled it
- Integrated high-resolution copy number and histomolecular analysis of diffuse hemispheric glioma, H3 G34-mutant reveals universal TP53 abnormalities.Brain pathology (Zurich, Switzerland) · 2026Article
- Development, validation, and utility of a clinically applicable methylation classifier for recurrence risk prediction in meningiomas.Acta neuropathologica communications · 2025Article
- Applicability of epigenetic age models to next-generation methylation arrays.Genome medicine · 2024Article
- Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice.Bioinformatics (Oxford, England) · 2024Article
- Association of self-identified race and genetic ancestry with the immunogenomic landscape of primary prostate cancer.JCI insight · 2023Article
- Accelerated epigenetic aging in newborns with Down syndrome.Aging cell · 2022Article
- Article
- The DNA methylome of cervical cells can predict the presence of ovarian cancer.Nature communications · 2022Observational
- MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions.Frontiers in bioinformatics · 2022Article
- Autosomal sex-associated co-methylated regions predict biological sex from DNA methylation.Nucleic acids research · 2021Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Recent technological and methodological developments have enabled the use of array-based DNA methylation data to call copy number variants (CNVs). ChAMP, Conumee, and cnAnalysis450k are popular methods currently used to call CNVs using methylation data. However, so far, no studies have analyzed the reliability of these methods using real samples. Data from a cohort of individuals with genotype and DNA methylation data generated using the HumanMethylation450 and MethylationEPIC BeadChips were used to assess the consistency between the CNV calls generated by methylation and genotype data. We also took advantage of repeated measures of methylation data collected from the same individuals to compare the reliability of CNVs called by ChAMP, Conumee, and cnAnalysis450k for both the methylation arrays. ChAMP identified more CNVs than Conumee and cnAnalysis450k for both the arrays and, as a consequence, had a higher overlap (~62%) with the calls from the genotype data. However, all methods had relatively low reliability. For the MethylationEPIC array, Conumee had the highest reliability (57.6%), whereas for the HumanMethylation450 array, cnAnalysis450k had the highest reliability (43.0%). Overall, the MethylationEPIC array provided significant gains in reliability for CNV calling over the HumanMethylation450 array but not for overlap with CNVs called using genotype data.
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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.