ArticleBioinformatics (Oxford, England)2010
A statistical framework for Illumina DNA methylation arrays.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers, 1 of them a synthesis that pooled it.
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Who cites it
65 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Epigenome-wide association study of mitochondrial genome copy number.Human molecular genetics · 2021Pooled it
- DNA methylation quality control decisions, removed beta values, and their influence on epigenetic clocks.Epigenomics · 2026Article
- ReMeDy: A Flexible Statistical Framework For Region-based Detection of DNA Methylation Dysregulation.bioRxiv : the preprint server for biology · 2026Article
- Association of Epigenetic Age Acceleration and Mitochondrial DNA-Based Aging Metrics Provides Insights Into Mechanisms of Aging-Related Diseases.Aging cell · 2025Article
- Article
- Sex differences in the intergenerational link between maternal and neonatal whole blood DNA methylation: a genome-wide analysis in 2 birth cohorts.Clinical epigenetics · 2023Article
- Integrative genomic analyses reveal mechanisms of glucocorticoid resistance in acute lymphoblastic leukemia.Nature cancer · 2020Article
- Penalized logistic regression based on L1/2 penalty for high-dimensional DNA methylation data.Technology and health care : official journal of the European Society for Engineering and Medicine · 2020Article
- Paternal DNA Methylation May Be Associated With Gestational Age at Birth.Epigenetics insights · 2020Article
- Epigenetic aging is accelerated in alcohol use disorder and regulated by genetic variation in APOL2.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2020Article
- A Network-guided Association Mapping Approach from DNA Methylation to Disease.Scientific reports · 2019Article
- SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.Nucleic acids research · 2018Article
- Frequency of heavy vehicle traffic and association with DNA methylation at age 18 years in a subset of the Isle of Wight birth cohort.Environmental epigenetics · 2018Article
- CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data.Nucleic acids research · 2018Article
- Article
- Changes in DNA Methylation from Age 18 to Pregnancy in Type 1, 2, and 17 T Helper and Regulatory T-Cells Pathway Genes.International journal of molecular sciences · 2018Article
- Modeling the Causal Role of DNA Methylation in the Association Between Cigarette Smoking and Inflammation in African Americans: A 2-Step Epigenetic Mendelian Randomization Study.American journal of epidemiology · 2017Article
- Accounting for tumor purity improves cancer subtype classification from DNA methylation data.Bioinformatics (Oxford, England) · 2017Article
- An epigenome-wide DNA methylation study of PTSD and depression in World Trade Center responders.Translational psychiatry · 2017Article
- Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies.Genome biology · 2017Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
motivationThe Illumina BeadArray is a popular platform for profiling DNA methylation, an important epigenetic event associated with gene silencing and chromosomal instability. However, current approaches rely on an arbitrary detection P-value cutoff for excluding probes and samples from subsequent analysis as a quality control step, which results in missing observations and information loss. It is desirable to have an approach that incorporates the whole data, but accounts for the different quality of individual observations.
resultsWe first investigate and propose a statistical framework for removing the source of biases in Illumina Methylation BeadArray based on several positive control samples. We then introduce a weighted model-based clustering called LumiWCluster for Illumina BeadArray that weights each observation according to the detection P-values systematically and avoids discarding subsets of the data. LumiWCluster allows for discovery of distinct methylation patterns and automatic selection of informative CpG loci. We demonstrate the advantages of LumiWCluster on two publicly available Illumina GoldenGate Methylation datasets (ovarian cancer and hepatocellular carcinoma). AVAILABILITY: R package LumiWCluster can be downloaded from http://www.unc.edu/∼pfkuan/LumiWCluster.
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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.