ArticleNucleic acids research2018
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 416 papers.
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Who cites it
416 citing papers in PubMed.
- Effects of daily multivitamin-multimineral and cocoa extract supplementation on epigenetic aging clocks in the COSMOS randomized clinical trial.Nature medicine · 2026Trial
- A predictive endocrine resistance index accurately stratifies luminal breast cancer treatment responders and nonresponders.The Journal of clinical investigation · 2025Trial
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- Non-parametric differential methylation analysis characterizes histotype-specific promoter regions in epithelial ovarian cancer.Epigenetics · 2026Article
- Differential methylation at novel putative imprinting control regions on chromosome 20 associated with childhood obesity.Epigenetics · 2026Article
- Clinical Epigenomics in Rare Diseases: Interpreting DNA Methylation Episignatures.Molecular genetics & genomic medicine · 2026Review
- Epigenome-Wide Association Study of Abdominal Aortic Aneurysm Identifies Central Role for Inflammatory Pathways.Circulation · 2026Article
- Recurrent mechanisms of biallelic epigenetic inactivation reveal new putative tumour suppressor genes in prostate cancer.Nature communications · 2026Article
- Posttraumatic Stress Disorder Epigenome-Wide Association Studies in the Million Veteran Program.medRxiv : the preprint server for health sciences · 2026Article
- Article
- DNA methylation profiling identifies long-range epigenetic silencing of clustered protocadherins as a key determinant of meningioma progression.Nature communications · 2026Article
- A skin-kidney neutrophil axis links ultraviolet exposure to renal angiogenesis and tissue remodeling in healthy and lupus kidneys.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- DNA methylation profiling enables subclassification of mucinous ovarian carcinoma and distinguishes it from extraovarian mucinous metastases.Cell reports. Medicine · 2026Article
- Sellar region neurocytomas exhibit a CIMP and neuroendocrine-like epigenetic signature distinct from other intra-axial neurocytomas.Acta neuropathologica · 2026Article
- Biallelic inactivating variants in the chromatin remodeler DMAP1 cause a syndromic neurodevelopmental disorder.The Journal of clinical investigation · 2026Article
- Longitudinal changes in epigenetic measures over 2 years: methodological implications.GeroScience · 2026Article
- DNA Methylation Profiling in IDH-Mutant Gliomas: Biological Evolution, Molecular Grading and Clinical Implementation.Neuropathology and applied neurobiology · 2026Review
- Depression, but not anxiety, is associated with epigenetic age accelerations among Asian older adults.Molecular psychiatry · 2026Article
- Leukocyte profiles reveal sex and age differences in immune investment in a polygynous bat.The Journal of animal ecology · 2026Article
- A machine learning approach to identify key epigenetic transcripts for ageing research in human blood (Epitage).Biogerontology · 2026Article
356 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
We report a new class of artifacts in DNA methylation measurements from Illumina HumanMethylation450 and MethylationEPIC arrays. These artifacts reflect failed hybridization to target DNA, often due to germline or somatic deletions and manifest as incorrectly reported intermediate methylation. The artifacts often survive existing preprocessing pipelines, masquerade as epigenetic alterations and can confound discoveries in epigenome-wide association studies and studies of methylation-quantitative trait loci. We implement a solution, P-value with out-of-band (OOB) array hybridization (pOOBAH), in the R package SeSAMe. Our method effectively masks deleted and hyperpolymorphic regions, reducing or eliminating spurious reports of epigenetic silencing at oft-deleted tumor suppressor genes such as CDKN2A and RB1 in cases with somatic deletions. Furthermore, our method substantially decreases technical variation whilst retaining biological variation, both within and across HM450 and EPIC platform measurements. SeSAMe provides a light-weight, modular DNA methylation data analysis suite, with a performant implementation suitable for efficient analysis of thousands of samples.
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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.