The integration of genomic and epigenomic data is an increasingly popular approach for studying the complex mechanisms driving cancer development. We have developed a method for evaluating both methylation and copy number from high-density DNA methylation arrays. Comparing copy number data from Infinium HumanMethylation450 BeadChips and SNP arrays, we demonstrate that Infinium arrays detect copy number alterations with the sensitivity of SNP platforms. These results show that high-density methylation arrays provide a robust and economic platform for detecting copy number and methylation changes in a single experiment. Our method is available in the ChAMP Bioconductor package: http://www.bioconductor.org/packages/2.13/bioc/html/ChAMP.html.
High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays
An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays
Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.
Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.
Comparative analyses of chromosome alterations in soft-tissue metastases within and across patients with castration-resistant prostate cancer.
Genome-wide DNA methylation analysis of archival formalin-fixed paraffin-embedded tissue using the Illumina Infinium HumanMethylation27 BeadChip.
Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis.
Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform.
Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms
Identification and functional validation of HPV-mediated hypermethylation in head and neck squamous cell carcinoma
An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform
Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors
DNA Methylation Adds Prognostic Value to Minimal Residual Disease Status in Pediatric T-Cell Acute Lymphoblastic Leukemia
Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis
Sensitivity Analysis of the MGMT-STP27 Model and Impact of Genetic and Epigenetic Context to Predict the MGMT Methylation Status in Gliomas and Other Tumors
CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array
BACOM2.0 facilitates absolute normalization and quantification of somatic copy number alterations in heterogeneous tumor
Malignant Transformation of a Dysembryoplastic Neuroepithelial Tumor (DNET) Characterized by Genome-Wide Methylation Analysis
An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation
Initiation of aberrant DNA methylation patterns and heterogeneity in precancerous lesions of human hepatocellular cancer
cnAnalysis450k: an R package for comparative analysis of 450k/EPIC Illumina methylation array derived copy number data
Obligatory and facilitative allelic variation in the DNA methylome within common disease-associated loci
Recurrent chromosomal and epigenetic alterations in oral squamous cell carcinoma and its putative premalignant condition oral lichen planus
Differential DNA methylation at birth associated with mental disorder in individuals with 22q11.2 deletion syndrome
In silico DNA methylation analysis identifies potential prognostic biomarkers in type 2 papillary renal cell carcinoma
Genomic structural variations lead to dysregulation of important coding and non-coding RNA species in dilated cardiomyopathy
Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes
Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors
Genome-wide genetic and epigenetic analyses of pancreatic acinar cell carcinomas reveal aberrations in genome stability
Neuro-radiological characteristics of adult diffuse grade II and III insular gliomas classified according to WHO 2016
The central nervous system tumor methylation classifier changes neuro-oncology practice for challenging brain tumor diagnoses and directly impacts patient care
Large-scale evaluation of SLC18A2 in prostate cancer reveals diagnostic and prognostic biomarker potential at three molecular levels
Global epigenetic profiling identifies methylation subgroups associated with recurrence-free survival in meningioma
Identifying mislabeled and contaminated DNA methylation microarray data: an extended quality control toolset with examples from GEO
Genome-wide methylomic analysis in individuals with HNF1B intragenic mutation and 17q12 microdeletion
Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions.
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions
Infarction with associated pseudosarcomatous changes mimics anaplasia in otherwise grade I meningiomas.
Malignant transformation and genetic alterations are uncoupled in early colorectal cancer progression.
Correlation between genomic index lesions and mpMRI and 68 Ga-PSMA-PET/CT imaging features in primary prostate cancer
An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays.
MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer.
Cancer Genomics (Keystone)
Cancer genomics approaches employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Discover the latest research using such technologies in this feed.
Cancer Epigenetics & Metabolism (Keystone)
Epigenetic changes are present and dysregulated in many cancers, including DNA methylation, non-coding RNA segments and post-translational protein modifications. The epigenetic changes may or may not provide advantages for the cancer cells. This feed focuses on the relationship between cell metabolism, epigenetics and tumor differentiation.
Cancer Epigenetics and Senescence (Keystone)
Epigenetic changes are present and dysregulated in many cancers, including DNA methylation, non-coding RNA segments and post-translational protein modifications. The epigenetic changes may be involved in regulating senescence in cancer cells. This feed captures the latest research on cancer epigenetics and senescence.