Computational protocol: An integrative pan-cancer-wide analysis of epigenetic enzymes reveals universal patterns of epigenomic deregulation in cancer

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Protocol publication

[…] For the ten cancer types mentioned above, DNAm data generated with the Illumina Infinium HumanMethylation450 BeadChip array [] were downloaded from TCGA data portal. The methylation level for each probe was obtained as the beta value, which was calculated from the intensity of methylated (M) and unmethylated (U) alleles: beta=Max(M,0)/[Max(M,0)+Max(U,0)+100]. The beta ranges from 0 (unmethylated) and 1 (fully methylated). Probes with missing data (i.e. NAs) in more than 70 % of the samples were removed. The rest of the probes with NAs were imputed using the k-nearest neighbors (knn) imputation procedure []. Subsequently, BMIQ was used to correct for the type II probe bias []. Data from each cancer type was then subjected to the same SVD quality control analysis, as done for gene expression. [...] Illumina 450k DNAm data for 30 normal samples (from healthy women), 21 normal samples adjacent to breast cancers, and 165 breast cancer samples were collected within the Bavarian Breast Cancer Cases and Controls Study 2. The Ethics Committee of the Medical Faculty, Friedrich-Alexander University approved the study (re. no. 4514) and all patients gave written informed consent. The study was done in adherence to the Declaration of Helsinki. Data are available in the Gene Expression Omnibus (accession number GSE69914). Raw data files were processed using the minfi, impute and BMIQ/ChAMP Bioconductor packages. […]

Pipeline specifications

Software tools BMIQ, minfi
Databases GEO TCGA Data Portal
Application DNA methylation array analysis
Diseases Neoplasms