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Illumina Infinium MethylationEPIC BeadChip (850k) data of primary cancer-associated fibroblasts (CAF) isolated from fresh ex vivo germ cell tumor (GCT) patient tissue

ABSTRACT: Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of primary CAF isolated from fresh ex vivo GCT patient tissue. Purity of CAF populations were verified by qPCR analysis of common CAF, GCT, endothelial and epithelial markers. 14 different CAF cultures from distinct GCT subtypes (seminoma(SE), non-seminoma(NS)) and 5 non-malignant fibroblast cultures were analyzed.

ORGANISM(S): Homo sapiens

PROVIDER: GSE228405 | GEO | 2024/06/21

REPOSITORIES: GEO

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RNA sequencing data of primary cancer-associated fibroblasts (CAF) isolated from fresh ex vivo germ cell tumor (GCT) patient tissue

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Illumina Infinium MethylationEPIC BeadChip (850k) data of germ cell tumor-related somatic-type maligancies

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Proteome characterization of germ cell tumor-related somatic-type malignancies for the identification of tissue origin, cisplatin resistance mechanisms, and putative therapeutic options

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DNA methylation profiling for 850k reannotation and normalization evaluation [850k]

Project description:Illumina Infinium DNA Methylation (5mC) profiling arrays are a popular technology to measure genome-scale distribution of 5mC at low cost and high throughput, especially in cancer and other complex diseases. Following the success of the HumanMethylation450 array (450k), Illumina released the MethylationEPIC array (850k) featuring increased coverage of enhancers in addition to regulatory regions primarily covered by the 450k (i.e. promoters, gene bodies). Despite its widespread use, the analysis of 850k data remains suboptimal as it mostly still relies on Illumina’s default annotation, which underestimates enhancers and long noncoding RNAs (lncRNAs). We thus developed an approach, based on ENCODE and LNCipedia databases, that greatly improves Illumina’s default annotation of enhancers and long noncoding transcripts. Comparisons between the re-annotated 850k and its precursor, the 450k, or RRBS, another high-throughput 5mC profiling technology, revealed that the 850k covers at least three times more enhancers and lncRNAs than the other two technologies. We further investigated the reproducibility of the three technologies and applied various normalisation methods to 850k data, showing that most of them reduce variability to a level below that of RRBS. When analyzed with our new annotation and normalization pipeline, profiling for 5mC changes in breast cancer biopsies with the 850k highlighted aberrant enhancers methylation as the predominant feature, confirming previous reports. In conclusion, our study provides an updated analysis pipeline for 850k data based on a refined probe annotation and normalization that allows for the improved analysis of methylation at enhancers and long noncoding transcripts.

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Project description:Compare the difference between pairwise aNOF and CAF samples for two patients patient #225: aNOF #225 vs CAF #225 patient #248: aNOF #248 vs CAF #248

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