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Epigenome wide DNA methylation assay of gingivo-buccal oral squamous cell carcinoma using single base resolution high throughput array

Gingivo-buccal oral squamous cell carcinoma (OSCC-GB) is the most common cancer among men in India and is associated with high mortality. Although OSCC-GB is known to be quite different from tongue cancer in its genomic presentation and its clinical behavior, it is treated identically as tongue cancer. Predictive markers of prognosis and therapy that are specific to OSCC-GB are, therefore, required. To achieve this, we have carried out epigenomic (n=87) profiling of paired tumor-normal tissues collected from OSCC-GB patients from India and genome-wide DNA methylation assays were performed. DNA was isolated using DNeasy Blood and Tissue Kit (Qiagen). The purity and concentration was estimated using NanoDrop 2000 (Thermo Fisher Scientific). Approximately 500 ng genomic DNA from each sample was used for sodium bisulfite conversion using the EZ DNA methylation Gold Kit (Zymo Research, USA). Genome-wide DNA methylation was assayed using iScan (Illumina), for paired tumour and adjacent normal samples of 25 patients using the Infinium Human Methylation450 BeadChip and of 62 patients using the Infinium MethylationEPIC BeadChip.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00010001850 Illumina Infinium 450K BeadChip Array; Illumina Infinium EPIC Beadchip Array 174
Publications Citations
Epigenomic dysregulation-mediated alterations of key biological pathways and tumor immune evasion are hallmarks of gingivo-buccal oral cancer.
Clin Epigenetics 11: 2019 178
Application of Random Forest and data integration identifies three dysregulated genes and enrichment of Central Carbon Metabolism pathway in Oral Cancer.
BMC Cancer 20: 2020 1219