Whole Genome DNA Methylation and Gene Expression Profiling of Oropharyngeal Cancer Patients in North-Eastern India

Methylation of CpG Islands within promoter regions of genes has been associated with gene silencing, suggesting loss of tumor suppressor function and tumorigenesis. The northeastern states of India are leaders in the country for cancers of several sites. Almost no reports are available of any DNA methylation biomarker for oropharyngeal cancers of the northeastern states. The present study aimed to identify targets of CpG hypermethylation and hypomethylation in oropharyngeal cancer prevalent in northeast India. Using Illumina Infinium Human Methylation 450K microarray platform a genome wide screening has been done for differentially methylated genes, including genes not previously implicated in carcinogenesis. Differential gene expression correlated to their methylation status was elaborated using transcriptome profiling. The new genes identified may be used to develop promising panels of DNA Methylation biomarkers for oropharyngeal screening and detection at a very early stage. Whole genome DNA methylation profiling of oropharyngeal cancer in patients from north-east India. The Illumina Infinium 450k Human DNA methylation Beadchip was used to screen the entire DNA methylation profiles across 485577 CpG sites per sample at single-nucleotide resolution. Bisulphite converted DNA from the 16 paired and 10 unpaired samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip