Transcriptomics

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A minimal DNA 5-methylcytosine signature of oral tongue squamous cell carcinoma [methylation]


ABSTRACT: Oral tongue squamous cell carcinomas (OTSCC) are a homogenous group of aggressive tumors in the head and neck region, with a rising incidence among younger population. The role of altered DNA methylation in OTSCC and its link with clinical parameters has not been fully assessed yet. We performed genome-wide methylation analysis of oral tongue primary tumors (n = 52) using 485, 512 probes and correlated altered methylation with differences in gene expression. We used an ensemble machine-learning algorithm to identify differentially methylated probes and regions predictive of survival, risk habits, nodal status, tumor stage, and HPV infection followed by validation using data from the cancer genome atlas (TCGA) project on oral tongue (n = 24) and tumors from all subsites of head and neck region (n = 50). Bisulphite converted DNA from the 52 tumor:matched control sample pairs were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

ORGANISM(S): Homo sapiens  

SUBMITTER: Kunal Dhas  Jayalakshmi Nair   binay panda   Vikram Kekatpure   Moni A Kuriakose   Binay Panda   Amritha Suresh   Gangotri Siddappa   Neeraja M Krishnan    

PROVIDER: E-GEOD-75537 | ArrayExpress | 2016-06-01

SECONDARY ACCESSION(S): GSE75537PRJNA304506

REPOSITORIES: GEO, ArrayExpress

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