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nci.nih.gov/tcga) (Table?(Table1).1). Tumor methylation data (M values) for CpG loci corresponding to the 22 CpG loci were extracted from DNA methylation data sets corresponding to these patients, and the samples sorted using hierarchical clustering. RNA-Seq data corresponding to the 33 OPSCC tumors from the TCGA were extracted for p14(ARF) and p16(INK4A) AZ191 (https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=HNSC&diseaseName=Head and Neck squamous cell carcinoma). Methods for sequencing and data processing of RNA using the RNA-Seq protocol have been previously described for TCGA 15. Briefly, RNA-Seq data were generated using Illumina TruSeq mRNA libraries, and sequenced by Illumina HiSeq2000. Workflow for processing and normalization of these data is described elsewhere (https://cghub.ucsc.edu/docs/tcga/UNC_mRNAseq_summary.pdf). Expression results were presented as normalized read counts. DNA methylation and gene expression data were not normalized or processed by our group in any way prior to analysis. Results HPV-positive OPSCC tumors display a unique epigenetic profile We showed previously that HPV+ oropharyngeal cancers exhibit significantly higher numbers of differentially methylated CpG loci (hyper- and hypomethylated) between tumors and adjacent normal mucosa compared to HPV? oropharyngeal, oral cavity, and laryngeal cancers 11 suggesting that a specific subset of CpG loci may be identified that could further stratify these cancers and reflect DNA methylation changes associated with LGK-974 supplier HPV. We tested a total of 46 patients undergoing treatment for histologically confirmed OPSCC at Montefiore Medical Center, Bronx, NY (Table?(Table1).1). When mining gene expression data from our head and neck cancer genomics database, HPV+ OPSCC tumors showed a significant increase in the expression of DNA methyltransferase 1 (DNMT1), the major eukaryotic DNA methyltranferase (unpaired t-test with Welsch correction, P?Apoptosis Compound Library clinical trial samples of 9 HPV-negative and 6 HPV-positive OPSCC primary tumors obtained previously from the Albert Einstein head and ... By analyzing genome-wide DNA methylation between tumor and matched normal tissue samples for a subset of OPSCC patients, 22 CpG loci were identified that showed a statistically significant difference in methylation (��M) when comparing HPV+ to HPV? OPSCC (Fig.?(Fig.1B).1B). Among these 22 CpG loci were four CDKN2A-specific loci located downstream of the p16(INK4A) transcription start site, two loci located within the CpG island of the GALR1 gene, and one associated with the PPP1R3D gene.