Metastasis of HPV-negative oral cavity tumors: an in silico study

Abstract

Methodology: 20 samples from a collaborator’s cohort (AC Camargo ACC) and 22 samples from The Cancer Genome Atlas (TCGA) were analyzed. The raw data from ACC was filtered and quality checked using FastQC and Trimmomatic, respectively. The ACC reads were then aligned against the human genome GRCh38 using star method and genes were counted with RSEM package. TCGA cohort already possess pre-processed data. Differentially expressed genes were evaluated by DESeq2, the enriched pathways by Webgestalt and tumor microenvironment by xCell. Exclusively for the TCGA available data, the HLA-I alleles were identified by Optitype and subsequent neoantigen prediction was accomplished by netMHCpan. T and B-cell receptors (TCR and BCR) repertoire were identified and analyzed by MiXCR.