Bioinformatics pipeline for the analysis of Tumor Mutational Burden and Enhancer RNAs

In this work Tumor Mutational Burden (TMB) and eRNAs have been stu- dided. In particular computational pipelines have been developed the analy- sis of NGS data in these context. The first project is a comprehensive study of Tumor Mutational Burden (TMB) in several type of cancer, conducted with the IOM Ricerca, Viagrande. The aim of the study is to establish a reliable signature of gene allowing the estimation of TMB from a targeted panel. TMB is a biomarker used in clinical practice that make possible to identify the patients who can more benefit from immunotherapy. It mea- sures the number of mutations per coding area of tumor genome. Our analysis can be divided into different phases: upstream and down- stream. In upstream analysis we performed the Alignment, Bam Process- ing, Variant calling and Annotation. In the downstream analysis we have performed Survival analysis, Enrichment analysis, Correlation Analysis, Lo- gistic regression and Microsatellite instability analysis. The second part of the work concerns the study of enhancer RNA, conduced in collaboration with the team of Dr. L. Cascione, at the Institute of On- cology Research (IOR), Bellinzona, Switzerland. The eRNA are non-coding RNA molecules transcribed from the DNA sequence of enhancer regions. They are linked to the development of the disease through the regulation of transcription. Indeed in recent years particular attention was paid to determining and knowing the exact role of the enhancer in gene regulation. In this work we mainly dealt with the bioinformatics part of the project, with the aim of quantifying the enhancer RNA for two different DLBCL cell lines (TMD8 and U2932). We have performed total RNA-Seq on RNA extracted from U2932 and TMD8, exposed to DMSO or PQR treatmenet for 4, 8, or 12 h. The first part of this analysis involved data preparation, in the second we conducted the differential expression analysis to quantify the eRNAs.