Characterizing Nsd3 Amplification In Lung Cancer

<strong>SGC Open Notebook Project to Characterize the HMTase NSD3</strong> <strong>Exp020 Objective: </strong>NSD3 (WHSC1L1) is amplified in ~5% of Non-Small Cell Lung Cancer patients( cBioPortal : Cerami et<br> al. Cancer Discov. 2012 and Gao et al. Sci. Signal. 2013). However, the implications of this event on the<br> formation and progression of the disease are unclear. While NSD3 may be a driver of lung cancer, it is also<br> plausible that this locus is simply amplified at a higher frequency in the context of cancer-associated genomic<br> instability. To dive deeper into this question I will use The Cancer Genome Atlas (TCGA) lung cancer<br> data-sets to look for associations between NSD3 amplification and mutational status as well as gene expression<br> profiles. This data has been generated by the TCGA Research Network: http://cancergenome.nih.gov/. I<br> hypothesize that if NSD3 amplification is a driving force in a subset of lung tumors, these samples will share<br> similar gene expression profiles and exhibit higher expression levels of NSD3. Here, I am using FirebrowserR<br> (Deng M., et al. Database. 2017 - PMID:28062517), an R client for Broad Institute’s Firehose Web API,<br> which allows TCGA data processed by the Firehose Pipeline to be directly imported into R for analysis.