Characterizing NSD3 Amplification in Lung Cancer

SGC Open Notebook Project to Characterize the HMTase NSD3

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