Transcriptomics, Genomics, and Neurological Disease

I was part of the Helios Scholars program through the Helios Education Foundation and the Translational Genomics Research Institute, a part of City of Hope. During this program, I worked on a research project in bioinformatics.

I looked into RNA in cerebrospinal fluid, which is extremely sparse. One ongoing question is understanding what makes up RNA that does not appear to map to the genome in CSF. We know that there is something in the transcriptome that is mapping to something in the genome, but much of it is not understood, or “hidden” due to this sparcity. My project specifically looked at integrating the TEtoolkit suite in a Jinja2 pipeline and analyzing the outpute of this pipeline using Bioconductor in R.

We wanted to know if transposable elements acted as potential biomarkers for Parkinson’s disease, so analyses using DESeq2, pheatmap, and EnhancedVolcanoPlot compared those diagnosed with PD and healthy controls. Results require further analysis, but transposable elements were found in CSF. The abstract submitted for this project can be found on TGen’s website.

After my work as a Helios Scholar was over, I became an intern and now work full-time at TGen under Dr. Kendall Van-Keuren Jensen. I have since worked with data related to neurodegenerative diseases such as Alzheimer’s and Parkinson’s Disease, Schizophrenia, and helped with projects related to ALS and COPD amongst many other diseases. I have also had the opportunity to look at RNA-seq data in many types of biofluid and tissue, such as urine, plasma, and CSF. Further, I have learned to use many packages with R programming and have helped to further add to our bioinformatics pipeline.

This is an example of some deidentified code to illustrate how DESeq2 is used:

See PsychNStuff/BioNStuff for more!