Mitochondrial Genetics and Espresso Shots

Winter 2014

Andy (Guan Xiang) Zeng

Schulich Leader at Simon Fraser University

This past summer, I did an internship at the Genome Sciences Centre (in the BC Cancer Agency) under Dr. Angela Brooks-Wilson (The corresponding picture is a 3AM selfie in front of the BCCA). The project that I was hired for involved investigating the mitochondrial genomes of ovarian cancer patients, and assessing for any associations between specific mitochondrial mutations and ovarian cancer susceptibility. The internship began with technical laboratory work, in which I did tumor extractions and amplified mitochondrial DNA as a means of sample preparation for DNA sequencing.  With over one thousand samples to process, it wasn't a surprise that the technical work got repetitive and tiring through the course of the summer.

In order to address this, I realized that I had to shift my perspective towards how I looked at the laboratory work.

I constantly reminded myself of the humanitarian aspect of the project: each tissue samples came from the tumor of a woman who either passed away from ovarian cancer, or is actively fighting it at present. Keeping this in mind instilled a strong humanitarian purpose into the work, and helped to keep everything in context so that the task would not be reduced to merely a matter of "sample processing". In addition to this, I also aimed to understand the theory behind the project and strived to contribute on a theoretical basis as well. I started burning through academic papers on mitochondrial DNA  sequence analysis, and it really shed light on the entire research project, allowing me to learn about the components of the research project that would entail after all of the sample processing and the DNA sequencing.

Reading through my first academic paper on mitochondrial DNA analysis was a very difficult process, and it took me nearly 2 weeks before I could fully understand the paper and all of the jargon it used. I started getting faster and faster and soon I would only take a few hours to get through each paper. Halfway into the summer, I had gained enough proficiency in my 'mitochondrial sequencing literacy' that it would only take me 20 minutes or so to go through a paper, identify the relevant pieces of information, and apply them towards my work. I realized that I was navigating through an S-shaped learning curve (of sorts), and the awareness of the process served to add more excitement to my readings. Nearing the end of the summer, I began to gain expertise in the field and started to look at things beyond the project that I was hired for. I proposed to do an independent project, which I am currently working on now. 

The premise of my research project is to extract mitochondrial DNA sequences from existing datasets of Whole Genome Sequencing data and run secondary analysis on it. Often, when researchers aim to inspect the DNA of cancerous cells, they may generate both Nuclear and Mitochondrial DNA Sequences (through their sequencing process), but will disregard the mitochondrial sequence as contaminant and only analyze specific components of the nuclear sequence. I am taking advantage of this, and 'dumpster diving' to characterize the mitochondrial genomes of their samples.  This eliminates the sample collecting and processing steps, and ultimately reveals insight into the genetic aberrations experienced by mitochondrial genomes in specific types of cancer.
At this point, I have veered into the realm of bioinformatics (quite a change from my physiology major), and must familiarize myself with statistics and computer science in order to properly analyze my data. Fueled by the 7th floor espresso machine, I am currently in the midst of drawing up a statistical plan for analyzing these mitochondrial genomes, and really looking forward to the results ahead.

My internship this summer has provided me with an abundance of opportunities, and helped me to transform my interest in research into a passion.