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Jaewon Oh - Week 5 and 6

To be frank, I have felt completely lost in the lab for the past 6 weeks. I thought I would be working with prostate cancer and phylogenetic trees in the spring. Then I read a paper on ALK receptors two weeks before coming to my lab. That didn't work out, so I moved on to doing all sorts of analyses of the p53 gene. I wish I had a set plan when I first came into the lab six weeks ago. I wish I could have seen a clear starting and end point to a project that I would be working on. But, I have learnt the hard way, that research is not what it seems. You may encounter all sorts of problems, or think of better ways to proceed with your investigation, that your methods and/or final goal may continuously change.

Finally, I am starting to have a sense of what my final project may look like. After being away at conferences for around a week and a half, Dr. Townsend came back to the lab and we had a meeting to discuss the RFS paper that Dr. Cannataro introduced to me while Dr. Townsend was away. We read through the article, and Dr. Cannataro and I showed him what we had been working on while he was away (comparing their RFS values with our selection intensity). He liked what we were doing with the data, but he decided that we focus on two specific graphs (Fig4 A and B). 

Our goal was to recreate the graphs by keeping their RFS values, but using our own p53 prevalence data. Then after recreating those graphs, we would divide it by our labs mutation rates, and hope to see a clustering of data points. The first problem we encountered was in using the correct prevalence data to compare to the RFS values. We first thought we could use our proportion values until we realised that the values were based on the number of patients in a study instead of across all tumors. So I had to calculate new proportion values for tumor specific mutations. Then we realised that we didn't have data on all the variants that appeared in the original Fig4A and B graphs because our data only contains values of mutations that are seen within the human population (explaining the fact that most the points we were getting had high RFS values). This is a problem that will be tackled starting next week.

I am undeniably scared that I won't have anything concrete to present when I get back to school. In the final two weeks that I have remaining, I hope we can find and also create the exact kinds of data needed to compare with the data from the RFS article.

Other than the stress I am feeling with the work I am doing in the lab, I was happy to see Mr. Sham. Being in New Haven by myself is quite a bore because I don't have anyone around me. #loner. It was nice to finally have someone to vent to about the stress of feeling lost in the lab, and not necessarily enjoying the type of research I am involved in. But like he said, it's a consequence that I brought upon myself and need to deal with. Don't get me wrong, I am finding value in my experience here, but if I looked at labs a little more carefully fall term junior year, I might not be sitting in front of a computer all day. ¯\_(ツ)_/¯ 

Link to article for reference: https://www.cell.com/molecular-cell/fulltext/S1097-2765(18)30454-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1097276518304544%3Fshowall%3Dtrue

Comments

  1. speretzAugust 6, 2018 at 6:08 AM

    Jaewon,
    Sounds like science! It can be frustrating. Experiments change, and you are there at the start of a new experiment which means that the path is not clear to you, but also not to the other members of the lab. Don't stress too much about your poster, you will just document what you did do, you will not be the only person who joined a lab at the start of an experiment. (Grab some New Haven pizza to cheer up when needed!)

    ReplyDelete

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