General Information

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Project Description

This project aims to unravel the impact of ARID2 mutations on immune escape in melanoma. By elucidating the functional consequences of ARID2 loss and mutation and investigating the association with immune escape mechanisms, this research will provide valuable insights for advancing melanoma treatment strategies and improving patient outcomes.

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Weekly Log

Week 1:

My first week I became familiarized with melanoma epidemiology and researched avaiable databses that contained melanoma mutation data. I also created my first presentation introducing my research goals.

Week 2:

After familiarizing myself with driver mutations in melananoma and the genes we will be studying my first task was to create a progam that collects data in an efficient way from cBioPortal where free data is available on mutations of melanoma patients. I created a program that specifically makes a tsv files with all the mutations of each patient as well as the oncogenic annotation of these mutations and the genetic subtype of the patients melanoma muatations. This program will help us collect data on gene mutations faster and more efficiently and prepare us for an easier stastistical analysis on the data.

Week 3:

I attended my first lab meeting, meeting all the other lab members working on other projects in cancer research. For this week we updated the code to make it repeatable for other melanoma case studies from other databases. I also organized the code according to mutation status to make stastistical analysis easier.

Week 4:

This week we met with stastistical professionals at Rutgers to discuss how we should procede with our data. We decided to use Fisher's exact test on our data, which has finally been programmed to the exact format needed for analysis. We filtered out any mutations that were not significant for our study.

Week 5:

With the cbioportal data neaerly finalized I worked on finding other databses with avavilable melanoma mutation data for us to solidify our results with more samples. The best database I found was ICGC, Internation Cancer Gene Consortium, which had over 700 samples for us to study.

Week 6:

I built a web scraper with selenium to scrape the ICGC database of over 150 mutations that we are interested in from BRAF, NF1, RAS, and ARID2 genes. The code took a long time to create and run through all these mutations but it collected all the data in a readabel format for us to study further.

Week 7:

We found an error with the cBioPortal data when applying fischers exact test. I found that there were not enough Triple WT samples but was able to fix the issue and we completely finalized the cbioportal data and are now working on fischers exact test and on studying mrna expressions from heatmaps.

Week 8:

This week was final presentations so I gathered all my code and data and created results. I created two bar graphs in Prism to show the distribution of ARID2 mutations across other melanoma associated mutations. I then worked on the rest of my presentation while finalizing my results.

Week 9:

This week my mentor was focused on teaching me how to write a good reserach paper. I gathered all the resources throughout the summer that taught me about melanoma mutations and epidemiology and used them as references. This week I completed all my REU goals!

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Presentations

• Final Presentation

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Additional Information

• My Mentors
  • Dr. Jian Cao
  • Connor Mattivi