Week 5 : Adil

Week 5 was a good mix of research and time in the clinic/OR. I continued to work with the ICSBCS datasets and preparing them for downstream analysis. This week I started selecting and preprocessing WGS data from the ICSBCS datasets. We plan to combine bulk RNA and WGS datasets for our downstream analyses. Since we do not have RNA seq/WGS data for each and every sample, we are currently trying to handle samples which have both types of data and will eventually shortlist them for downstream analysis. I am also trying to get access to a docker image of a deconvolution package which we plan to use for our downstream analysis.

On the clinical front, I attended the MDC tumor board on Monday. There were many cases from multiple doctors this week. Most of Dr. Newman's cases were follow-ups from her earlier surgeries - radiation and medical treatments were discussed. Later in the week I shadowed Dr. Newman for a few patient sessions in her clinic. Most of them were new cases wherein Dr. Newman discussed surgical plans for their treatments. Two cases particularly were advised mastectomies - one patient had a huge mass for her breast size and the other patient and multiple pre cancerous calcifications throughout her breast. In the OR, I shadowed Dr. Newman for a bilateral mastectomy and a bilateral sentinel lymph node biopsy.