Thea Nikolaou/Dr. Solomon - Week 2

 This week I spent more time looking at slides with Dr. Solomon and learning the process pathologists use to identify cancerous cells and tumor content in biopsies or resections. I also learned more about the cancer staging guidelines and how that is facilitated by surgical pathologists. I was invited to attend pathology resident conferences where I got to hear about interesting call cases in pathology with issues ranging from a lack of weekend service and emergency testing requests to uncertainty in the protocol to be followed in specific cases. They also discussed the assay and equipment validation processes there, as the validation of properly working procedures is extremely important for reliable results that can be used to form conclusions and adjust patient diagnosis and treatment. It was also interesting to learn more about new findings in pathology from various papers discussed at the resident conferences. 

 I got to find out more about the molecular testing that occurs prior to bone marrow transplant with Dr. Rennert. She explained the types of tests performed and went through some cases where she determined which of the tested biomarkers are good candidates to monitor post-transplant to confirm the success of the operation as donor cells dominate over recipient cells. She explained the algorithm they use to determine these candidate biomarkers and how a patient's ability to receive the transplant depends on these findings: if no good biomarkers are identified, the recipient/donor pair is no longer considered a good match. I also got to spend some time in GI pathology and look at slides with Dr. Hissong where most cases were confirmations of normal GI tissue post treatment but also included some cases where the tissue was inflamed and patients were experiencing various symptoms. Dr. Hissong also arranged for me to spend some time in the gross room next week where the biopsied or resected tissues are prepared for microscopic observation. Finally, last Sunday I attended Dr. Prince's MRI course where we learned some MRI basics, how patients are prepped for a scan, how the machines are operated, and how to use the software to scan a patient. 

I'm excited to have a project underway for mutational signature identification from TSO500 data as well as one that I have started discussing with Dr. Solomon and Dr. Velu with image analysis to for an algorithm based determination of tumor content rather than relying only on a visual estimation. Determining sample tumor content could help filter out the noise in the assay results for a better analysis or direct pathologists to request better samples containing a higher percentage of tumor cells.  

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