The goal of this project is to analyze the patterns in methylation across breast tumor, tumor-adjacent, opposite quadrant, and opposite breast tissue.
(Work in progress. Jotting down quick notes at the moment)
- Conventionally, breast cancer researchers have commonly used adjacent normal tissue as a comparison to tumor tissue in various genomic characterizations of breast cancer.
- The overarching hypothesis of this project is that the adjacent normal is in fact too similar to the tumor, sharing many of their genomic aberrations.
- We explore this hypothesis by comparing DNA methylations of tissues from tumor, tumor-adjacent, opposite quadrant, and opposite breast from breast cancer patients, as well as normal patients without breast cancer.
- Our results, whether it supports our hypothesis or not, will offer useful insight to the researcher community. If shown that the adjacent normal tissue is sufficiently different from tumor, it validates past methods. If our results show that adjacent normal tissue is quite similar to tumor and that other tissues (opposite quadrant or opposite breast) should be used, this will be informative for future experimental design.
All analysis surrounding this project was performed on Northwestern University's HPC Quest. The R/4.3.0 module was used.