BLT Stages

Abstract 2020-2021: AUTOMATIC CONSULTATION OF VARIOUS KEY SOURCES REQUIRED FOR BRCA1/2 VARIANT ANNOTATION

In the pathological department of the UZA biomarker analysis is done on tumors to determine the type of tumor, the pathogenicity and possible therapeutics for these tumors.

BRCA1 and BRCA2 are two genes that are linked to ovarium, breast and prostate cancer. After these genes are identified using next generation sequencing techniques, the genes are classified in one of five different classes according to their pathogenicity.

The classification is done by manually assessing databases. The goal of the project is to automize the consultation of these diverse sources needed for the classification. A python script is created that will automatically access these databases using modules to read excel, text and pdf files in the case of locally stored databases or access online databases through their available API or web scraping. The script will then extract the required information and summarize the clinical significance in a word document. To make the script user friendly a GUI was created and the script was converted into a stand-alone windows executable file.