Our team this year was inspired by the More Than Pharm to Table Challenge because we understand that integrating genomics in medicine is required to provide better guidance for prescribing physicians.
What it does
PGxInsight software was developed as part of the Hudson Alpha Tech Challenge 2022 in efforts to afford more comprehensive pharmacogenomic services to providers which integrate multiple pharmacogenomic databases & allow easy query of genetic test results.
How we built it
CPIC sql databases were parsed in pgAdmin 4 with postgresql. A csv file of each CPIC table was exported from pgAdmin4. The CPIC csv files & PharmGKB tsv files were converted to tab delimited text utilizing sed 's/,/\t/g' in bash. An Rscript was then utilized to perform full joins on the database based on a column with a common field. The Sample_Genetic_Data.json was parsed in Excel and converted to tab delimited text. The Sample_Genetic_Data.txt file was utilized to search gene variants in the integrated CPIC & PharmGKB database from the command line which generated the PharmGenResults1.txt report. A web-interface developed with python delivered through a service called Streamlit. It was created to allow providers the ease of uploading their genomic data reports which are then searched against an integrated PharmGKB and CPIC database to generate a pdf report tailored to a laboratory director's preference.
Challenges we ran into
Designing a user interface and integrating PharmGKB and CPIC databases was not any easy task. We were unfamiliar with the structure of pharmacogenomics data as well as how to tackle app development. We gained many new skills over the course of this challenge that were slightly outside our areas of expertise.
Accomplishments that we're proud of
We are proud that we overcame many obstacles during this challenge, and that we were successful in achieving the tasks that were set in front of us.
What we learned
We learned how to query sql data in postgresql, parse json files, design our own app, and generate pdf files for the first time.
What's next for PGxInsight
We hope that our application will lead to the development of better patient care in pharmacogenomics.
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