Biomarker Informatics

Our client had an ex vivo tumor evaluation platform that maintained the tumors’ cellular structure. The platform collected data on the efficacy of various drug treatment candidates with the intention of biomarker identification for more personalized medicine. We defined strategies and technologies and provided bioinformatics and statistical analysis on provided patient sample data. Since they did not have in house bioinformatics capabilities, we performed an assay statistical analysis resulting in data interpretations and visualizations to guide their bioinformatics strategy..

Delivery

Strategy and Requirements Gathering:

We evaluated appropriate technologies (Python, AWS) for bioinformatics support and analysis and selected appropriate visualization tools required to produce publication quality visualizations.

We defined and road-mapped future technology platform to streamline and automate the way in which project data analysis was performed. Moreover, we worked with the R&D and immuno-oncology scientific teams to bridge bioinformatics and data science expertise for a growing number of projects.

Analysis and Informatics Execution:

DNA SNPs mutation were identified by Dicer1 analysis across multiple cell lines. We analyzed RNA transcriptomics by Nanostring and RNA Seq, interrogated high-dimensional flow and mass cytometry, integrated quantitative pathology, and other next-generation approaches.

We derived signatures, patterns, mechanisms, and other biological phenomena that associated with therapy responses across dozens of solid tumor types and responses to dozens of drug regimens and combinations.

We implemented Python data visualization scripts and

 conducted statistical analysis across multiple studies that used for publications.

We established initial AWS infrastructure and compute resources and used AWS Elastic Cloud Computing in order to ramp up for future analysis.

Value

Arrayo was able to propose a strategy based on the specific needs of our client, taking account for their in-house capabilities. The road map was utilized to show future value of implementing a data science and analytics platform to the C suite. All informatics pipeline and NGS analysis and visualization tasks were prioritized and completed. The results of these analysis and visualizations supported the overall direction and strategy of the company.