Situation
Our Client, a biotechnology company developing novel cancer therapeutics, needed to identify cancer types containing a specific cell population of interest. This identification was crucial for developing a therapeutic that selectively targets these cells. Lacking the internal resources to conduct this complex bioinformatics analysis, the company partnered with Bridge Informatics (BI) to leverage our expertise in data mining and analysis.
Strategy
BI, after understanding Client’s objectives and goals, provided an experienced bioinformatician to collaborate with their research team who drafted and executed on a statement of work that included the following:
- Mining public data: Utilized The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) for bulk transcriptional analysis to identify potential cancer types expressing markers suggestive of Client’s target cell population.
- Acquiring and processing single-cell data: Downloaded relevant scRNA-seq datasets from NCBI Gene Expression Omnibus (GEO), focusing on recent publications with human samples of the identified cancers. A cloud environment was utilized for efficient data management and processing ensuring high scalability and speed.
- Performing in-depth single-cell analysis: Employed the Seurat pipeline for quality control, normalization, dimensionality reduction, clustering, and differential gene expression analysis of the scRNA-seq data, pinpointing the cell type of interest and novel marker genes.
- Delivering actionable results: Provided Client with a prioritized list of cancer types and a detailed CSV file containing a dataframe of novel marker genes for targeted therapeutic development.
Results
Within two weeks, BI delivered valuable insights to Client, enabling them to accelerate their drug development process:
- Data-driven target identification: Client received a prioritized list of cancer types likely to contain their target cell population, supported by both bulk and single-cell transcriptomic evidence.
- Novel marker gene discovery: Client obtained a list of novel marker genes uniquely expressed by the target cell population, facilitating the development of highly specific therapeutics.
By leveraging BI’s bioinformatics expertise and data mining capabilities, our Client gained crucial insights for developing targeted cancer therapies, optimizing their research strategy and accelerating their progress towards more effective treatments.
Interested in partnering with Bridge Informatics? Contact us to learn more about our team of bioinformaticians with experience at the bench whose core specialty is understanding and analyzing biological data.
Jessica Corrado, Head of Business Development & Commercial Operations, Bridge Informatics
As the Head of Business Development & Commercial Operations, Jessica is responsible for driving strategic growth initiatives and overseeing the company’s commercial activities. She has both a keen understanding of the life sciences industry and a strong track record in building successful partnerships.
Prior to joining Bridge, Jessica held a number of leadership roles across sales, marketing, and communications. Outside of work, Jessica is responsible for the majority of marketing and event planning for Shore Saves, a non-profit animal rescue. She enjoys reading and is often reading at least two books of various genres at a time. If you’re interested in reaching out, please email [email protected].
