Back in March, I wrote about Biomarkers and Personalized Medicine Meetings in 2011 that I was interested in attending. One of the meetings that somehow didn’t make the list was Cambridge Healthtech Institute’s ADAPT Congress, Making Personalized Medicine a Reality, which runs later this week in Philadelphia (September 7-9th). If you’re on Twitter, you can follow along using the hashtag #ADAPT2011.
As it turns out, I’ll be speaking at the conference on Friday, September 9th. Covance is sponsoring a breakfast presentation during the Biomarker Discovery Informatics Track to describe their new BioPathways resource located on Covance.com. I played and am playing a significant role in the development of BioPathways, so it made sense for me to present it at the conference.
I ran a story about this on Friday last week over at Biomarker Commons: Covance BioPathways for Biomarker Discovery. Below are the slides I’ll be showing during my presentation at the ADAPT Congress.
Slide 1: My name is Walter Jessen. I’m a computational biologist with the Covance Biomarker Center of Excellence in Greenfield, Indiana. Today I’m going to talk to you about Covance BioPathways for Biomarker Discovery.
Slide 2: The Biomarker Center of Excellence is a division of Covance Discovery and Translational Services (DTS), which was formed last year. Computational biology in Covance DTS spans two service lines: the Biomarker Center of Excellence and Covance Genomics Laboratory (what used to be Rosetta; in 2009, Covance bought the genomic analysis division of Merck’s Rosetta operation).
Slide 3: There were three key drivers in the formation of Covance DTS, all of which are focused on helping our clients bring the miracles of medicine to market sooner.
Slide 4: Currently, there are over 740 validated assays between Covance Central Labs (GCP compliant, CAP/CLIA certified laboratory) and the Biomarker Center of Excellence (research environment laboratory, follows SOP-based “Good Research Practices”).
Slide 5: One of the problems we found that our clients have is the problem of information in the decision pathway. It’s often difficult for clients to identify validated assays; there’s often a disconnect between the analyte to be tested and gene/protein; and assays aren’t presented in the context of data.
Slide 6: In addition, we’re moving from target-based biomarker discovery using 1 or 2 genes to pathway-based biomarker discovery using gene signatures.
Slide 7: Thus, a “desirable biomarker” today is not only (1) easily & objectively measured, and (2) reflects an endpoint, but it also (3) can be evaluated with other biomarkers simultaneously and is (4) useful in many contexts.
Slide 8: To address these issues, we’re mapping all of Covance’s assays and antibody products onto biological and disease pathways.
Slide 9: This contextualizes Covance’s scientific capabilities around biological and disease pathways and provides several benefits to clients.
Slide 10: We’re calling this tool, which maps validated assays and antibody products — something we think is novel in the space — Covance BioPathways.
Slide 11: The Covance BioPathways homepage allows users to search by keyword, restrict their search to cateories or browse pathway categories.
Slide 12: Pathways are organized into three main categories — Regulatory processes, Diseases and Protein Regulatory Pathways — each of which contain a number of sub-categories.
Slide 13: The search results page lists individual pathways on the right and, in the left sidebar, maps them onto subcategories.
Slide 14: On an individual pathway page, the header lists categories and subcategories the pathway maps onto. Every pathway includes links for custom assay development and validation, and custom antibody services. The pathway map itself is interactive — mousing over a pathway node will show available services/products. Every node that has a service and/or product associated with it is currently indicated with a shopping cart.
Slide 15: Below each pathway is a description and list of references.
Slide 16: Clicking on a pathway node will populate the sidebar with detailed information.
Slide 17: At top, there are links to an assay request form (if an assay is available) and/or to the Covance Antibody Products store (if an antibody is available). Below are gene/protein details with links to Entrez, Swiss-Prot, OMIM, Ensembl, UniGene and dbSNP records.
Slide 18: Covance BioPathways is the information solution. BioPathways makes it easy for clients to identify validated assays; it links analyte with gene/protein; Covance services and products are presented in the context of data; and it accelerates the path forward to decisions.
Slide 19: Covance DTS in Greenfield indiana has three buildings with over half-a-million square feet of laboratory space, housing the Biomarker Center of Excellence, Imaging, Flow Cytometry, In vivo Pharmacology, Pathology, and other services.
Walter Jessen is a digital strategist, writer, web developer and data scientist. You can typically find him behind the screen something with an internet connection.