October 14, 2004 | A clinical researcher compares gene-expression profiles from two tissues — one diseased, the other normal. A drug researcher looks at changes in expression profiles after administration of a small chemical compound. The data from these experiments are a lengthy list of genes that are upregulated, downregulated, or unchanged. And typically, the bemused researcher asks, "What does it all mean?"

Deciphering such vast volumes of genomic data is tedious, confusing, and might not lead to the desired result — a clear understanding of what is going on inside the cell. This elusive understanding of biological data is the primary gating factor to realizing the full benefits of the genomics revolution and substantial investments to date.

Several companies, including Entelos, Gene Network Sciences, Genstruct (see The Russell Transcript, page 66), and Ingenuity Systems market applications that can interpret genomic data, identify interacting partners, and generate biological pathways diagrams. Pathways analysis applications are being introduced into all phases of the pharmaceutical value chain, and may well be the key to finally realizing significant returns on -omics investments.

Life Science Insights recently completed a survey of scientists and executives at major biopharmaceutical companies who use the pathways analysis application developed by Ingenuity Systems. Although this software has been commercially available for only a year, Ingenuity claims nine of the top 10 pharmaceutical companies as customers, including Pfizer, Wyeth, GlaxoSmithKline, and Aventis.

Many Happy Returns Our report concluded that companies that broadly deploy pathways analysis applications throughout the drug development process received a considerable return on investment. Additional findings indicate that organizations may gain the following extraordinary benefits: Increase overall product development productivity by approximately 10 percent Reduce the cost of developing a drug by $90 million Limit the number of failures by one-third Speed time to market and increase revenue by extending patent protection Increase sales by improving life-cycle management via competitive differentiation and reaching target patient populations Add value through increasing collaboration and communication, both internally and externally, such as with the FDA during the submission process

The Ingenuity application enables scientists to analyze multiple data sets concurrently across different experimentation platforms and identify key functions and pathways that distinguish biological states. The Web-delivered application makes use of the Ingenuity Pathways Knowledge Base, touted as the world's largest curated database, consisting of millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases.


Applications and Benefits 
Although pathways analysis has many possible applications, three scenarios are worth highlighting.

The first scenario identifies the value of incorporating pathways analysis during target identification and validation. Researchers using pathways analysis achieve greater understanding of the relevant biology and a higher level of experimental confidence. Pathways analysis also identifies targets not observed during gene-expression analysis because they were not differentially expressed. Researchers performing target validation prioritized potential drug targets based on data provided through pathways analysis.

A senior executive at a large pharmaceutical company shared a second scenario. This individual's experience recommended pathways analysis during preclinical studies and, in particular, in choosing the appropriate animal model. Performing preclinical studies on the wrong model, based on preliminary data or literature analysis, may lead to failures, costly delays, and repeated work. Pathways analysis implementation during the preclinical phase provides a complete picture of the biological landscape necessary to make the most informed decision of which animal model to investigate during preclinical studies.

The final scenario is that of a researcher comparing his or her company's drug and that of a competitor. Pathways analysis effectively demonstrated that the competitor's drug activated an unrelated pathway that may lead to unidentified adverse side effects. Such data could provide a competitive market advantage, possibly boosting sales.  

Zachary Zimmerman is a senior research analyst for Life Science Insights. Email: zzimmerman@idc.com. 


The full report, "The Return on Investment for Ingenuity Pathways Analysis Within the Pharmaceutical Value Chain," is available free of charge at www.ingenuity.com/ROI.