Ahead of the digital 11th World Clinical Biomarkers & CDx Summit (Sept29– 30), Dr Jude O’Donnell spoke to World CB & CDx on her experience of planning ahead when it comes to clinical trial assay and CDx development and tying this to Dx performance, regulatory compliance and downstream success of a drug development program.
Read the full article below- total read time 10 minutes.
You can also register for World CB & CDx here.
Dr Stewart McWilliams, VP of Quality and Regulatory Affairs at Almac Diagnostic Services, in conjunction with John Wise and Mike Furness from the Pistoia Alliance and Simon Patton from EMQN have produced an interesting paper on CDx, NGS and Regulation – Five Perspectives.
Companion diagnostics (CDx) are essential to the practice of precision medicine. Next-generation sequencing is an increasingly important tool in the development of CDx. However, for CDx to be deployed, many different biopharma industry sectors need to collaborate. This paper outlines some of the challenges and opportunities perceived by the biopharmaceutical industry, the Europe Molecular Quality Network, a regulatory agency, a notified body, and a CDx service provider.
Background:
There is a clear need for assays that can predict the risk of metastatic prostate cancer following curative procedures. Importantly these assays must be analytically robust in order to provide quality data for important clinical decisions. DNA microarray based gene expression assays measure several analytes simultaneously and can present specific challenges to analytical validation. This study describes the analytical validation of one such assay designed to predict metastatic recurrence in prostate cancer using primary formalin fixed paraffin embedded tumor material.
Conclusion:
The Metastatic Assay was found to be highly reproducible and precise. In conclusion, the studies demonstrated an acceptable analytical performance for the assay and support its potential use in the clinic.
Almac Diagnostic Services are a personalized medicine company focused on the discovery, development and commercialization of diagnostic and companion diagnostic tests. They have unique expertise in working with multidimensional genomics data and utilizing a disease subtyping approach to diagnostic development. Almac’s highly complex and innovative bioinformatics pipeline incorporated multiple technologies and was labor and compute intensive with a full run of the pipeline taking 1-3 weeks, depending on the dataset complexity, with around 15 manual steps.
Almac worked with Analytics Engines to migrate its proprietary processes and algorithms to Analytics Engine’s XDP™. The Analytics Engines platform utilized big data technologies to streamline the process using scalable storage and scalable compute to industrialize the analytics. Analytics Engines re-architected and optimized the pipeline to take advantage of the big data platform.
The pipeline can now be set up to run with 15 minutes of hands on time and results returned within 3-4 hours. Depending on the complexity of the dataset and analysis, this saves 20-50 hours of FTE per analysis and enables Almac to take a data driven discovery approach. The pipelines are now run reliably, reproducibly and repeatably with a full audit trail.
Austin Tanney and Peter Kerr describe how Almac has utilized its expertise in working with formalin fixed paraffin embedded (FFPE) tissue in developing diagnostics for partner companies and in the development of its own pipeline of molecular diagnostics from preclinical biomarker discovery through to full companion diagnostic development and clinical test delivery.
