Comparing two assays for clinical genomic profiling: the devil is in the data

Abstract

Rachel M Squillace, Garrett M Frampton, Phil J Stephens, Jeffrey S Ross, Vincent A MillerFoundation Medicine Inc., Cambridge, MA, USAWe read with concern the paper “Evaluation and comparison of two commercially available targeted next-generation sequencing platforms to assist oncology decision- making”.1 The study directly compared results for the Paradigm Cancer Diagnostic test to the FoundationOne test for formalin-fixed, paraffin-embedded specimen pairs from 21 advanced cancer cases. We believe this study is fundamentally flawed, misleading, and potentially dangerous for patient care, for the reasons outlined herein.The paper neglected to address innumerable discordances between a rigorously analytically validated test (FoundationOne) and the experimental assay. It erroneously ascribes categorization of many genomic alterations detected on FoundationOne as “none”, when in fact available drugs have demonstrated activity or mechanism-based clinical trials exist, and it claims high levels of actionability based on the results of RNA-expression profiling of a single gene – TOPO2A.Read the original paper by Weiss et al.