A Comprehensive Guide to Achieving New York State Clinical Laboratory Evaluation Program Approval for Next-Generation Sequencing Assays

Abstract

The US Food and Drug Administration's recent move to regulate laboratory-developed tests as in vitro diagnostics has raised significant interest and concerns regarding its implementation. The New York State Department of Health's Clinical Laboratory Evaluation Program (CLEP) provides a useful framework for understanding laboratory-developed test oversight, particularly through its guidelines for next-generation sequencing assays. These CLEP requirements for analytical validation are widely recognized as a national standard, yet there is limited peer-reviewed literature detailing the studies needed for CLEP approval. This study presents the validation of the Rapid Pan-Heme (RPPH) assay, a genomic profiling tool for hematopoietic neoplasms, developed in compliance with CLEP standards. The RPPH assay features a comprehensive next-generation sequencing panel targeting >400 genes with clinically relevant variants, including single-nucleotide variants, insertions and deletions, and fusions critical for classifying hematopoietic malignancies. CLEP approval mandates detailed documentation, quality control metrics, validation studies (accuracy, precision, and reproducibility), and compliant clinical reporting. It is demonstrated that RPPH achieves CLEP's stringent analytical sensitivity and reproducibility criteria. Variants were orthogonally validated, and proper controls were implemented. Additionally, it is outlined how RPPH's clinical reports align with CLEP requirements. Overall, this study establishes RPPH as a robust molecular diagnostic tool and provides actionable insights for researchers navigating regulatory compliance and assay validation in clinical settings.