Development and validation of the JAX Cancer Treatment Profile™ for detection of clinically actionable mutations in solid tumors.

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Algorithms, Computational Biology, DNA, Neoplasm, Gene Expression Regulation, Neoplastic, High-Throughput Nucleotide Sequencing, Humans, Molecular Sequence Annotation, Mutation, Neoplasm Proteins, Neoplasms, Paraffin Embedding, Prognosis, Sequence Analysis, DNA

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Exp Mol Pathol 2015 Feb; 98(1):106-112.








BACKGROUND: The continued development of targeted therapeutics for cancer treatment has required the concomitant development of more expansive methods for the molecular profiling of the patient's tumor. We describe the validation of the JAX Cancer Treatment Profile™ (JAX-CTP™), a next generation sequencing (NGS)-based molecular diagnostic assay that detects actionable mutations in solid tumors to inform the selection of targeted therapeutics for cancer treatment.

METHODS: NGS libraries are generated from DNA extracted from formalin fixed paraffin embedded tumors. Using hybrid capture, the genes of interest are enriched and sequenced on the Illumina HiSeq 2500 or MiSeq sequencers followed by variant detection and functional and clinical annotation for the generation of a clinical report.

RESULTS: The JAX-CTP™ detects actionable variants, in the form of single nucleotide variations and small insertions and deletions (≤50 bp) in 190 genes in specimens with a neoplastic cell content of ≥10%. The JAX-CTP™ is also validated for the detection of clinically actionable gene amplifications.

CONCLUSIONS: There is a lack of consensus in the molecular diagnostics field on the best method for the validation of NGS-based assays in oncology, thus the importance of communicating methods, as contained in this report. The growing number of targeted therapeutics and the complexity of the tumor genome necessitate continued development and refinement of advanced assays for tumor profiling to enable precision cancer treatment. Exp Mol Pathol 2015 Feb; 98(1):106-112.