Development and validation of the JAX Cancer Treatment Profile™ for detection of clinically actionable mutations in solid tumors.
Document Type
Article
Publication Date
2-1-2015
Keywords
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
JAX Source
Exp Mol Pathol 2015 Feb; 98(1):106-112.
ISSN
1096-0945
PMID
25562415
Grant
CA034196
Abstract
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.
Recommended Citation
Ananda G,
Mockus S,
Lundquist M,
Spotlow V,
Simons AK,
Mitchell T,
Stafford G,
Philip VM,
Stearns TM,
Srivastava A,
Barter M,
Rowe LB,
Malcolm J,
Bult CJ,
Karuturi R,
Rasmussen K,
Hinerfeld D.
Development and validation of the JAX Cancer Treatment Profile™ for detection of clinically actionable mutations in solid tumors. Exp Mol Pathol 2015 Feb; 98(1):106-112.