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

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 (≤50bp) 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 necessitates continued development and refinement of advanced assays for tumor profiling to enable precision cancer treatment.

Genomic alterations in BCL2L1 and DLC1 contribute to drug sensitivity in gastric cancer

“…Among the 342 significantly altered genes, we also found previously known critical genetic drivers including TP53, ARID1A, PIK3CA, KRAS, MYC, FAT4, CTNNB1, and ERBB2 (SI Appendix, Table S9) (6,19). Using the JAX Cancer Treatment Profile analysis pipeline, we also identified clinically actionable mutations in 144 genes as candidate targets for clinical application (JAX-CTP; Dataset S3) (20).…”

<b>Optimizing an ion semiconductor sequencing data analysis method to identify somatic mutations in the genomes of cancer cells in clinical tissue </b><b>samples </b>

“…We identified somatic mutations by comparing mutations detected in tumor and blood samples and custom filters to extract the most likely candidates. Subsets of SNVs found in cancer-related genes (2,7,12,16,18,20,23,24,37,38,42) were randomly selected, and a two-step validation was performed to obtain a set of high-confidence somatic mutations. Optimization of parameters and filtering rules were performed according to the results of the validation.…”

A Comprehensive Evaluation of Solid Tumor Analysis in the Clinical Space

“…In cases where multiple nucleotides are incorporated in a row, the intensity of the light fluoresces will dictate how many bases were added. 454's technology allowed for sequencing of longer reads, reaching up to 1 Kb, compared to some of the other available platforms at that time [24,25].…”

“…Taking Illumina's idea one step further, other companies have designed their own custom targeted panels which can then be developed as clinical tests to be offered to physicians. As an example, the Jackson Laboratory for Genomic Medicine offers a custom targeted sequencing panel, the JAX Cancer Treatment Profile TM (JAX-CTP TM ), which analyses 358 cancer-associated genes in a diverse subset of cancer types [24]. Accompanying the 358 gene panel, a targeted fusion detection assay is incorporated to detect gene fusions in 53 genes linked to solid tumors.…”