Development and Clinical Validation of a Large Fusion Gene Panel for Pediatric Cancers.

Gene fusions are one of the most common genomic alterations in pediatric
cancer. Many fusions encode oncogenic drivers and play important roles in
cancer diagnosis, risk stratification, and treatment selection. We report
the development and clinical validation of a large custom-designed RNA
sequencing panel, CHOP Fusion panel, using anchored multiplex PCR
technology. The panel interrogates 106 cancer genes known to be involved in
nearly 600 different fusions reported in hematological malignancies and
solid tumors. The panel works well with different types of samples,
including formalin-fixed, paraffin-embedded samples. The panel demonstrated
excellent analytic accuracy, with 100% sensitivity and specificity on 60
pediatric tumor validation samples. In addition to identifying all known
fusions in the validation samples, three unrecognized, yet clinically
significant, fusions were also detected. A total of 276 clinical cases were
analyzed after the validation, and 51 different fusions were identified in
104 cases. Of these fusions, 16 were not previously reported at the time of
discovery. These fusions provided genomic information useful for clinical
management. Our experience demonstrates that CHOP Fusion panel can detect
the vast majority of known and certain novel clinically relevant fusion
genes in pediatric cancers accurately, efficiently, and cost-effectively;
and the panel provides an excellent tool for new fusion gene discovery.