Mentor Name: Brian Crompton

NTRK1/2/3 gene fusions (TRK fusions) occur in a range of pediatric cancers and are estimated to occur in 2.22% of all pediatric solid tumor cases. Although treatment with TRK inhibitors is highly effective at first, resistance and progressive disease is seen. Biomarkers are also needed to determine which patients are likely to have better and worse outcomes utilizing first generation TRK inhibitors, and which patients may benefit from being moved onto later generation inhibitors prior to relapse/progression occurring. Circulating tumor DNA (ctDNA) found in blood of pediatric patients with various solid tumors has shown promise as an early prognostic biomarker and predictive marker of treatment response. However, more sensitive assays are needed for detection of minimal residual disease (MRD) during treatment and off-treatment surveillance. In this proposal we will leverage a patient-specific approach to detect ctDNA as a biomarker in patients recently enrolled on a phase 2 trial. Oncogenic fusions that drive some pediatric cancers, such as NTRK1/2/3 gene fusions, are expressed from DNA-level translocations that have intronic breakpoints that are unique to every patient. Disease specific hybrid capture assays can detect these patient-specific breakpoints in tumor samples or plasma samples with high ctDNA content. Once these breakpoints are identified, droplet digital polymerase chain reaction (ddPCR), using patient-specific primer sets, can detect the presence of ctDNA when it makes up as little as 0.01% of the total cell-free DNA in a plasma sample. Therefore, ddPCR is a promising approach for detecting MRD in patients with TRK fusions. Through the Alex’s Lemonade Stand Foundation POST award, we will have the opportunity to develop patient-specific ddPCR assays, validate them, and test patient’s plasma samples for the presence of circulating tumor DNA through patient-specific breakpoint identification. We believe that this work has the potential to lead directly to new clinical surveillance tests for patients with TRK fusions that could improve the effectiveness of relapse therapy by allowing early initiation of treatment when recurrent disease burden is still low.