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PURPOSE Multiple FGFR inhibitors are currently in clinical trials enrolling adults with different solid tumors, while very few enroll pediatric patients. We determined the types and frequency of FGFR alterations ( FGFR1-4) in pediatric cancers to inform future clinical trial design. METHODS Tumors with FGFR alterations were identified from two large cohorts of pediatric solid tumors subjected to targeted DNA sequencing: The Dana-Farber/Boston Children's Profile Study (n = 888) and the multi-institution GAIN/iCAT2 (Genomic Assessment Improves Novel Therapy) Study (n = 571). Data from the combined patient population of 1,395 cases (64 patients were enrolled in both studies) were reviewed and cases in which an FGFR alteration was identified by OncoPanel sequencing were further assessed. RESULTS We identified 41 patients with tumors harboring an oncogenic FGFR alteration. Median age at diagnosis was 8 years (range, 6 months-26 years). Diagnoses included 11 rhabdomyosarcomas, nine low-grade gliomas, and 17 other tumor types. Alterations included gain-of-function sequence variants (n = 19), amplifications (n = 10), oncogenic fusions ( FGFR3:: TACC3 [n = 3], FGFR1:: TACC1 [n = 1], FGFR1:: EBF2 [n = 1], FGFR1:: CLIP2 [n = 1], and FGFR2:: CTNNA3 [n = 1]), pathogenic-leaning variants of uncertain significance (n = 4), and amplification in combination with a pathogenic-leaning variant of uncertain significance (n = 1). Two novel FGFR1 fusions in two different patients were identified in this cohort, one of whom showed a response to an FGFR inhibitor. CONCLUSION In summary, activating FGFR alterations were found in approximately 3% (41/1,395) of pediatric solid tumors, identifying a population of children with cancer who may be eligible and good candidates for trials evaluating FGFR-targeted therapy. Importantly, the genomic and clinical data from this study can help inform drug development in accordance with the Research to Accelerate Cures and Equity for Children Act.

Somatic gene translocations are key to making an accurate diagnosis in many cancers including many pediatric sarcomas. Currently available molecular diagnostic approaches to identifying somatic pathognomonic translocations have limitations such as minimal multiplexing, high cost, complex computational requirements, or slow turnaround times. We sought to develop a new fusion-detection assay optimized to mitigate these challenges. To accomplish this goal, we developed a highly sensitive multiplexed digital PCR-based approach that can identify the gene partners of multiple somatic fusion transcripts. This assay was validated for specificity with cell lines and synthetized DNA fragments. Assay sensitivity was optimized using a tiered amplification approach for fusion detection from low input and/or degraded RNA. The assay was then tested for the potential application of fusion detection from FFPE tissue and liquid biopsy samples. We found that this multiplexed PCR approach was able to accurately identify the presence of seven different targeted fusion transcripts with a turnaround time of 1 to 2 days. The addition of a tiered amplification step allowed the detection of targeted fusions from as little as 1 pg of RNA input. We also identified fusions from as little as two unstained slides of FFPE tumor biopsy tissue, from circulating tumor cells collected from tumor-bearing mice, and from liquid biopsy samples from patients with known fusion-positive cancers. We also demonstrated that the assay could be easily adapted for additional fusion targets. In summary, this novel assay detects multiple somatic fusion partners in biologic samples with low tumor content and low-quality RNA in less than two days. The assay is inexpensive and could be applied to surgical and liquid biopsies, particularly in places with inadequate resources for more expensive and expertise-dependent assays such as next-generation sequencing.

Oncogenic FGFR alterations in the form of activating mutations, amplifications, and fusions are detected in a variety of solid tumors, including those in children. Major advances in FGFR-targeted drug development have led to investigation of multiple generations of FGFR inhibitors in adult clinical trials. In contrast, there are few clinical trials of FGFR inhibitors enrolling children. There is a need to identify and characterize molecular targets including oncogenic FGFR alterations in pediatric cancers so that drug development can occur in accordance with the RACE (Research to Accelerate Cures and Equity) for Children Act. The goal of this study was to determine the frequency and types of FGFR alterations in pediatric cancers to inform future clinical trial design. Tumors with FGFR alterations were identified from two large cohorts of pediatric solid tumors subjected to targeted DNA sequencing: The Dana-Farber/Boston Children’s Profile Study (n=888) and the multi-institution GAIN/iCAT2 (Genomic Assessment Improves Novel Therapy) Study (n=571). Data from the combined patient population of 1,395 cases (64 patients were enrolled in both studies) were reviewed and cases in which an FGFR alteration was identified by OncoPanel sequencing were further assessed. We identified 42 patients with tumors harboring an oncogenic or possibly oncogenic FGFR alteration (FGFR1 in 22; FGFR2 in 4; FGFR3 in 5; FGR4 in 11). Median age at diagnosis was 8 years (range 6 months-26 years old). Diagnoses included 11 rhabdomyosarcomas, 8 low-grade gliomas, 3 high-grade gliomas, and 16 other tumor types. We identified 20 patients with a gain-of-function (GoF) mutation, 10 patients with amplifications (copy number ≥7), 7 patients with fusions, 4 patients with a variant of uncertain significance (VUS) assessed and determined to be possibly oncogenic, and 1 patient with an amplification and VUS. Four of the fusion cases had oncogenic FGFR3-TACC3 (n=3) and FGFR1-TACC1 (n=1) fusions previously reported in the literature. Three cases had novel fusions (FGFR1-EBF2, FGFR1-CLIP2, FGFR2-CTNNA3) found in a spindle cell sarcoma and two low-grade gliomas. Tumors with an FGFR missense mutation were primarily those with oncogenic hotspot mutations in FGFR1 [N546K (n= 5); K656E (n=4)] and FGFR4 [N535K/D (n=2); V550L/E (n=5)]. In summary, this study identified oncogenic FGFR alterations in 42 of 1395 patients (3%) with solid and brain tumors sequenced through the Profile and GAIN/iCAT2 studies who would potentially be eligible for clinical trials evaluating FGFR-targeted therapy. Citation Format: Lorena Lazo De La Vega, Alanna J. Church, Hannah Comeau, Wenjun Kang, AeRang Kim, Navin R. Pinto, Margaret E. Macy, Luke D. Maese, Steven G. DuBois, Bruce E. Johnson, Katherine A. Janeway, Suzanne J. Forrest. Rare FGFR oncogenic alterations in sequenced pediatric solid and brain tumors suggest FGFR is a relevant molecular target in childhood cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3893.