# NIH grant: Clinical validation of FGFR-Dx in plasma cell-free DNA from patients with FGFR-altered advanced pancreatic cancer (1UH3CA313817-01) — retained record

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NIH grant 1UH3CA313817-01: Clinical validation of FGFR-Dx in plasma cell-free DNA from patients with FGFR-altered advanced pancreatic cancer
Institute: {'code': 'CA', 'abbreviation': 'NCI', 'name': 'National Cancer Institute', 'admin_org_id': '12500008', 'admin_funding_url': ''}. PI: Sameek  Roychowdhury. Award: $327020.
Start: 2026-07-17T00:00:00.
PROJECT SUMMARY
Commercial cell-free DNA (cfDNA) assays are not sufficient for fibroblast growth factor receptor (FGFR) fusion
detection with sensitivities ranging from 20-50%. Due to the large genomic content in these cfDNA panels (>100
genes) and depth of coverage required for cfDNA variant calling, these assays are limited in their ability to target
repetitive intronic regions that would increase off-target sequencing. As a result, gene fusions occurring in these
regions are missed. Motivated by the need for a highly sensitive test to monitor FGFR-positive
cholangiocarcinoma patients receiving FGFR targeted therapy, we developed and analytically validated FGFR-
Dx. FGFR-Dx comprehensively targets introns in FGFR1-3 previously shown to be involved in gene fusions as
well as all coding exons. Analytic validation of FGFR-Dx revealed a sensitivity of 92.9% for fusion detection,
which is a considerable improvement over commercial assays. Through basket trials for FGFR kinase inhibitors,
we have observed exceptional clinical outcomes in four patients with FGFR2 fusion-positive pancreatic cancer.
We estimate FGFR alterations are present in 1.5% of pancreatic cancers (~900 patients per year). Strengthened
by telemedicine experiences during the COVID19 pandemic, we have launched a nationwide telemedicine
prospective phase 2 therapeutic trial of pemigatinib for FGFR-altered pancreatic cancer. This is accompanied by
a nationwide patient registry for FGFR-positive pancreatic cancer. Telemedicine has the potential to radically
accelerate drug development for such rare precision oncology targets. Our telemedicine study includes remote
collection of serial blood for correlative cfDNA analysis. cfDNA has emerged as a new tool for precision oncology,
but the dynamics have not been adequately studied, and how test results should be utilized is not certain. To
date, most studies have evaluated just two blood timepoints: before starting treatment and at first radiologic
imaging. There is a knowledge gap to understand the early temporal kinetics of cfDNA for both initial response
and development of resistance. Additionally, no studies have evaluated cfDNA when patients have breaks or
dose reductions from therapy that are either planned or due to toxicities. We hypothesize that cfDNA dynamics
of FGFR will inform therapy and clinical decision-making in pancreatic cancer and more broadly serve as a
blueprint for other targeted therapies. We propose the following Aims : 1) Clinical validation of FGFR-Dx in cfDNA
from pancreatic cancer patients, including accuracy, precision and reportable range; 2) Establish the dynamics
of serial FGFR-Dx in response to treatment, including the ideal time frame to measure the impact of therapy,
lead time between increasing cfDNA alterations and disease progression, acquired resistance in response to
FGFR targeted therapy in pancreatic cancer, and dynamics related to chemotherapy treatment (naïve or resistant
to FGFR inhibitors).
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