Identification of targetable BRAF ΔN486_P490 variant by whole genome sequencing leading to dabrafenib-induced remission of a BRAF-mutant pancreatic adenocarcinoma

The tumor genome of a patient with advanced pancreatic cancer was sequenced to identify potential therapeutic targetable mutations after standard of care failed to produce any significant overall response. Matched tumor-normal whole genome sequencing revealed somatic mutations in BRAF, TP53, CDKN2A, and a focal deletion of SMAD4. The BRAF variant was an in-frame deletion mutation (ΔN486_P490), which had been previously demonstrated to be a kinase-activating alteration in the BRAF kinase domain. Working with the Novartis patient assistance program allowed us to treat the patient with the BRAF-inhibitor, dabrafenib. The patient’s overall clinical condition improved dramatically with dabrafenib. Levels of serum tumor marker dropped immediately after treatment, and a subsequent CT scan revealed significant decrease in the size of both primary and metastatic lesions. The dabrafenib-induced remission lasted for six months. Preclinical studies published concurrently with the patient’s treatment showed that the BRAF in-frame mutation (ΔNVTAP) induces oncogenic activation by a mechanism distinct from that induced by V600E, and that this difference dictates the responsiveness to different BRAF inhibitors. This study describes a dramatic instance how high level genomic technology and analysis was necessary and sufficient to identify a clinically logical treatment option that was then utilized and shown to be of clinical value for this individual.

 2019 Sep 13. pii: mcs.a004424. doi: 10.1101/mcs.a004424.


Other Contributors

Author information

New York Genome Center;
New York Genome Center.
The Rockefeller University.
Renaissance School of Medicine, Stony Brook University.
IBM Watson Health.
Stony Brook Cancer Center.