Detection and Quantification of KIT Mutations in ctDNA by Plasma Safe-SeqS

Area of Science:

• Oncology
• Genetics
• Molecular Biology

Background:

• Gastrointestinal stromal tumors (GIST) are often driven by mutations in the KIT gene.
• Secondary resistance to targeted therapies like regorafenib is a significant clinical challenge in GIST management.
• Sensitive detection of emerging mutations is crucial for understanding treatment response and resistance mechanisms.

Purpose of the Study:

• To develop and validate a highly sensitive assay for detecting de novo KIT gene mutations.
• To apply this assay to plasma samples from GIST patients undergoing regorafenib treatment.
• To identify known and novel mutation sites associated with secondary resistance to regorafenib.

Main Methods:

• Design and implementation of a highly sensitive assay utilizing Safe-SeqS technology.
• Application of the assay to serial plasma samples from GIST patients in the GRID III clinical trial.
• Genomic DNA extraction from plasma and subsequent sequencing to detect low-frequency mutations.

Main Results:

• The Safe-SeqS assay demonstrated high sensitivity in detecting de novo KIT mutations.
• Analysis of patient samples revealed mutations at known and previously unidentified sites.
• Identified mutations provide insights into mechanisms of secondary resistance to regorafenib.

Conclusions:

• The developed Safe-SeqS assay is a powerful tool for monitoring GIST patients and detecting resistance mutations.
• Understanding the mutational landscape during treatment can inform future therapeutic strategies.
• This technology aids in the early identification of resistance mechanisms, potentially improving patient outcomes.