ctDNA testing (liquid biopsy) is more effective than tissue biopsy for identifying ESR1 mutations. It samples DNA from all metastatic sites, capturing the disease's genetic heterogeneity and reflecting the most active resistance mechanisms, unlike a single-site needle biopsy which can miss them.

A major limitation of menin inhibitor monotherapy is acquired resistance. Up to 39% of patients on revumenib develop mutations in the menin (MEN1) gene. These mutations prevent the drug from binding to its target, leading to rapid relapse and highlighting the need for combination therapies or next-generation agents.

While not yet validated, ctDNA is being used by clinical experts as a de-escalation tool to provide confidence when stopping long-term maintenance therapies like PARP inhibitors. This novel application focuses on reducing treatment burden rather than solely detecting disease progression.

A study switching therapy based on ctDNA-detected ESR1 mutations revealed patients felt significantly better after the switch, even without visible tumor progression on scans. This counterintuitive finding suggests molecular progression has a subclinical impact on quality of life, supporting proactive, biomarker-driven treatment changes before patients clinically deteriorate.

The original Signatera assay used 16 personalized probes based on whole-exome sequencing to find ctDNA. The next-generation version, based on whole-genome sequencing, expands this to 64 probes. This is expected to significantly increase sensitivity, detect molecular relapse earlier, and provide a longer window for clinical intervention.

The InVigor11 study was the first to show that detecting recurrence via a ctDNA test before it's visible on scans is not just a prognostic sign, but an actionable clinical state. Intervening with therapy at this early stage was proven to improve patient outcomes, establishing a new paradigm for cancer surveillance.

For post-progression biopsies, which are often small and contain necrotic tissue, institutions may prioritize DNA-based NGS panels. This strategy is based on the rationale that most resistance mechanisms are genetic mutations detectable by DNA sequencing, reserving RNA panels primarily for identifying less common fusion events.

Circulating tumor DNA (ctDNA) analysis allows for early detection of resistance mechanisms, such as secondary FGFR2 mutations, before tumors show growth on scans. This provides a potential window to adjust treatment strategies proactively, offering an advantage over traditional imaging-based monitoring.

The standard of care for GIST is evolving to mandate molecular testing at two key points: initial diagnosis and at the time of progression on first-line therapy. Using ctDNA at progression is now deemed critical to identify acquired resistance mechanisms, which directly informs the selection of subsequent, more effective therapies and avoids ineffective treatments.