Circulating tumor DNA as a marker of treatment response in BRAF V600E mutated non-melanoma solid tumors

Abstract

PurposeWe evaluated longitudinal tracking of BRAF V600E in circulating cell-free DNA (cfDNA) as a marker of treatment response to BRAF inhibitor (BRAFi) combination therapies in non-melanoma solid tumors included in the Copenhagen Prospective Personalized Oncology (CoPPO) program.Experimental designPatients with BRAF V600E-mutated tumors were treated with combination therapies including BRAFi. Quantification of mutant cfDNA from plasma was determined and correlated to clinical outcomes. Exome sequencing was performed to identify possible resistance mutations.ResultsTwenty-three patients had BRAF-mutated tumors out of 455 patients included in CoPPO and 17 started BRAFi combination (EGFRi/MEKi) therapy. Tumor responses were achieved in 8 out of 16 evaluable patients and the median overall- and progression-free survival (OS and PFS) was 15 and 4.8 months, respectively. Longitudinal measurements of BRAF V600E-mutant cfDNA indicated disease progression prior to radiological evaluation and a reduction in the mutant fraction of more than 50% after 4 and 12 weeks of therapy was associated with a significantly longer PFS (p=0.003 and p=0.029) and OS (p=0.029 and p=0.017). Furthermore, the baseline mutant fraction and total level of cfDNA positively correlated with tumor burden (p=0.026 and p=0.024). Finally, analysis of cfDNA at progression revealed novel mutations potentially affecting the MAPK pathway.ConclusionBRAFi combination therapies showed a response rate of 50% in BRAF V600E-mutated non-melanoma tumors. The fraction of BRAF-mutant cfDNA represent a sensitive indicator for clinical outcomes with plasma collected at week 4 and 12 as crucial time points for monitoring response and disease progression.

Whole exome sequencing of cell-free DNA – A systematic review and Bayesian individual patient data meta-analysis

“…In total, 20 studies were included in this review of which the individual patient data of 12 studies were included for the meta-analyses of SNV sensitivity and agreement ( Fig. 1) [5,[15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33].…”

“…Four studies performed only WES on samples with a high tumor fraction, i.e. ≥ 10% [15,17] and ≥ 25% [33] or "high" was not further specified [26]. Overall, the median tumor fraction of all samples from which individual tumor fractions were available, was 37% based on estimation by different platforms such as ultra-low pass whole genome sequencing (ULP-WGS), Sequenza [34] or maximum MAF of variants.…”

“…Final selection of variants based on MAF, coverage and sequencing quality was highly variable (Table A4). For example, some studies only called SNVs based on a minimum MAF ranging from 1 [31,33] to 5% [16,17]. Sequencing quality scores involved either in-house developed algorithms or Phred scores with different cut-offs.…”

“…Sequencing quality scores involved either in-house developed algorithms or Phred scores with different cut-offs. Finally, not all studies performed an exome-wide final analysis and only reported data on cancer-associated genes [16] or genes involved in MAPK-pathway analysis [17] limiting the number of detected SNVs per patient. We further studied the correlation between total numbers of detected SNVs in cfDNA and ctDNA fraction on IPD which showed a positive correlation, p = 0.016 ( Fig.…”

“…To calculate a pooled sensitivity and agreement between WESdetected SNVs in cfDNA versus tumor tissue we performed a Bayesian random-effect meta-analysis on this subset ( Table 2; Table A5 for IPD). Most studies compared SNVs between metastatic tumor tissue and cfDNA [15][16][17]21,26,27,32], whilst three studies analyzed primary tumors [20,29,38] and two studies analyzed both [19,23]. The pooled sensitivity of WES-detected SNVs in cfDNA using tumor tissue as reference was 50% (95% CI: 29-72%) (Fig.…”