Utility of Genomic Profiling of cfDNA to Inform Clinical Care for Patients with Advanced Biliary Tract Cancer

Results from the the largest and most comprehensive study to date on the clinical utility of cell-free DNA (cfDNA) from 2,068 plasma samples obtained as a routine part of clinical care of 1,671 patients with advanced biliary tract cancer point out to several findings of clinical relevance. Profiling of cfDNA identifies similar frequencies of clinically actionable alterations compared to tissue profiling, detects most IDH1 mutations, BRAF V600E mutations, and FGFR2 extracellular domain mutations, but is suboptimal for detecting FGFR2 fusions, reveals a high degree of clonality for the most clinically actionable alterations (IDH1 mutations, BRAF V600E mutations, and FGFR2 fusions) suggesting that these are early driver events in biliary tract cancer, uncovers novel mechanisms of resistance to targeted therapy not detected on tumour biopsy, and provides prognostic and predictive data to integrate into clinical decision making. Findings are published by Dr. Lipika Goyal of Mass General Cancer Center in Boston, MA, US and colleagues on 8 September 2022 in the Annals of Oncology.

The authors wrote in the background that large-scale genomic profiling efforts have transformed the treatment opportunities for patients with biliary tract cancer by identifying clinically actionable alterations in several genes, including FGFR2, IDH1, BRAF, NTRK, RET, and HER2. The frequency of these alterations varies by anatomic subtype of biliary tract cancer. FGFR2 fusions and IDH1 mutations occur at a frequency of 13-14% in intrahepatic cholangiocarcinoma and rarely in the other subtypes. HER2 amplification is seen in approximately 14-16% of gallbladder cancer and less frequently in the other subtypes. BRAF V600E mutations (3-4%), NTRK fusions (<1%), and RET fusions (<1%) are rare across all subtypes. Precision medicine strategies have emerged from identification of these targets.

As a desmoplastic and often necrotic, biliary tract cancer is difficult to profile, with more than 25% of metastatic tumour biopsies yielding insufficient tumour content or DNA quality for analysis by next-generation sequencing (NGS). Cholangiocarcinoma displays a significant degree of intratumoural heterogeneity, especially at the periphery of tumours, which may be missed with a single tumour biopsy from the centre of a lesion. Capturing tumour heterogeneity may be particularly important for assessing resistance to FGFR inhibitors as the resistance is in part mediated by subclonal populations of FGFR2 kinase domain mutations.

cfDNA analysis is an attractive approach for cancer genomic profiling that can overcome many of the limitations of tissue-based analysis. In particular, cfDNA can provide genomic information when tissue is unobtainable or insufficient in quantity or quality, tumour DNA is shed into the blood from multiple lesions and thus may better capture intrapatient tumoural heterogeneity, serial cfDNA analysis can facilitate the study of tumour evolution and resistance and cfDNA can also provide predictive and prognostic information.

In this report, the investigators analyzed results from 2,068 cfDNA samples obtained as a routine part of clinical care of 1,671 patients with advanced biliary tract cancer. The goal was to assess the utility of cfDNA to detect clinically actionable alterations and to generate novel insights into biology of biliary tract cancer. NGS data of cfDNA samples were generated with Guardant360. The study team performed clinical annotation on a multi-institutional subset to assess intrapatient cfDNA-tumour concordance and the association of cfDNA variant allele fraction (VAF) with clinical outcomes.

Genetic alterations were detected in cfDNA in 84% of patients, with targetable alterations detected in 44% of patients. FGFR2 fusions, IDH1 mutations, and BRAF V600E were clonal in majority of cases, affirming these targetable alterations as early driver events in biliary tract. Concordance between cfDNA and tissue for mutation detection was high for IDH1 mutations (87%) and BRAF V600E (100%), and low for FGFR2 fusions (18%).

cfDNA analysis uncovered novel putative mechanisms of resistance to targeted therapies, including mutation of the cysteine residue (FGFR2 C492F) to which covalent FGFR inhibitors bind.

High pre-treatment cfDNA VAF associated with poor prognosis and shorter response to chemotherapy and targeted therapy.

The study team also reported the frequency of promising targets in advanced biliary tract cancer currently under investigation in other advanced solid tumours, including KRAS G12C (1.0%), KRAS G12D (5.1%), PIK3CA mutations (6.8%), and HER2 amplifications (4.9%).

The authors commented that patients with advanced biliary tract cancer are prime candidates for molecular profiling by cfDNA analysis. Rates of tumour shed are high with 84% of patients in this study having detectable somatic variants in cfDNA. The frequency of clinically actionable variants is high, with 44% of patients in this study having such variants, compared to 25-47% in biliary tract cancer tissue profiling studies and 43-55% in smaller biliary tract cancer cfDNA studies.

Biliary tract cancer also harbours many other genetic alterations of unclear significance, and as clinical and functional characterisation of these variants improves, the utility of genomic profiling can only increase. With more than 50 active clinical studies investigating targeted therapies in biomarker-selected patients with biliary tract cancer, it is hoped that the number of patients with biliary tract cancer who can benefit from molecularly-guided treatment will grow substantially in the coming years.

The study findings support a role for cfDNA analysis in current clinical practice and highlight the importance of incorporating cfDNA into clinical studies to further define its utility as a non-invasive predictive and prognostic biomarker in patients with biliary tract cancer. However, the authors emphasized that clinicians should recognise the limitations of cfDNA for the detection of FGFR2 fusions and consider tumour biopsies as a complementary approach.

This work was supported by the RARE Initiative.