Abstract 734: Monitoring of dynamic changes and clonal evolution in circulating tumor DNA from patients with IDH-mutated cholangiocarcinoma treated with IDH inhibitors
Authors: Lapin Morten , Huang Helen J. , Javle Milind , Shroff Rachna T. , Pant Shubham , Raina Anjali , Madwani Kiran , Holley Veronica R. , Call S. Greg , Lanman Richard B. , Kwong Lawrence , Meric-Bernstam Funda , Raymond Victoria M. , Janku Filip 
Published: September 2020

Abstract
Background: IDH mutations are prevalent in up to 30% of patients with cholangiocarcinoma and IDH inhibitors are in the late stage of clinical development. Circulating tumor DNA (ctDNA) can offer a source of tumor DNA, which can be used for molecular diagnostics, monitoring and mapping of clonal evolution to better understand response and resistance patterns.
Methods: We isolated ctDNA from plasma from patients with IDH-mutated advanced cholangiocarcinoma collected at baseline, on therapy and at progression on IDH inhibitors. Molecular testing of ctDNA was done using droplet digital PCR (ddPCR; QX200, Bio-Rad) utilizing the tumor tissue informed approach. In addition, baseline and progression ctDNA samples were tested, while blind to tissue results, using targeted digital NGS for oncogenic aberrations in 74 genes (Guardant360, Guardant Health). Baseline results were compared to molecular profile of archival tissue (targeted NGS) to establish concordance and sensitivity. Quantity of ctDNA (variant allele frequency, VAF) and dynamic changes were compared to clinical outcomes. Progression samples were analyzed for emergence of mutations plausibly associated with therapeutic resistance.
Results: Of 32 patients with IDH1 R132 (n=26) or IDH2 R172 mutations (n=6) in the tumor tissue, IDH mutations were detected in ctDNA from 27 of 32 (84%) patients analyzed by ddPCR and in 25 of 30 (83%, 2 samples failed QC) ctDNA samples analyzed by NGS. Detection rates for known simultaneous mutations other than IDH in tumor tissue were 60% for ddPCR of ctDNA and 100% for NGS of ctDNA. Patients with low amount of IDH-mutated ctDNA (VAF ≤ median) at baseline compared to those with high amount (VAF &gt; median) demonstrated a trend towards longer median time-to-treatment failure (TTF) for NGS (p=0.1) and ddPCR (p=0.2). Also, patients with low amount of ctDNA by the VAF for all detected molecular alterations combined by NGS at baseline had longer TTF compared to patients with high combined VAF (3.6 vs 1.8 months, p=0.01). Dynamic changes in quantity of IDH-mutated ctDNA in serially collected samples by ddPCR demonstrated that patients with decrease in VAF of IDH-mutated ctDNA compared to no change/increase had a trend to longer survival (P=0.06), but not TTF (P=0.4). In 12 patients, NGS of ctDNA collected at progression detected alterations (range 1-5/patient) not detected at baseline with ARID1A mutations (n=3) and TP53 mutations (n=3) being most frequent.
Conclusions: To our knowledge this is the first systematic assessment of serially collected ctDNA in patients with IDH -mutated cholangiocarcinoma treated with IDH inhibitors. Our data demonstrate that ddPCR and NGS of ctDNA are feasible and concordant with archival tumor tissue. In addition, NGS of ctDNA can be associated with clinical outcomes and detect emerging mutations plausibly associated with therapeutic resistance.
Citation Format: Morten Lapin, Helen J. Huang, Milind Javle, Rachna T. Shroff, Shubham Pant, Anjali Raina, Kiran Madwani, Veronica R. Holley, S. Greg Call, Richard B. Lanman, Lawrence Kwong, Funda Meric-Bernstam, Victoria M. Raymond, Filip Janku. Monitoring of dynamic changes and clonal evolution in circulating tumor DNA from patients with IDH-mutated cholangiocarcinoma treated with IDH inhibitors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 734.