Molecular profiling of ctDNA from NCI-MATCH patients enrolled for treatment with mTOR1/2 inhibitor sapanisertib (arm M) and the Hedgehog pathway inhibitor vismodegib (arm T).
Authors: LoCoco Jennifer S. , Das Biswajit , Rahmanian Sorena , Chang Ting-Chia , Silhavy Jennifer , Chen Li , Harrington Robin , Peach Amanda , Fu Yao , McShane Lisa , Li Jessica , Chen Alice P. , Takebe Naoko , Harris Lyndsay , Patton David R. , Pawlowski Traci L. , Febbo Phillip G. , Doroshow James H. , Williams P. Mickey , Karlovich Chris Alan 
Published: June 2023

3047

Background: The National Cancer Institute Molecular Analysis for Therapy Choice (NCI-MATCH) multi-arm phase II clinical trial tested biopsies from patients with advanced refractory cancer to assign treatment based on tumor molecular profile. Enrollment criteria for treatment with the mTOR1/2 inhibitor sapanisertib in Arm M, or the Hedgehog pathway inhibitor vismodegib in Arm T, included detection of mutations in TSC1/TSC2 or PTCH1/SMO in tissue, respectively. For a subset of patients enrolled on these two arms, matched plasma was also collected at time of enrollment or on treatment to evaluate ctDNA. Methods: Screening for NCI-MATCH was based on tissue sequencing that was initially performed centrally using the 143-gene Oncomine Comprehensive Assay version 2 (OCAv2) and later referred to NCI-MATCH Designated Laboratory (DL) Network to perform sequencing for patient referral. Cell-free DNA (cfDNA) extracted from plasma collected in Streck tubes was input at 10 – 30 ng into a modified version of the Illumina TruSight Oncology 500 assay (TSO 500). Following error correction and read collapsing post-sequencing, variant calls were made and concordance between cfDNA libraries meeting prespecified QC criteria and tissue was evaluated. Results: Plasma, representing multiple collection timepoints, was available for 30/49 Arm M and 21/34 Arm T enrolled patients. A total of 95 cfDNA libraries, including replicates, were constructed and sequenced. Unique patient samples were tested across various timepoints (n = 35 pretreatment; n = 35 Cycle 2 Day 1; n = 8 at progression) plus replicates, with 90 (94.7%) libraries passing all prespecified QC criteria. Among Arm M patients there were 3 patients whose enrollment variant did not overlap with the TSO 500 gene panel. In total, 14 of 27 (51.8%) patients in Arm M and 18 of 21 (85.7%) patients in Arm T were concordant for enrollment mutation for at least one collection timepoint. In Arm T, 85.7% (n=38) of patient samples had at least one oncogenic or likely oncogenic (O/LO) mutation in the tumor sample at enrollment, with 73.6% (n = 28) of those also being detected by cfDNA. Interestingly, within Arm M and Arm T, a total of 7 patient samples were detected as MSI-H, with corresponding bTMB scores ranging from ~6 to > 100 Mut/Mb (median = 86.7). Conclusions: Detection of the enrollment mutations in treatment arms was observed in 51.8% - 85.7% of patients tested by ctDNA with overall variant concordance between tissue and ctDNA of at least 73.6%. These findings support the use of liquid biopsy as a tool for understanding genomic profiles of cancer patients both at diagnosis and progression, less invasively than standard tissue biopsies. In addition, 7 patients were identified as MSI-H, suggesting that blood-based testing could complement tissue testing for identifying patients who may benefit from targeted therapy.