Blood-based detection of actionable alterations from NCI-MATCH patients with no tissue results.
Authors: Harrington Robin , Peach Amanda , Howell D'Andra , Das Biswajit , Pauly Rini , Chang Ting-Chia , LoCoco Jennifer S. , Chen Li , Jiwani Shahanawaz , Lee Jennifer , McShane Lisa , Chen Alice P. , Febbo Phillip G. , Pawlowski Traci L. , Takebe Naoko , Tricoli James V. , Doroshow James H. , Williams Paul M. , Karlovich Chris Alan 
Published: June 2022

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Background: The National Cancer Institute Molecular Analysis for Therapy Choice (NCI-MATCH) multi-arm phase II clinical trial tested tumor tissue from 5,954 patients with advanced refractory cancer to assign treatment based on the molecular profile. Molecular profiling was successful for 93% of patients. For 267 of the patients who were not enrolled because molecular profiling was not successful, plasma cfDNA was evaluated to provide insight into the potential utility of blood-based testing in a broad spectrum of histologies when tissue is not evaluable. Methods: Cell-free DNA was extracted from plasma collected from Streck blood tubes and quantitated. Libraries were constructed using ³ 15 ng cfDNA into the Illumina TruSight Oncology 500 ctDNA RUO Assay, including unique molecular identifiers and duplex barcodes for error correction. Libraries were sequenced on the NovaSeq 6000 with S4 XP flow cells. Results: Of the 267 samples, 250 samples (94%) were evaluable, representing 72 histologies, including colorectal cancer (N = 36), lung adenocarcinoma (N = 15), pancreatic adenocarcinoma (N = 14), and invasive breast carcinoma (N = 12). Of these, 231 (92%) had ³ 1 OncoKB annotated mutation, with 208 patients (83%) having putative somatic mutations detected in genes not commonly associated with clonal hematopoiesis. The most common somatic mutations were in TP53, KRAS, APC, and PIK3CA, reported in 51%, 20%, 12%, and 12% of patients respectively. A total of 109 patients (44%) had ³ 1 actionable mutation of interest (aMOI) reported that could have been used for treatment assignment in the NCI-MATCH clinical trial. After applying histology and molecular exclusions, 75 patients (30%) had ³ 1 aMOI. The most common assignable treatment arms were Z1B/Z1BX1 (palbociclib with CCND1/2/3, N = 13), Z1F (copanlisib with PIK3CA Mutations, N = 13), S1/S1X1 (trametinib with NF1 mutation, N = 12), and Z1C/Z1CX1 (palbociclib with CDK4/CDK6 Amplification and Rb Expression by IHC, N = 10). Mutations in genes commonly associated with clonal hematopoiesis (CH) were prevalent in this population. Along with the expected high frequency of DNMT3A (21% of patients) and TET2 (11%) mutations, PPM1D mutations were the highest amongst CH genes, with 61 patients (24%) having ³ 1 PPM1D mutation, likely due to the heavily pre-treated nature of these patients. Conclusions: Variants observed in the blood are consistent with what is reported in the tissue. Using liquid biopsy when tissue is not evaluable can expand the ability of patients to obtain mutation information that can inform treatment compared to using tumor tissue only. Cell-free DNA provided valuable mutation information for these patients and could have resulted in up to an additional 75 patients being eligible for treatment selection based on their mutation profile. These results indicate that blood-based screening could be a tool for future NCI-sponsored clinical studies.