Pilot study of cell-free DNA (cfDNA) for measurable residual disease monitoring following autologous hematopoietic cell transplant in multiple myeloma

Abstract Introduction Measurable residual disease (MRD) in bone marrow has become an important surrogate endpoint in multiple myeloma studies and is prognostic of overall (OS) and progression-free survival (PFS). However, repeat bone marrow sampling can be painful and logistically challenging. Conventional blood-based assays like serum protein electrophoresis and serum free light chain testing are available but uninformative for patients with non-secretory or oligosecretory disease where M-protein is absent. Consequently, there is an unmet need for a sensitive and widely applicable blood-based assay to assess global residual tumor burden during therapy. Circulating tumor DNA (ctDNA), fragments of DNA shed by tumor cells into the bloodstream has emerged as a reliable prognostic biomarker in solid tumors and lymphoma. Herein, we report the initial results of a retrospective pilot study assessing the utility of a tumor-informed ctDNA assay (SignateraTM, Natera, Inc.) in multiple myeloma. Methods Patients who consented to participate in our institutional myeloma biobank (HRPO: 201102270) were reviewed for inclusion. Patients were included if they 1) had a biopsy-confirmed diagnosis of multiple myeloma, 2) underwent autologous hematopoietic cell transplant (AHCT), 3) had adequate pretreatment tumor samples (bone marrow aspirate slides (preferred) and/or cryopreserved bone marrow aspirate; plasma), 4) adequate germline samples (cheek swab or skin), and 5) had available cryopreserved plasma samples at day +100 post-AHCT. Tumor-specific single-nucleotide variants were identified via whole-exome sequencing (WES) of tumor-normal pairs to design a locked 16-plex assay used to track ctDNA in plasma samples (median of 2.9 mL per sample). Results Of the 9 eligible patients, 8 had a successfully designed tumor-informed assay and were included in this analysis. The median age was 59.5 years, 6/8 (75%) were male, and 7/8 underwent AHCT in first complete remission (CR1). By IMWG criteria, 5, 2, and 1 patients had complete response (CR), partial response (PR), and stable disease (SD) at day +100, respectively. 4 patients had matched MRD results using the clonoSEQ assay (Adaptive Biotechnologies, Seattle, WA), with 1 patient being MRD+ at >10-5. Four patients progressed post-transplant (at day 402, 581, 1134, and 1309); The remaining 4 were in remission at the last follow-up. In terms of ctDNA testing for the 8 patients, 7 had an available baseline result, and all were ctDNA-positive. One baseline sample failed due to a pre-analytic error. At day +100, 25% (2/8) patients were ctDNA-positive, while 75% (6/8) were ctDNA-negative, all 6 of whom remained relapse-free for at least 1 year post AHCT. Strikingly, one patient who was ctDNA-positive at day +100 had was in an MRD-negative CR at day +100, but had rapid progression at day 402 after transplant, suggesting this assay may capture a unique risk mechanism. Conclusion Initial pilot data demonstrate the feasibility of designing personalized, tumor-informed ctDNA assays with a 100% detection rate at baseline in most patients with multiple myeloma. In one case, ctDNA-positivity on day +100 post was associated with early recurrence with a lead time of 8 months. Correlation with traditional markers of disease assessment is low, raising the possibility that ctDNA may capture an independent process driving risk. Given the minimally invasive nature of this assay, additional data, particularly serial monitoring, are needed to further delineate the utility of this assay in multiple myeloma. Analyses on an additional 26 patients are underway.