Background Measurable residual disease (MRD) is an important predictor of survival outcomes in both newly diagnosed and relapsed/refractory multiple myeloma (MM). Currently, it is assessed by bone marrow aspirate, either using next-generation sequencing or multi-color flow cytometry. However, not only does it require an invasive procedure, it may not capture the spatial heterogeneity of the tumor. Here, we apply cell-free DNA liquid biopsies via Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq) to detect circulating tumor DNA (ctDNA) and quantitatively track in MM patients undergoing anti-BCMA CAR T-cell therapy.

Methods We performed CAPP-Seq for the detection of ctDNA using a MM-specific gene panel, which we previously developed.¹ A total of 252 plasma, germline and tumor samples from 28 patients receiving BCMA directed standard of care CAR-T therapy (idecabtagene vicleucel, n=23 or ciltacabtagene autoleucel, n=5) were sequenced to assess the dynamics of ctDNA. Clinical MRD was performed on day 90 (+/- 15 days) after CAR infusion by ClonoSeq (Adaptive Biotechnologies), or by multiparametric flow cytometry (Mayo Clinic) in patients without a trackable sequence for ClonoSeq. The clinical MRD and ctDNA levels at matched timepoints were assessed for correlation. These metrics were also correlated with patient outcomes.

Results Using CAPP-Seq, a median of 90 SNVs (range 2–264) were detected per case; 24/28 patients (86%) had a sufficient number of variants for tumor monitoring. On day 90, 14 patients had evaluable plasma. For clinical MRD, 24/28 patients were submitted for identification of trackable sequences by ClonoSeq including 6 patients who already had identified clones during prior therapy; 8/24 patients (33%) failed the identification of dominant sequences. For these patients, MRD flow cytometry was sent on day 90. Overall, 16 patients had clinical MRD data (ClonoSeq, n=13; flow, n=3). For patients who had both day 90 ctDNA and clinical MRD (n=14), there was a significant correlation in quantification by respective measures (rho=0.71, p=0.007; figure 1A). Kaplan-Meier analysis showed progression-free survival (PFS) significantly correlated with day 90 ctDNA level (p=0.03; figure 1B) as well as clinical MRD (p=0.008).

Conclusions MRD has emerged as an important prognostic biomarker in MM. However, current methods depending on bone marrow aspirates limit the frequency of assessment. ctDNA assessment by CAPP-Seq can quantitatively follow the disease burden and assess MRD. ctDNA-MRD levels correlate with clinical MRD, and ctDNA negativity on day 90 is associated with improved PFS. ctDNA-MRD can potentially provide comparable information to clinical bone marrow MRD.

Reference

1. Hosoya H, Carleton M, Tanaka K, Sworder B, Hovanky V, Duran G, Zhang T, Khodadoust M, Miklos D, Arai S, Iberri D, Liedtke M, Sidana S, Kurtz D. Disease Characterization and Response Prediction in Myeloma Patients Undergoing Conventional and Cellular Therapies from Circulating Tumor DNA. Blood 2022;140(Supplement 1):1546–1548.

Ethics Approval This study has obtained ethics approval by Stanford IRB under protocol number of #18329 and #5019.

All the participants gave informed consent before taking part.

• Download figure
• Open in new tab
• Download powerpoint

Abstract 160 Figure 1

Assessment of MRD by circulating tumor DNA. (A) Correlation between day 90 ctDNA level and clinical bone marrow MRD assay (ClonoSeq, n=11; MRD flow, n=3). (B) Kaplan-Meier curve of progression-free survival (PFS) according to the ctDNA positivity at day 90.