Measurable Residual Disease Detection in Mantle Cell Lymphoma (MCL) Subjects Using NGS B-Cell MRD Assay

Abstract Background Mantle Cell Lymphoma (MCL) is an aggressive, rare form of non-Hodgkin B-cell lymphoma. Measurable Residual Disease (MRD) assessment can provide useful information when assessing and tracking response to therapy, refining treatment and predicting clinical outcome for subjects with B-cell lymphoproliferative diseases. One method of MRD detection is to identify and track specific clonal immunoglobulin heavy chain (IGH) gene rearrangement sequences on a next-generation sequencing (NGS) platform. Here, we present the NGS-based B-cell MRD Assay with 10−6 sensitivity for detecting MRD in malignancies in mantle cell lymphoma (MCL). Methods Residual DNA samples from different specimen types (44 BM and 77 PB) at different post-treatment time points were obtained from anonymized 47 MCL subjects that had been enrolled in a study approved by the Spanish Group of Lymphoma and Autologous Stem Cell Transplantation (clinical trial: NCT02682641, publication reference: 10.1200/JCO.21.02321). 121 of these follow up samples were tested by the B-cell MRD Assay by tracking the clonal sequences detected in corresponding baseline samples. Among them, 90 follow up samples were paired PB and BM samples. The B-cell MRD Assay workflow consists of DNA extraction and PCR based library preparation with proprietary multiplex master mixes (MMx) targeting either IGH Framework 1 (FR1) or 3 (FR3) regions, which both track the patient- and tumor-specific CDR3 sequence. Purified libraries are then equimolar pooled and sequenced on Illumina’s NextSeq Dx platform. The FASTQ output files from sequencing are analyzed using Invivoscribe’s B-Cell MRD Software-NextSeqDx. Results from Invivoscribe were compared to the results from Salamanca lab that were generated by qPCR. Results Based on the results from B-cell MRD Assay, 115/121 (95%) samples were valid, 42/115 (37%) valid samples had, “MRD Detected”, and 73/115 (63%) samples had, “MRD Not Detected”, with an “MRD Detection” rate of 28% in PB and 50% in BM specimen types. When comparing MRD detectable status between paired PB and BM samples from 36 MCL subjects, 30/44 (68%) paired samples had same MRD call and were concordant, whereas 14/44 (32%) calls were discordant. More specifically, 12/14 (86%) discordant samples had PB specimen type with a “MRD Not detected” call, whereas the paired BM specimen showed a “MRD Detected” call. Overall, in comparison with the MRD results (n = 84) provided by Salamanca lab using qPCR method, the B-cell MRD Assay demonstrated concordance of 80%, PPA of 79%, and NPA of 80% for MRD detection in MCL samples. Conclusion Good concordance was observed between the qPCR used at Salamanca and Invivoscribe’s B-cell MRD assay. It was important to note that the BM specimen type was determined to be more sensitive in detecting MRD when compared to PB in assessment of paired PB and BM samples. These results demonstrate that the B-cell MRD Assay can be utilized for MRD detection in follow-up sample types for MCL subjects.