Standardized Minimal Residual Disease Detection by Next-Generation Sequencing in Multiple Myeloma

Abstract

Next-generation sequencing (NGS) has been applied to monitor minimal residual disease (MRD) in multiple myeloma (MM). Standardized DNA input and sequencing depth is essential for achieving a uniform sensitivity in NGS-based MRD study. Herein, the sensitivity of 10−5 was verified by a standardized experimental design based on triplicate measurements of 1 μg DNA input and 1 million sequencing reads using the LymphoTrack-MiSeq platform. MRD level was defined as the mean MRD burden of the triplicates. Two spike-in controls at concentrations of 0.001% tumor plasma cells (PC) for verifying the sensitivity of 10−5 and 0.01% (or 0.005%) for MRD normalization were systematically analyzed. The spike-in control of 0.001% MRD was consistently detected in all samples, confirming a sensitivity of 10−5. Moreover, this standardized NGS approach yielded MRD measurements concordant with serological response and comparable to allele-specific oligonucleotide (ASO) real-time quantitative (RQ)-PCR. Moreover, NGS showed an improved sensitivity and provided quantification of MRD for cases assigned “positive but not quantifiable” (PNQ) by ASO RQ-PCR, even without the use of patient-specific probes/primers. Issues regarding the specificity of myeloma-specific sequences as MRD target, optimal input for spike-in normalization, and interpretation of MRD from triplicates are discussed. Herein, the standardized LymphoTrack-MiSeq-based method is verified to carry a sensitivity of 10−5, hence an effective tool for MRD monitoring in MM. As only a small number of samples are tested here, further study with a larger number of patients is warranted.