Genomic discovery and clonal tracking in multiple myeloma by cell-free DNA sequencing

Summary: Development of drug resistance and clonal evolution is a major problem in multiple myeloma (MM) and may be due to genetic heterogeneity and clonal evolution but its longitudinal genetic characterization has been impractical, thus far. We have developed a genomic discovery method to monitor genetic evolution of the disease through whole exome sequencing and low-pass whole genome sequencing of myeloma-derived circulating cell-free DNA (cfDNA). Low-pass whole genome sequencing of 110 cfDNA samples from 75 randomly selected MM patients was used to develop an approach to predict the utility of further whole exome sequencing based on cfDNA concentration as a quick and cost-effective marker. Whole exome sequencing of cfDNA, matched normal blood cells, and bone marrow MM cells obtained from five myeloma patients at the same time point demonstrated that identification of clonal somatic mutations was robust and highly concordant between cfDNA and bone marrow, and provided sufficient resolution to define the subclonal composition by cfDNA. cfDNA allowed longitudinal tracking of disease burden and captured clonal evolution of MM. We provide a framework for effectively utilizing comprehensive discovery-oriented cfDNA sequencing in MM.