Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides

Abstract

The longitudinal evolution of a myeloma genome from diagnosis to plasma cell leukemia has not previously been reported. We used whole-genome sequencing (WGS) on 4 purified tumor samples and patient germline DNA drawn over a 5-year period in a t(4;14) multiple myeloma patient. Tumor samples were acquired at diagnosis, first relapse, second relapse, and end-stage secondary plasma cell leukemia (sPCL). In addition to the t(4;14), all tumor time points also shared 10 common single-nucleotide variants (SNVs) on WGS comprising shared initiating events. Interestingly, we observed genomic sequence variants that waxed and waned with time in progressive tumors, suggesting the presence of multiple independent, yet related, clones at diagnosis that rose and fell in dominance. Five newly acquired SNVs, including truncating mutations of RB1 and ZKSCAN3, were observed only in the final sPCL sample suggesting leukemic transformation events. This longitudinal WGS characterization of the natural history of a high-risk myeloma patient demonstrated tumor heterogeneity at diagnosis with shifting dominance of tumor clones over time and has also identified potential mutations contributing to myelomagenesis as well as transformation from myeloma to overt extramedullary disease such as sPCL.

Figure 1

Frequency of somatic mutations in genes of interest within other tumor cohorts. Genes containing SNV identified in this case study patient were compared against the MMRC cohort of 38 myeloma genomes and the COSMIC database of other tumor types to determine the frequency of all somatic mutations in these genes within larger populations. This graph illustrates the frequency (percentage) of all somatic mutations in the MMRC cohort and in other tumors present in the COSMIC database. Frequencies with < 0.5% were counted as absent and were not included in the graph.

Figure 2

Clonal divergence of validated variant alleles. Graph illustrating the presence of shared and unique SNV at each tumor time point. There are 15 variants common to all time points and shared by a common ancestor. Six variants are common to only the diagnostic and second relapse, while no variants are common to the first relapse and sPCL. The greatest divergence is observed between the first relapse and sPCL, with 7 unique variants detected in each sample.

Figure 3

Circos plot depicting the summary of structural variation in the sPCL. The center, line plots indicate the presence of discordant read pairs. The middle ring contains the array CGH plot, and the outermost ring indicates mutated or deleted genes.