Clonal evolution revealed by whole genome sequencing in a case of primary myelofibrosis transformed to secondary acute myeloid leukemia

Abstract

Clonal architecture in myeloproliferative neoplasms (MPNs) is poorly understood. Here we report genomic analyses of a patient with primary myelofibrosis (PMF) transformed to secondary acute myeloid leukemia (sAML). Whole genome sequencing (WGS) was performed on PMF and sAML diagnosis samples, with skin included as a germline surrogate. Deep sequencing validation was performed on the WGS samples and an additional sample obtained during sAML remission/relapsed PMF. Clustering analysis of 649 validated somatic single-nucleotide variants revealed four distinct clonal groups, each including putative driver mutations. The first group (including JAK2 and U2AF1), representing the founding clone, included mutations with high frequency at all three disease stages. The second clonal group (including MYB) was present only in PMF, suggesting the presence of a clone that was dispensable for transformation. The third group (including ASXL1) contained mutations with low frequency in PMF and high frequency in subsequent samples, indicating evolution of the dominant clone with disease progression. The fourth clonal group (including IDH1 and RUNX1) was acquired at sAML transformation and was predominantly absent at sAML remission/relapsed PMF. Taken together, these findings illustrate the complex clonal dynamics associated with disease evolution in MPNs and sAML.

Figure 1. Spectrum of transition and transversion mutations per sample

The percentage of somatic single nucleotide variants (SNVs) in the PMF, sAML, or specific for the sAML sample are categorized by transition and transversion mutation types.

Figure 2. Comparison of variant allele frequencies across tier 1 somatic single nucleotide variants (SNVs)

The variant allele frequency for each tier 1 SNV across the PMF, sAML, and sAML remission/relapsed PMF samples is shown. The genes with the SNVs are divided based on whether the SNV was present predominantly in all three samples (Shared SNVs), only the PMF sample (PMF SNVs), low in the PMF sample but high in sAML and sAML remission/relapsed PMF samples (Low PMF SNVs), and only in the sAML sample (sAML SNVs).

Figure 3. Clustering and clonal evolution across disease progression

Unsupervised clustering of 649 SNVs identified clusters of mutations with similar variant allele frequencies corresponding to the founding clone (green), subclone 1 (light blue), subclone 2 (red), and subclone 3 (dark blue). (A) Frequency of mutations in PMF versus sAML. (B) Frequency of mutations in sAML remission/relapsed PMF versus sAML. (C) A model of clonal evolution based on the median values for the VAFs in each of the four clusters at each stage of progression in (A) and (B) as shown below the plot. Abbreviations: PMF, primary myelofibrosis; sAML, secondary acute myeloid leukemia; sAML REM, secondary acute myeloid leukemia remission/relapsed PMF.