Clonal and subclonal driver mutations in MDS. (A) Variant allele fractions (y-axis) for driver mutations identified in 4 illustrative patients. The points show the observed allele fraction, with the vertical bars denoting 95% CIs in this fraction. The leftmost patient shows 4 driver mutations all at the same allele fraction. The second patient from the left shows statistical evidence for clonal heterogeneity, but the variant allele fractions are too low to establish phylogenetic relationships among mutations unambiguously. The rightmost 2 patients have statistically significant differences in observed allele fractions among driver mutations with some definitive phylogenetic structure. The phylogenetic tree cannot always be fully resolved (see possible trees for the 4th patient), but even with this uncertainty, 4 informative pairwise precedences can be unambiguously stated. (B) Pie chart showing the distribution of clonality and subclonality among 313 patients with 2 or more driver mutations. (C) Results of a Bradley-Terry model showing the relative temporal order of genes involved in at least 5 pairwise precedences. The estimates are calculated in relation to ASXL1 as the reference point, and standard errors are shown as horizontal bars. Genes are colored by their general biological function. A total of 107 patients contributed informative precedences.