Figure S4.

Phasing Pairs of Subclonal Point Mutations, Related to Figure 3

(A) Phasing of subclonal mutations (stars) with other nearby subclonal mutations allows determination of whether they are in separate phylogenetic lineages, in which case no sequencing reads will report both variants together (mutually exclusive pair of mutations).

(B) Similar phasing analysis can identify cases where the later subclonal mutation has arisen on an allele linked with a previous subclonal mutation.

(C) Example of a mutually exclusive pair of mutations from PD4120a. Sequencing read pairs are shown as yellow and blue bars linked by a dotted line. Base calls varying from the reference genome are shown as red squares. Two nearby mutations, indicated by arrows, are never found on the same read pair.

(D) Example of a pair of mutations showing subclonal evolution in PD4120a. The right-hand subclonal mutation occurred on an allele already carrying the left-hand mutation, as evidenced by the existence of reads reporting both together, the left-hand but not the right-hand mutation but never the right-hand mutation without the left-hand one.

(E) A pair of mutations, both of which phase with the subclonally deleted copy of chromosome 13, but are mutually exclusive.