Extended Data Figure 10. Mutations in a B lymphocyte clone in a cirrhotic liver.

(A) Illustration of a portion of the B-cell receptor (IGH) region on chromosome 14. Shown are the coverage tracks of an LCM sample that does not belong to the lymphocyte lineage (top) and a sample that belongs to the lymphocyte lineage (middle). In the center of the displayed region there is a drop of copy number in the lymphocyte track, indicating a structural rearrangement. The bottom track shows the paired-end reads that contribute to a rearrangement event in the lymphocyte sample, co-localised with the drop in copy number.

(B) Application of the pigeonhole principle – if two clusters of heterozygous mutations in regions of diploid copy number are in different cells, then their median variant allele fractions must sum to ≤0.5 (if they sum to >0.5, equivalent to a combined cellular fraction of >1, there must be some cells that carry both sets of mutations – hence one cluster would have a subclonal relationship with the other). Cluster 10 is the cluster with the unique VDJ rearrangement of IGH shown in panel A and the large number of mutations attributed to signature 9. Clearly, samples from clusters 2, 11 and 55 etc have VAFs which, when combined with cluster 10, sum to >0.5. Therefore, they must be subclonal to cluster 10, even though they do show signature 9.

(C-H) Representative pairwise decision graphs for clusters of mutations. Median cellular fraction is shown for pairs of clusters across every sample from the patient. Where at least one sample falls above / to the right of the x+y=1 diagonal line, those two clusters must share a nested clonal-subclonal relationship.