Extended Data Fig. 7. Inference of SCNAs using CITE-seq data from the CLL_24 sample.

(a) InferCNV⁴⁸ analysis of 3,919 high quality CLL cells, and 540 control cells (cells sequenced by CITE-seq not originating from the B-cell lineage; see Supplementary Fig. 25), profiled by CITE-seq. This analysis did not discover any subclones in CLL_24. (Note that the high variability observed on the 6p-arm, not only seen in CLL cells but also in control cells, likely arose from the presence of MHC genes in this locus, whose expression is cell cycle dependent¹¹³.) (b) CONICSmat based targeted SCNA recalling of the 10q-terDel (previously discovered in SCb; see Fig. 4b) using the high-resolution breakpoints derived from Strand-seq. Use of these SV breakpoints allowed CONICSmat to confidently call the 10q-terDel in 82 single cells from the CITE-seq data.