Extended Data Fig. 9: Deciphering subclonal progenitor identities using multiplex GoT, and targeting loci that are distant from transcript ends using circularization GoT.

a, Single-cell cloning assay of peripheral blood cells from patient MF05 (Methods). b, Rate of targeted locus capture (per cent) as a function of gene expression and the distance of the targeted locus from the transcript ends. c, Distance of the mutation locus from transcript ends for pan-cancer drivers, and their frequencies (based on the number of times they are reported in the COSMIC database). Mutations are annotated as oncogenes, tumour-suppressor genes or passengers (as previously defined^60,61). Relative density of each subclass of mutations from the closer end (that is, 3′ or 5′) is shown in the top panel. d, Schematic of analysis of ONT sequencing reads. e, Frequency of SF3B1-mutant and wild-type reads of linear GoT amplicon library sequenced with ONT. f, Analysis of SF3B1 amplicon reads sequenced by ONT for inter-transcript PCR recombination by mapping 50 bp at the opposite end of the targeted locus, showing only the 2.2% of fragments that reflect inter-transcript recombination. g, Pairwise difference of read lengths for duplicate reads (that is, reads with the same cell barcode and UMI) of the SF3B1 amplicon library sequenced with ONT, showing consistent read lengths of duplicate reads that support a low rate of intra-transcript PCR recombination. h, Comparison of genotype assignment for CALR in sample MF01 between linear GoT and circularization GoT after downsampling reads to 300,000 with 10 iterations (n = 320 cells). i, Comparison of CALR-mutant UMI fraction per cell in sample MF01 between linear GoT and circularization GoT after downsampling reads to 300,000 with 10 iterations (n = 320 cells, Pearson’s correlation, F-test).