Figure 3. Haplotype-specific NO analysis shows local effects of a copy-neutral driver SV in AML.

(a) Balanced t(8;21) translocation in AML_1, discovered based on strand co-segregation (P-value for translocation discovery using strand co-segregation²⁴: P=0.00003, FDR-adjusted Fisher’s exact test, Fig. S16). The SV breakpoint was fine-mapped to the region highlighted in light blue. Composite reads shown were taken from all informative cells in which reads could be phased (WC or CW configuration; Methods). (b) A violin plot demonstrates haplotype-specific NO at the RUNX1T1 gene body (10% FDR; two-sided wilcoxon ranksum test followed by Benjamini Hochberg multiple correction; n = 17 single-cells; boxplot was defined by minima = 25th percentile - 1.5X interquartile range (IQR), maxima = 75th percentile + 1.5X IQR, center = median, and bounds of box = 25th and 75th percentile), consistent with aberrant activity of the locus on der(8). (c) Haplotype-specific NO around the SV breakpoint. Fold changes of haplotype-specific NO, measured between the RUNX1-RUNX1T1 containing derivative chromosome (der(8)) and corresponding regions on the unaffected homologue (Ref), are shown in black, and -log10(P-values) in light blue. Enhancer-target gene physical interactions based on chromatin conformation capture^56–93 are depicted in orange (interactions involving RUNX1 and RUNX1T1) and grey (involving other loci). (d) Significant CREs located within the distal peak region, demonstrating haplotype-specific absence of NO on der(8) at 10% FDR, suggesting increased CRE accessibility on der(8). Within the segment ~0.8 to 1.1Mb upstream of RUNX1, which showed pronounced haplotypespecific NO, we tested 69 CREs for haplotype-specific NO, which identified two significant CREs. (e) Haplotype-specific NO measured between der(8) and corresponding regions of the unaffected homologue. Red: regions corresponding to the fused TAD. (f) A beeswarm plot shows that the fused TAD (red) is an outlier in terms of haplotype-specific NO on der(8) (P-values based on KS tests; n = 83 TADs in der(8); boxplot was defined by minima = 25th percentile - 1.5X interquartile range (IQR), maxima = 75th percentile + 1.5X IQR, center = median, and bounds of box = 25th and 75th percentile).