Fig. 3: SPRINTER identifies tumor clone proliferation heterogeneity in patient CRUKP9145 with NSCLC.

a, The distributions of SPRINTER’s inferred S fractions (bottom, y axis) for each NSCLC clone (x axis) with varying cell numbers (top, y axis) in primary (top) and metastatic (bottom) samples were calculated by bootstrapping (300 repeats; dashed lines represent sample-level averages). Clone S fractions were compared per sample using a two-sided chi-square test, combined using the minimum and a Benjamini–Hochberg correction was applied (family-wise error rate = 0.1; red asterisks indicate significant P values). Sample-level S fraction 95% CIs (between axes) were computed by bootstrapping cells per sample. *P < 0.1, **P < 0.05 and ***P < 0.005. b, Ki-67 staining from one representative slide in primary and metastatic samples, indicating areas with high and low Ki-67 (boxes) that were consistent with SPRINTER clone S fractions (red asterisk). c, Top, nuclear diameter (x axis, micrometers, normalized by sample mean) was measured by DLP+ nozzle-based imaging for 14,569 cells with successfully recorded images inferred to be in G1, S or G2 phase by SPRINTER (y axis), with each pair of distributions compared using a one-sided Mann–Whitney U test (P values on right). Bottom, the nuclear diameter per clone (x axis) was calculated using the minimum diameter across the cells in each clone (each dot) that were assigned to different cell cycle phases by SPRINTER (y axis). Across cell cycle phases, clones are linked by lines, such that the line width is proportional to clone size and the line color indicates whether the nuclear diameter per clone has increased as expected (red) or not (blue). Nuclear diameters in different cell cycle phases were compared per clone using a one-sided Wilcoxon signed-rank test (P values on right). Right, example microscopy images of nuclei in each phase. d, For five primary tumor samples in this study (colored circles on photo) and three additional samples (gray circles), each bulk clone identified in previous analysis (hexagons comprising clones with different inner shapes of size proportional to cell proportion) was assigned to the most similar SPRINTER clone using SNVs (colors, with legend marker size proportional to SPRINTER’s inferred S fraction). In a and c, box plots show the median and the IQR with whiskers denoting values within 1.5 times the IQR from the first and third quartiles. CI, confidence interval.