Fig. 3: Clonal complexity decreases during tumor regression, residual disease, and recurrence.
From: Adaptation and selection shape clonal evolution of tumors during residual disease and recurrence
a Pie charts showing the relative frequency of barcodes in early residual tumors (4 weeks following Dox withdrawal). b Pie charts showing the relative frequency of barcodes in late residual tumors (8 weeks following Dox withdrawal). c Number of unique barcodes detected in primary tumors and residual tumors 4 and 8 weeks following Dox withdrawal. *P < 0.05, **P < 0.01. Primary vs. 4-week residual tumors, P = 2.6 × 10−3; Primary vs. 8-week residual tumors, P = 1.1 × 10−3; 4-week residual tumors vs. 8-week residual tumors, P = 0.024. Significance determined by Welch Two-Sample T-test (two-sided). n = 6 biologically independent tumors in each cohort. d Shannon Diversity Index showing barcode complexity in primary tumors and residual tumors 4 and 8 weeks following Dox withdrawal. *P < 0.05, ***P < 0.001. Primary vs. 4-week residual tumors, P = 4.8 × 10−4; Primary vs. 8-week residual tumors, P = 1.1 × 10−4; 4-week residual tumors vs. 8-week residual tumors, P = 0.02. Significance determined by Welch Two-Sample T-test (two-sided). n = 6 biologically independent tumors in each cohort. e Cumulative abundance plots for primary tumors and residual tumors 4 and 8 weeks following Dox withdrawal. Barcode complexity decreased following tumor regression and continued to decrease during the persistence of residual disease. **P < 0.01, ***P < 0.001. Primary vs. 4-week residual tumors, P = 3.3 × 10−4; Primary vs. 8-week residual tumors, P = 2 × 10−4; 4-week residual tumors vs. 8-week residual tumors, P = 8 × 10−3. Significance determined by Welch Two-Sample T-test (two-sided) between the number of barcodes composing 50% of reads. f Pie charts showing the relative frequency of barcodes in recurrent tumors. g Shannon Diversity Index showing barcode complexity in primary and recurrent tumors. n = 6 biologically independent primary tumors and n = 12 biologically independent recurrent tumors. h Barcode diversity in recurrent tumors is not correlated with time to recurrence.
