Fig. 4

Evolutionary inference during HER2 amplification in DCIS from HER2-positive patients. We inferred copy number variations (CNVs) from Smart-3SEQ data and used CNVs called on chr1-15 for the following analysis. a Number of CNVs detected in DCIS with different HER2 amplification status. b Percentage of CNVs that are unique to DCIS_amp, unique to DCIS_noamp, or shared between two DCIS groups for each patient. A CNV is called if it is detected in ≥2 DCIS samples within each group. c Phylogenetic trees built by maximum parsimony (left) and hierarchical clustering (right) on inferred CNVs in DCIS for patients 3 and 5. Branches with the approximately unbiased p value (au) >=95% are considered statistically significant and highlighted by red rectangles (right). d Frequency of the CNVs detected among all patients by two DCIS groups along the chromosome location. Red: gain; blue: loss. The red dotted line denotes the value of (Q3+1.5×IQR) as the threshold. 1q gain, 8p loss, and 8q gain are called statistically significant in DCIS_amp; whereas 1q gain and 8p loss are called statistically significant in DCIS_noamp