Receiver Operating Characteristic (ROC) curves showing the association of the <i>PIK3CA</i>-GS with <i>PIK3CA</i> mutation status. A.

<p>Dataset A, n = 22/58 (38.5%) AUC = 0.67, 95%CI: 0.5–0.8, p = 0.04), <b>B.</b> Dataset B n = 6/23 (26%) AUC 0.77, 95%CI : 0.6–0.96, p =  = 0.059). <b>C</b> and <b>D</b> show the individual samples for each dataset and distinguish between sequenced kinase (exon 20- squares) and helical (exon 9-circles) mutations and wild-type (WT-black) <i>PIK3CA</i>.</p

Additional file 2: Figure S1. of An immune stratification reveals a subset of PD-1/LAG-3 double-positive triple-negative breast cancers

Prognostic value of the binary tumor-infiltrating lymphocytes (TILs) cutoff ≥ 20% in triple-negative breast cancer (TNBC) patients of the discovery cohort stratified by nodal status. Figure S2. Correlation between the expression of PD-1 and LAG-3 and the presence of CD8+ cells in triple-negative breast cancer (TNBC). (PDF 397 kb

Associations between PIK3CA-GS and relative change in phosphorylated S6. A

<p>Dataset B: relative percentage change in pS6 (S240) as measured by IHC from baseline to day 15 according <i>PIK3CA</i> genotype <b>B</b> Regression line for relative change in pS6 from baseline to day 15 according to <i>PIK3CA</i>-GS in dataset B <b>C</b> Dataset A: Relative percentage change in phosphorylated S6 (S240) as measured by IHC from baseline to day 15 according <i>PIK3CA</i> genotype and treatment arm.</p

Regression lines for relative change in %Ki67 from baseline to day 15 according to <i>PIK3CA</i>-GS scores by treatment arm by <i>PIK3CA</i> genotype in dataset A. A

<p>PIK3CA WT; <b>B</b> PIK3CA mutant Relative change in %Ki67 from baseline to day 15 by treatment arm and according to increasing tertiles of the <i>PIK3CA</i>-GS by <i>PIK3CA</i> genotype in dataset A <b>C</b> PIK3CA WT; <b>D</b> PIK3CA mutant.</p

Baseline characteristics of the two datasets used in this analysis.

<p>The second column compares the dataset A with the original previously published global trial population.</p><p># as previously published in Baselga et al, JCO 2009 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053292#pone.0053292-Dowsett1" target="_blank">[11]</a> (original cohort of which the Dataset A is a subset); Dataset B published by Sabine et al, BCR 2010 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053292#pone.0053292-Ellis2" target="_blank">[13]</a>.</p>**<p>As previously defined in Dowsett et al (CCR 2007) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053292#pone.0053292-Kalinsky1" target="_blank">[9]</a>;</p

Relative change in %Ki67 from baseline to day 15 by treatment arm.

<p>According <i>PIK3CA</i> genotype in <b>A</b> dataset A; B dataset <b>B</b> According to <i>PIK3CA</i>-GS scores by treatment arm: regression lines for relative change in %Ki67 from baseline to day 15 <b>C</b> dataset A; <b>D</b> dataset B <b>E</b> Relative change in %Ki67 from baseline to day 15 by treatment arm and according to increasing tertiles of the <i>PIK3CA</i>-GS in dataset A; <b>F</b> Number of Absolute D15 responders by treatment arm and according to increasing tertiles of the <i>PIK3CA</i>-GS in dataset A.</p

Mutational signatures in TN1 and ER2, and ctDNA assays in ER2.

<p>(A) Reconstruction of mutational context plot with deconstructSigs for TN1 using COSMIC signatures 17, 24, and 29. 5′ and 3′ nucleotides are indicated by colour code on <i>x</i>-axis. (B) Contribution of each signature per sample. (C) Subclonal phylogeny for TN1 showing private and public subclones. Private subclones in dark blue. Mutations arising from signature 17 represented in pink along branches. (D) Reconstruction of mutational context for ER2 using APOBEC signatures 2 and 13 detected with deconstructSigs, with origin of key mutations overlaid. Colour codings as for (A). (E) Subclonal phylogeny for ER2, with private subclones in dark blue. (F) Bar charts show ctDNA results at time of liver biopsy and later at death. <i>y</i>-axis unit is copies per millilitre.</p

Heatmap of copy number across all samples.

<p><i>x</i>-axis shows all coding genes in order of chromosomal coordinate. Grey areas on map represent difficulty in calling allele-specific copy number in FFPE samples. Horizontal blue lines indicate areas of LOH. Deep red is high level amplification, pale red is amplified with four or more copies, and blue is deleted with less than two copies. White is two to three copies. Ploidy is displayed in last column on right. <i>y</i>-axis terms correspond to Figs <a href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1002204#pmed.1002204.g002" target="_blank">2</a>–<a href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1002204#pmed.1002204.g005" target="_blank">5</a>.</p

Workflow diagram giving overview of methodology.

<p>Workflow diagram giving overview of methodology.</p