Additional file 2: of Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier
Creators: name: Chen, Youdinghuan
name: Wang, Yue
name: Salas, Lucas
name: Miller, Todd
name: Mark, Kenneth
name: Marotti, Jonathan
name: Kettenbach, Arminja
name: Cheng, Chao
name: Christensen, Brock
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Plant Biology

description: Figure S1. Details of SVM BRCA1-like classifier. (A) Overview of copy number mapping algorithm for generating the input for training the SVM BRCA1-like classifier. (B) Receiver-operation characteristic curves (ROC) of the classifier applied to training and test set (AUC = 1.00 and 0.75, respectively). (C-D) Correlation of SVM BRCA1-like probability scores with published HR-deficiency metrics (HRD-LOH and LST scores). ***P &lt; 0.001. Figure S2. Comparison of Ki-67 (MKI67) gene expression as a surrogate marker for cellular proliferation in METABRIC hormone-receptor-positive breast tumors. P value indicates statistical significance from a linear model adjusting for age, tumor stage, ER, PR and HER2 positivity. ***P &lt; 0.001. Figure S3. Five-year overall survival comparison between BRCA1-like and non-BRCA1-like ER-positive/PR-positive, HER2-negative breast tumors in TCGA and METABRIC (combined). Table inset shows hazards ratio (95% CI) and P value from Cox proportional hazards regression adjusting for potential confounders. ***P &lt; 0.001. Figure S4. miR124–2 with hypermethylation exhibit reduced gene expression in TCGA BRCA1-like receptor positive tumors. P value indicates statistical significance from a linear model adjusting for age, tumor stage, and ER, PR, and HER2 positivity. *P &lt; 0.05. Figure S5. Comparison of heterogeneity between the “BRCA1-like methylation cluster” and “non-BRCA1-like methylation cluster” generated by hierarchical clustering of 350 most differential CpGs identified by DMRcate (all FDR &lt;0.05 and |log2∆beta| ≥ 3.50). (A) Heat map showing unsupervised clustering (Euclidean distance, complete linkage) of the 350 DMRcate-identified CpGs. (B) Rank-ordered inter-sample variance in beta-values of the 350 differentially methylated CpGs. Horizontal dotted lines indicate mean inter-sample variance distribution for each group. Figure S6. Differential gene expression of DNA methyltransferases (DNMT1/3A/3B) in TCGA receptor-positive BRCA1-like breast tumors. A P value indicates statistical significance from linear model adjusting for age, tumor stage, and ER, PR, and HER2 positivity. ***P &lt; 0.001. Figure S7. Comparison of Somatic Mutational Signature 1 contributed to by genome-wide cytosine-to-thymine (C &gt; T) deamination events in TCGA hormone-receptor-positive breast tumors. A P value indicates statistical significance from linear model adjusting for age, tumor stage, and ER, PR, and HER2 positivity. **P &lt; 0.01. (PDF 3058 kb)