Additional file 2: of Integrated genomics approach to identify biologically relevant alterations in fewer samples

Additional Tables S1-S8: Copy number alterations of known genomic locations identified in HNSCC cell lines. Copy number alterations in halmark genes identified in HNSCC cell lines. Gene expression of hallmark genes by RNA sequencing and qPCR. Features of whole exome and transcriptome sequencing. Validation of mutations in hallmark and novel genes. Details of mutations identified by integrated analysis in HNSCC cell lines. Primer sequences used for Sanger sequenicng based validation of mutations. Primers used for copy number and gene expression study using qPCR. (ZIP 249 kb

Supplementary Table S4 from Natural History of Germline <i>BRCA1</i> Mutated and <i>BRCA</i> Wild-type Triple-negative Breast Cancer

This tables shows the copy number variation data for all patients on this study</p

TABLE 1 from Natural History of Germline <i>BRCA1</i> Mutated and <i>BRCA</i> Wild-type Triple-negative Breast Cancer

Detailed description of patient samples and applied genomic assays</p

Supplementary figure S5 from Natural History of Germline <i>BRCA1</i> Mutated and <i>BRCA</i> Wild-type Triple-negative Breast Cancer

This figure shows the SGOL score for all patient samples with clinically relevant genes.</p

FIGURE 2 from Natural History of Germline <i>BRCA1</i> Mutated and <i>BRCA</i> Wild-type Triple-negative Breast Cancer

Graphical representation of clonal evolution observed in sequentially collected samples over time in 3 patients with TNBC. Timepoints are depicted on the X-axis and Cellular Prevalence (Clonal Prevalence) is shown on the Y-axis. Different colors in each patient represent various clones and their changing dynamics over time. Clonal phylogeny for each patient is shown on the left side of main figure. A, Patient_02. B, Patient_04. C, Patient_07.</p

Supplementary Table S5 from Natural History of Germline <i>BRCA1</i> Mutated and <i>BRCA</i> Wild-type Triple-negative Breast Cancer

This table shows the annotation information from Annovar for clonal architecture of Patient P2</p

Supplementary Table S8 from Natural History of Germline <i>BRCA1</i> Mutated and <i>BRCA</i> Wild-type Triple-negative Breast Cancer

This table shows the genes in the germline sequencing panel for the targetted germline mutation assay.</p

Supplementary Data from Natural History of Germline <i>BRCA1</i> Mutated and <i>BRCA</i> Wild-type Triple-negative Breast Cancer

This file contains supplementary data for this study.</p