Additional file 1 of Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma

Additional file 1: Table S1. Clinical annotations of MPM patients. Table S2. List of biomarkers included in MCP-counter. Table S3. Variants with structural consequences in genes and variants in the TERT promoter. A Germline mutations identified by whole exome sequencing. B Variants correspondence between sequencing methods. C Somatic variants with structural consequences in genes and variants in the TERT promoter identified by whole exome sequencing. D Variants with structural consequences in genes and variants in the TERT promoter identified by DNA targeted sequencing. E DNA targeted sequencing of multiple sections of the T227LE fresh tumor sample used to generate the MPM_83 primary cell line. Table S4. Clonality of the protein-altering somatic variants detected by whole exome sequencing. A Cancer cell fraction (CCF) values of protein-altering variants. B Clonality per patient based on protein-altering variants. C Cancer cell fraction (CCF) values of copy number variations (CNV) based on FACET analysis. D Clonality per patient based on FACET analysis. Table S5. Fusion transcripts identified by RNA-seq. Table S6. Pathway dysregulation between paired tumor samples. A Differentially expressed protein coding genes between paired tumor samples. B Pathways dysregulated between paired tumor samples in the GeneOntology Biological Process non-redundant database. C Pathways dysregulated between paired tumor samples in the KEGG database. D Pathways dysregulated between paired tumor samples in the Reactome database. E Pathways analysis using single sample Gene Set Enrichment Analysis (ssGSEA) in the GeneOntology Biological Process, KEGG and Reactome databases. Table S7. Epigenetic dysregulation between paired tumor samples. A Differentially methylated CpG between paired tumor samples. B Pathways dysregulated between paired tumor samples based on differentially expressed protein coding genes associated with differentially methylated CpG in the GeneOntology Biological Process non-redundant, KEGG and Reactome databases.