Additional file 1 of Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors
Creators: name: Smith, Christopher
name: Moser, Tina
name: Mouliere, Florent
name: Field-Rayner, Johanna
name: Eldridge, Matthew
name: Riediger, Anja
name: Dineika Chandrananda
name: Heider, Katrin
name: Wan, Jonathan
name: Warren, Anne
name: Morris, James
name: Hudecova, Irena
name: Cooper, Wendy
name: Mitchell, Thomas
name: Gale, Davina
name: Ruiz-Valdepenas, Andrea
name: Klatte, Tobias
name: Ursprung, Stephan
name: Sala, Evis
name: Riddick, Antony
name: Tevita Aho
name: Armitage, James
name: Perakis, Samantha
name: Pichler, Martin
name: Seles, Maximilian
name: Wcislo, Gabriel
name: Welsh, Sarah
name: Matakidou, Athena
name: Eisen, Tim
name: Massie, Charles
name: Rosenfeld, Nitzan
name: Heitzer, Ellen
name: Stewart, Grant
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences

description: Table S1. Summary of patient characteristics of the DIAMOND cohort. Table S2. Summary of patient characteristics of the MonReC cohort. Table S3. Summary of filters applied to somatic single nucleotide variants (SNV) calls from Mutect2, for mutation calling of DIAMOND tissue samples. Table S4. Genes targeted for open reading frame sequencing. Table S5. Summary of samples with detected ctDNA at baseline of the MonReC cohort. Table S6. Mutations identified in tissue of in VHL, PTEN, TP53, SETD2, PBRM1, and BAP1 of patients subsequently analyzed with INVAR-TAPAS (n = 29). Table S7. Mutations identified at baseline in the MonReC cohort using a QIASeq custom panel targeting 10 frequently mutated genes in RCC. Fig. S1. Clinical records of select DIAMOND patients. Fig. S2. Schematic explaining the INVAR-TAPAS approach. Fig. S3. Summary of SCNA observed in matched tumor tissue from select DIAMOND patients. Fig. S4. tMAD - interrogation of plasma and urine data. Fig. S5. Assessment of SCNA landscape of matched tumor tissue supports their classification as oncocytoma. Fig. S6. Improved detection of SCNA by in silico size selection. Fig. S7. Comparison of the distribution of ichorCNA tumor fraction and tMAD score at baseline, and assessment of ichorCNA scores between cancer types from the MonReC cohort. Fig. S8. Summary of tumor tissue WES of the DIAMOND patients. Fig. S9. Tumor heterogeneity in RCC. Fig. 10. Summary of global ctDNA levels relative to informative reads in INVAR-TAPAS data from patient plasma and urine. Fig. S11. Correlation of tumor size and ctDNA detection. Fig. S12. Correlation of venous tumor thrombus and cell proliferation rates with ctDNA detection. Fig. S13. Confirmation of pathological classification as oncocytoma. Fig. S14. Application of a fragmentation feature based random forest model to predict patients with detected ctDNA. Fig. S15. Summary of ctDNA detection in all patients and all biofluids. Fig. S16. Comparison of z-score distribution at baseline, during treatment and when progression occurred. Fig. S17. Longitudinal monitoring of mutations detected with the QIAseq custom panel and ichorCNA tumor fractions. Fig. S18. Comparison of imaging data and ctDNA levels (as predicted by INVAR.TAPAS and tMAD). Fig. S19. Comparison of SCNA landscape of matched tumor tissue, normal adjacent tissue, and longitudinal plasma samples from DIAMOND patient 5634. Fig. S20. Comparison of imaging data and ctDNA levels (as predicted by INVAR.TAPAS and tMAD). Fig. S21. Tumor map of patient 5842. Fig. S22. Comparison between mAF and mutation representation in tumor lesions. Fig. S23. Representation of private mutations in the baseline plasma and USN samples of patient 5842. Fig. S24. Representation of mutations private to tumor regions in plasma and urine. Fig. S25. Distribution of mAF of patient specific mutations in plasma and urine from patient 5842. Fig. S26. Assessment of tumor heterogeneity representation in plasma from patient 5634.