Supplementary data from Circulating DNA Demonstrates Convergent Evolution and Common Resistance Mechanisms during Treatment of Colorectal Cancer

Abstract

<p>Legend Supplemental Table S1 : Point mutations tested by plasma analysis in the KPLEX R study, (A). Comparison of point mutations tested by tumor tissue and plasma analysis, (B). Legend Supplemental Table S2: Concordance between tumor-tissue analysis and cfDNA analysis before treatments. Legend Supplemental Table S3: Mutation load at baseline in mutant patients with the equivalent type of mutation as determined by tumor tissue and plasma analysis are heterogneous from 31.83% to 0.009% Legend Supplemental Table S4: Mutation load values of emerging mutant subclones during treatments for both cohorts are reported in (A). Most emerging mutant subclones appears with a mutation load below 0.5% including down to 0.1%, (B). Sensitive methods is needed to track emergence of mutant subclones during targeted therapies. ND, non detected; NQ, scored positive but non quantified. Legend Supplemental table S5 : Compilation of cfDNA data, CEA level and imaging for both cohorts before and during treatments. Legend Supplemental Table S6: Concordance between tumor-tissue analysis and cfDNA analysis before treatments when considering if patients having primary tumor in place or not in place when entering in the study. Legend Supplemental Table S7: Mutant patients and point mutations determined at baseline with different mA% thresholds. Legend supplemental table S8: Description of all point mutations found from plasma analysis at baseline according to increasing allelic frequencies and the mutational status as determined with tumor tissue analysis. Legend Supplementary Table S9: Evolution of increasing mA% from baseline to end of treatment Supplemental Figure S1: Patient's Flow chart Legend Supplemental Figure S2 : Time lag between tumor tissue collection and blood drawing. Legend Supplemental Figure S3A: Total concentration of cfDNA (RefA) at baseline as determined by targeting BRAF and KRAS wild type sequence. Legend Supplemental Figure S3B: KRAS/BRAF ratio before treatment as determined by targeting BRAF and KRAS wild type sequence. KRAS/BRAF ratio before initiation of treatments (n=41). Supplemental Figure S4: RefA values do not differ at baseline between cohorts 1 and 2 Supplemental Figure S5: RefA values do not differ at baseline between patients stopped treatment before C4 and others Supplemental Figure S6: Concentrations of mutant cfDNA do not differ at baseline between cohorts 1 and 2 Supplemental Figure S7: Concentration of mutant cfDNA do not differ at baseline between patients stopped treatment before C4 and others Supplemental Figure S8: Mutation load do not differ at baseline between cohorts 1 and 2 Legend supplementary Figure S9: Validation of point mutation detection/quantification under the Poisson law. Supplemental Figure S10: Illustration of point mutation detection at very low frequency with IntPlex ASB QPCR method in mCRC patients in the study.</p>