Fig. 2

Orthogonal ctDNA sequencing approaches are highly concordant. Somatic SNV and INDEL calling of whole exome sequencing (WES; average depth 150X) and targeted panel sequencing (TPS; nominal sequencing depth 10,000X) were completed on the Terra/Firecloud platform using gatk-Mutect2 pipelines (McKenna et al., 2010). a Variant recall assessment of TPS on somatic variants discovered in one or more WES assays. Only variants intersecting theoretical capture regions of TPS were considered. Variants used in assessment were those called in WES at any point, which also overlapped in genomic position with target or bait regions included in the TPS. X’s indicate a lack of adequate sequencing depth in the TPS. Center and right panels compare variant allele frequency (VAF) data from each assay. b Scatter plot comparing estimated VAF in TPS and WES sequencing across all individuals and time points. 1:1 line drawn for reference. c WES and ULP-WGS based algorithmic estimates of sample purity (a.k.a. tumor fraction) across samples and time points with high tumor fraction (TFx > 10%). d Algorithm estimation of ploidy (averaged copy number state across genome) across WES and ULP-WGS-based methods at time points with high tumor fraction. ABSOLUTE Soln.1 and Soln.2 represent the top two proposed solutions by model likelihood (Included here, as ABSOLUTE often suggests manual curation and/or override of the top solution)