a, Association between tumour-informed ctDNA detection and the number of mutations tracked using the population-based lung-cancer-focused CAPP-Seq panel. All patients were considered and binned by the number of mutations identified in matched tumour biopsy samples. b, Association between the number of mutations identified in matched tumour samples and tumour-informed ctDNA detection using the population-based lung-cancer-focused CAPP-Seq panel. c, ctDNA detection statistics in 17 patients with early-stage NSCLC profiled with both the population-based lung-cancer-focused CAPP-Seq panel (left) and customized capture panels designed using tumour exome sequencing data (right). Whereas ctDNA in all 17 patients was undetectable using the population-based method, it was detected in 10 (59%) patients using customized panels. For patients with detectable ctDNA, the mean VAF observed across all tracked mutations is depicted (blue circles). For samples without detectable ctDNA, the corresponding patient-specific analytical LOD is shown (open circles). LOD was determined on the basis of the binomial distribution, number of mutations tracked and the median unique molecular depth in the sample. When calculating the LOD in samples sequenced with the population-based panel, deduped depth was considered. When calculating the LOD in samples sequenced with customized panels, duplex depth was considered if this gave an LOD below the deduped error rate. In both scenarios, if the LOD was less than the background error rate for the cfDNA molecule type being considered (either deduped or duplex), the background error rate was used. d, Comparison of the patient-specific analytical LOD in patients with and without detectable ctDNA using tumour-informed CAPP-Seq. LOD was determined as in c and the LOD in samples sequenced with the population-based lung-cancer-focused CAPP-Seq panel only (n = 68) and samples sequenced with customized capture panels designed using tumour exome sequencing data (n = 17) are displayed. e, Detection of clonal and subclonal SNVs in cfDNA. The fraction of all clonal and subclonal SNVs detected in plasma are depicted in pie charts (two-sided Fisher’s exact test, P = 0.039) and the VAFs of clonal and subclonal SNVs detectable in plasma are compared using violin plots in which horizontal dashed lines depict the median and interquartile range. All mutations identified using the population-based lung-cancer-focused CAPP-Seq panel are considered. f, The fraction of all mutant and wild-type cfDNA molecules (defined as in Fig. 1d) with fragment sizes falling within the size windows found to be ctDNA-enriched in Fig. 1e. g, Violin plot displaying the enrichment of SNV VAFs following in silico size selection for the cfDNA fragment sizes found to be ctDNA-enriched in Fig. 1e. Enrichment is defined as the ratio of the SNV VAF after size selection to that observed before size selection. All mutations identified in matched tumor samples and detectable in plasma before size selection (n = 323 mutations) were considered. In the box plot, the centre line denotes the median, the box contains the interquartile range, and the whiskers denote the extrema that are no more than 1.5 × IQR from the edge of the box (Tukey style). h, Comparison of SNV VAFs before and after size selection. The dot plot displays the VAF of SNVs in plasma before and after size selection. The bar plot depicts the fraction of SNVs for which the VAF increased, decreased or became undetectable after size selection. All mutations identified in matched tumor samples and detectable in plasma before size selection were considered. i, Comparison of SNV VAFs before size selection in SNVs for which the VAF increased, decreased, or became undetectable after size selection. All mutations identified in matched tumor samples and detectable in plasma before size selection were considered. j, Tumour-informed ctDNA detection rates before and after size selection in patients sequenced with the population-based lung-cancer-focused CAPP-Seq panel (n = 85 patients) and customized capture panels designed using tumour exome sequencing data (n = 17 patients).