Extended Data Fig. 2: Comparison of sequence depth and raw error rate distributions across cancer cohorts (n=124) and non-cancer controls (n=47).
From: High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
(a) Comparison of deduplicated and uncollapsed mean target sequence depth between cfDNA and WBC. The p values were obtained using paired two-sided Mann-Whitney U-tests comparing cfDNA against WBC. (b) Deduplicated and collapsed mean target sequence depth in cfDNA and WBC between the different cancer cohorts and non-cancer controls. (c) Association between the amount of cfDNA used for library preparation and the mean target deduplicated and collapsed sequencing depth. The diagonal line represents a linear regression with 99% confidence intervals. The p value was obtained using an F-test. (d) Distribution of mean target deduplicated and collapsed sequencing depth across the different cohorts. (e,f) Comparison of (e) raw substitution error rate and (f) raw substitution and indel error rate across the different cohorts. In (b) and (d–f), the p values were obtained from pairwise comparisons using two-sided Mann-Whitney U-tests and adjusted for multiple testing using the Bonferroni method. In (e), the substitution error rate represents the percentage of collapsed bases with non-reference base. Similarly, in (f) the combined error rate represents the percentage of collapsed bases with non-reference base or indels. In all panels, the cohorts consist of n = 39 MBC, n = 41 NSCLC and n = 44 CRPC patients and n = 47 non-cancer controls. In (a, b) and (d–f), the horizontal bars indicate the median and the boxes represent the interquartile range (IQR). The whiskers extend to 1.5 x IQR on either side.
