Fig. 2: Concordance between WMS and WGS in cfDNA copy number and fragmentation profiling.

a, c depict the genome-wide CNA and FSI profiles of a colorectal cancer patient GCP0088 as an example. b, d analyze 225 healthy controls and 287 cancer patients for cohort-level comparison. a Log2 ratio over the mean baseline coverage in 100-kb bins across the genome of Patient GCP0088 profiled by WGS and WMS respectively. Bins with log2 ratio above 0.3 (copy number gains) are colored in red, and bins with log2 ratio below −0.3 (copy number loss) are colored in green. b Scatter plot of PA scores derived from matched WGS and WMS data of all samples. The regression line is colored in red. Pearson correlation coefficient (R) of 0.988 (95% confidence interval: 0.986–0.990) and the p value (<2.2 × 10⁻⁶, two-sided) are indicated on the plot. c FSI of 5-Mb windows across the genome of Patient GCP0088 profiled by WGS and WMS respectively. The coverage ratio of short to long fragments for each bin is normalized by z-score across the genome. Patient FSI profile is colored in black against 225 gray healthy reference FSI profiles. d Scatter plot of Pearson correlations between FSI profiles of individual samples with the reference FSI profile, assessed with WGS and WMS data respectively. The regression line is colored in red. Pearson correlation coefficient (R) of 0.961 (95% confidence interval: 0.954–0.968) and the p value (<2.2 × 10⁻⁶, two-sided) are indicated on the plot. Source data are provided as a Source Data file.