Figure 1 from Cell-Free DNA–Derived Immune Cell Ratios Uncover Cancer-Associated Systemic Changes

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cfDNA coverage at TSSs enables deconvolution of blood cell type contributions. A, Schematic overview of the analytic approach. Plasma cfDNA is subjected to WGS at a target depth of 20–30×. GC-corrected coverage at TSS of protein-coding genes is computed using Griffin (15). TSS coverage is then correlated with gene expression profiles from the Tabula Sapiens single-cell reference dataset (14) to generate cell type ranks, reflecting relative contributions to the cfDNA pool. B, Mean cfDNA coverage in healthy individuals across ±1,000 base pairs surrounding the TSS of the top 2,000 highly expressed (red) and unexpressed (blue) genes in blood. Expression categories were defined using the GTEx dataset, with highly expressed genes ranked by TPM and unexpressed genes defined as those with TPM = 0. C, Distribution of median TSS coverage for all protein-coding genes in healthy individuals, overlaid with gene expression categories from GTEx: unexpressed (blue), expressed (red), and all other genes (gray). D, Inferred cell type ranks in healthy individuals grouped by cell type categories in healthy controls. Higher ranks indicate greater relative cfDNA contribution. Prog., progenitor. E, Same as D, grouped by cell type compartment defined by Tabula Sapiens. F, Cell types contributing to the Immune compartment grouped by tissue. G, Cell type ranks for individual immune cell types. CRC, colorectal cancer; eff., effector; NK, natural killer; Sec., secreting; thy.-der., thymus-derived.

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