Extended Data Fig. 3: Case-level information of samples profiled by EPIC-Seq.

Cohorts and cell-free DNA samples profiled by EPIC-seq in this study, including Cancer Cases and Control Subjects. (a) Schema depicts the full set of specimens profiled by EPIC-Seq (n = 373), including those meeting Quality Control (QC) criteria (n = 352, 95%). A subset of samples were used for the initial gene expression model tuning (n = 2) and TSS filtering (n = 21). The remaining 329 samples were profiled by EPIC-Seq to address disease-specific questions, including utility for cancer detection, classification of histology and cell-of-origin, and response monitoring. These included 252 samples (76.6%) from 226 subjects that comprised our Discovery/Training cohort (large light purple rectangle), as well as subsequent profiling of a Validation Cohort of 77 samples (23.4%) from 69 subjects, after models were ‘locked down’ (large light green rectangle). A subset of 22 NSCLC patients where a pair of serial blood samples were monitored for ICI response (to allow comparisons of both EPIC-Seq and CAPP-Seq and assess biological plausibility), but this exercise was not subject to any model training. No samples were shared between Training and Validation exercises, with all models locked down before independent validations. Four healthy subjects (4.5%) provided more than one cfDNA specimen with one used for Training and the second for Validation. (b) Distribution of demographic, clinical, anatomic, and pathological variables for subjects profiled by EPIC-Seq. Tabulated are the relevant indices for cancer cases (235 blood samples 201 patients), including NSCLC patients (light blue; 109 blood samples from 87 patients), DLBCL patients (light orange; 126 blood samples from 104 patients), and non-cancer control subjects (gray; 94 blood samples from 87 adults).