In addition to healthy individuals, the Nguyen WGBS dataset and our cfNano dataset also contained individuals being treated for lung adenocarcinoma, marked as “LuAd” in Fig. 1B, C. In the Nguyen WGBS study, samples were collected at the time of acquired resistance to EGFR inhibitors and were divided into those that acquired resistance mutations in EGFR itself (labeled “on-target”) vs. those that acquired amplifications in alternative oncogenes MET/ERBB2 (labeled “off-target”). Here, ERBB2 is linked to lung adenocarcinoma.