Fig. 3

ScfDNA profile in cancer vs. noncancer donors. (A) ScfDNA insert size profile with multiple peaks and valleys below 100 bp using single-stranded library preparation for noncancer donors (Turquoise solid line) and an additional peak at ~ 167 bp for cancer donors (Peach solid line). (B) Peak-valley index of the ScfDNA fragment profile decreases in cancer subjects. The peak-valley index represents upward and downward inflections of the ScfDNA size distribution (Supplementary Fig. 2). P value = 0.0012, Student’s t test, Welch’s correction. (C) Receiver operating curve for prediction of gastric cancer based of peak-valley of insert size profile, area under receiver operating curve 0.93. (D) Human and microbial origins of salivary cell-free DNA from cancer and noncancer donors. Percentage of reads of ScfDNA mapping to humans and microbes. (E) Chromosomal locations of human mapped ScfDNA in noncancer and cancer donors increased ScfDNA reads at telomeric portions in noncancer donors when compared to cancer donors. Box shows zoomed in view of chr 19–22. (F) Volcano plot demonstrating over 1500 chromosomal locations significantly different between cancer and noncancer donors following multiple t tests, without considering the consistency of SD, false discovery rate Benjamini, Krieger and Yekutieli method, p value < 0.05, q value < 0.05. (G) Top 20 significant chromosomal locations, p value < 0.05, multiple t test, corrected FDR. (H) Differences in mitochondrial ScfDNA, t test p value < 0.014, (I) Area under receiver operating curve = 0.86