Cell‐free DNA copy number variations in plasma from colorectal cancer patients

To evaluate the clinical utility of cell‐free DNA (cf DNA ), we performed whole‐genome sequencing to systematically examine plasma cf DNA copy number variations ( CNV s) in a cohort of patients with colorectal cancer ( CRC , n  = 80), polyps ( n  = 20), and healthy controls ( n  = 35). We initially compared cf DNA yield in 20 paired serum–plasma samples and observed significantly higher cf DNA concentration in serum (median = 81.20 ng, range 7.18–500 ng·mL −1 ) than in plasma (median = 5.09 ng, range 3.76–62.8 ng·mL −1 ) ( P  < 0.0001). However, tumor‐derived cf DNA content was significantly lower in serum than in matched plasma samples tested. With ~10 million reads per sample, the sequencing‐based copy number analysis showed common CNV s in multiple chromosomal regions, including amplifications on 1q, 8q, and 5q and deletions on 1p, 4q, 8p, 17p, 18q, and 22q. Copy number changes were also evident in genes critical to the cell cycle, DNA repair, and WNT signaling pathways. To evaluate whether cumulative copy number changes were associated with tumor stages, we calculated plasma genomic abnormality in colon cancer ( PGA ‐C) score by summing the most significant CNV s. The PGA ‐C score showed predictive performance with an area under the curve from 0.54 to 0.84 for CRC stages I‐ IV . Locus‐specific copy number analysis identified nine genomic regions where CNV s were significantly associated with survival in stage III ‐ IV CRC patients. A multivariate model using six of nine genomic regions demonstrated a significant association of high‐risk score with shorter survival ( HR  = 5.33, 95% CI  = 6.76–94.44, P  < 0.0001). Our study demonstrates the importance of using plasma (rather than serum) to test tumor‐related genomic variations. Plasma cf DNA ‐based tests can capture tumor‐specific genetic changes and may provide a measurable classifier for assessing clinical outcomes in advanced CRC patients.