Journal Article

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

Druliner, Brooke R., Dittmar, Rachel L., Huang, Chiang‐Ching, Boardman, Lisa, Zhang, Huijuan, Xia, Shu, Wang, Liang, Li, Jian, Du, Meijun

2017

Overview

To evaluate the clinical utility of cell‐free DNA (cfDNA), we performed whole‐genome sequencing to systematically examine plasma cfDNA copy number variations (CNVs) in a cohort of patients with colorectal cancer (CRC, n = 80), polyps (n = 20), and healthy controls (n = 35). We initially compared cfDNA yield in 20 paired serum–plasma samples and observed significantly higher cfDNA 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 cfDNA 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 CNVs 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 CNVs. 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 CNVs 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 cfDNA‐based tests can capture tumor‐specific genetic changes and may provide a measurable classifier for assessing clinical outcomes in advanced CRC patients. A liquid biopsy approach has been advocated for assessing the genetic makeup of solid tumors. In this study, we sequenced cell‐free DNA from plasma samples from 131 subjects. We identified stage‐dependent copy number variations in patients with colorectal cancer and determined six genomic regions for survival predictions. Our study also demonstrates the importance of using plasma rather than serum for testing tumor‐related genomic variations.

• Publisher: John Wiley & Sons, Inc,John Wiley and Sons Inc
• Subject: Adult / Aged / Aged, 80 and over / Biopsy / Cancer / Cancer therapies / Care and treatment / Cell cycle / cell‐free DNA / Chromosomes, Human - genetics / Circulating Tumor DNA - blood / Circulating Tumor DNA - genetics / Colon cancer / Colonoscopy / Colorectal cancer / Colorectal carcinoma / Colorectal Neoplasms - blood / Colorectal Neoplasms - genetics / Copy number / copy number variation / Deoxyribonucleic acid / DNA / DNA Copy Number Variations / DNA repair / DNA sequencing / Female / Gene Amplification / Genetic aspects / Genomes / Genomics / Humans / Kinases / Male / Medical research / Medicine, Experimental / Middle Aged / Mutation / next‐generation sequencing / Patients / Plasma / Polyps / Studies / survival / Wnt protein / Wnt Signaling Pathway - genetics