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

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

Research output: Contribution to journalArticle

22 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1099-1111
Number of pages13
JournalMolecular Oncology
Volume11
Issue number8
DOIs
StatePublished - Aug 1 2017

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Keywords

  • cell-free DNA
  • colon cancer
  • copy number variation
  • next-generation sequencing
  • survival

ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Cancer Research

Cite this

Li, J., Dittmar, R. L., Xia, S., Zhang, H., Du, M., Huang, C. C., Druliner, B. R., Boardman, L. A., & Wang, L. (2017). Cell-free DNA copy number variations in plasma from colorectal cancer patients. Molecular Oncology, 11(8), 1099-1111. https://doi.org/10.1002/1878-0261.12077