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

Molecular Oncology
Jian LiLiang Wang

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 0.5...Continue Reading

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Citations

Oct 28, 2018·Cellular Oncology (Dordrecht)·Heidi FettkeArun A Azad
Feb 9, 2018·Oncotarget·Irma G Domínguez-VigilHugo A Barrera-Saldaña
May 31, 2020·Cancers·Drahomír KolenčíkPeter Kuhn
Aug 9, 2018·Frontiers in Oncology·Hariti SalujaErin L Symonds
Jan 31, 2020·Frontiers in Genetics·Zhiqiang ChangWenyuan Zhao
Jan 11, 2019·Journal of Hematology & Oncology·Mu XuShukui Wang
Oct 9, 2020·Molecular Biology Reports·Gayathri BaburajMahadev Rao
Aug 11, 2020·Molecular Therapy. Methods & Clinical Development·Zhiqiang ChangYan Xu
May 11, 2021·Indian Journal of Thoracic and Cardiovascular Surgery : Official Organ, Association of Thoracic and Cardiovascular Surgeons of India·Dhruva SharmaPreksha Sharma
Jan 1, 2020·Seminars in Cancer Biology·Shawn Baldacchino, Godfrey Grech

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Methods Mentioned

BETA
biopsies
biopsy
blood draw
Chip
PCR

Software Mentioned

Partek Genomics Suite
GraphPad
SeqMan

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