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- Title
Somatic copy number profiling from hepatocellular carcinoma circulating tumor cells.
- Authors
Court, Colin M.; Hou, Shuang; Liu, Lian; Winograd, Paul; DiPardo, Benjamin J.; Liu, Sean X.; Chen, Pin-Jung; Zhu, Yazhen; Smalley, Matthew; Zhang, Ryan; Sadeghi, Saeed; Finn, Richard S.; Kaldas, Fady M.; Busuttil, Ronald W.; Zhou, Xianghong J.; Tseng, Hsian-Rong; Tomlinson, James S.; Graeber, Thomas G.; Agopian, Vatche G.
- Abstract
Somatic copy number alterations (SCNAs) are important genetic drivers of many cancers. We investigated the feasibility of obtaining SCNA profiles from circulating tumor cells (CTCs) as a molecular liquid biopsy for hepatocellular carcinoma (HCC). CTCs from ten HCC patients underwent SCNA profiling. The Cancer Genome Atlas (TCGA) SCNA data were used to develop a cancer origin classification model, which was then evaluated for classifying 44 CTCs from multiple cancer types. Sequencing of 18 CTC samples (median: 4 CTCs/sample) from 10 HCC patients using a low-resolution whole-genome sequencing strategy (median: 0.88 million reads/sample) revealed frequent SCNAs in previously reported HCC regions such as 8q amplifications and 17p deletions. SCNA profiling revealed that CTCs share a median of 80% concordance with the primary tumor. CTCs had SCNAs not seen in the primary tumor, some with prognostic implications. Using a SCNA profiling model, the tissue of origin was correctly identified for 32/44 (73%) CTCs from 12/16 (75%) patients with different cancer types.
- Subjects
LIVER cancer; CANCER genetics; DNA copy number variations; CIRCULATING tumor DNA; NUCLEOTIDE sequence
- Publication
NPJ Precision Oncology, 2020, Vol 4, Issue 1, p1
- ISSN
2397-768X
- Publication type
Article
- DOI
10.1038/s41698-020-0123-0