Ultra-Deep Sequencing of Plasma-Circulating DNA for the Detection of Tumor- Derived Mutations in Patients with Nonmetastatic Colorectal Cancer

Abstract

Identification of tumor-derived mutation (TDM) in liquid biopsies (LB), especially in early-stage patients, faces several challenges, including low variant-allele frequencies, interference by white blood cell (WBC)-derived mutations (WDM), benign somatic mutations and tumor heterogeneity. Here, we addressed the above-mentioned challenges in a cohort of 50 nonmetastatic colorectal cancer patients, via a workflow involving parallel sequencing of paired WBC- and tumor-gDNA. After excluding potential false positive mutations, we detected at least one TDM in LB of 56% (28/50) of patients, with the majority showing low-patient coverage, except for one TDM mapped to KMT2D that recurred in 30% (15/30) of patients.

Keywords:

• Cell-free DNA
• circulating tumor DNA
• early detection
• colorectal cancer
• tumor-specific mutations

Acknowledgement

The author would like to thank Dr. Curt Balch (Bioscience Advising, Ann Arbor, MI, USA) for proofreading the manuscript.

Author contributions

Conceptualization, Anh Vu Hoang, Hoang Bac Nguyen, Kiet Truong Dinh, Hoai-Nghia Nguyen, Thanh-Thuy Thi Do, Hoa Giang and Diep Tuan Tran; Data curation, Huu-Thinh Nguyen, Duc-Huy Tran, Quoc Dat Ngo, Truong Vinh Ngoc Pham, Minh Triet Le, Ngoc An Trinh Le, Trung Kien Le and Le Son Tran; Formal analysis, Bac An Luong, Le Gia Hoang Le, Quoc Chuong Ho, Hue-Hanh Thi Nguyen, Cao Minh Nguyen, Vu Uyen Tran, Thanh Luan Nguyen, Hong-Anh Thi Pham, Hong Thuy Le, Hong Diep Thi Duong and Le Son Tran; Funding acquisition, Thanh-Thuy Thi Do and Diep Tuan Tran; Methodology, Huu-Thinh Nguyen, Hoa Giang and Le Son Tran; Project administration, Huu-Thinh Nguyen, Hoai-Nghia Nguyen and Le Son Tran; Software, Trong-Hieu Nguyen, Minh-Duy Phan and Hoa Giang; Supervision, Diep Tuan Tran; Writing – original draft, Le Son Tran; Writing – review & editing, Hoai-Nghia Nguyen and Diep Tuan Tran.

Institutional review board statement

this study was approved by The Ethics Committee of University of Medicine and Pharmacy at Ho Chi Minh City, Vietnam (Ethic number: 383/ĐHYD-HĐĐĐ)

Informed consent statement

Informed consent was obtained from all subjects involved in the study.

Declaration of interest

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This research was funded by Ho Chi Minh city Department of Science and Technology under grant number 52/2019/HĐ-QP T KHCN (to DT T).]