Ultra-deep massively parallel sequencing with unique molecular identifier tagging achieves comparable performance to droplet digital PCR for detection and quantification of circulating tumor DNA from lung cancer patients


Autoři: Le Son Tran aff001;  Hong-Anh Thi Pham aff001;  Vu-Uyen Tran aff001;  Thanh-Truong Tran aff001;  Anh-Thu Huynh Dang aff004;  Dinh-Thong Le aff005;  Son-Lam Nguyen aff005;  Ngoc-Vu Nguyen aff005;  Trieu-Vu Nguyen aff006;  Binh Thanh Vo aff001;  Hong-Thuy Thi Dao aff001;  Nguyen Huu Nguyen aff001;  Tam Huu Tran aff007;  Chu Van Nguyen aff008;  Phuong Cam Pham aff009;  Anh Tuan Dang-Mai aff010;  Thien Kim Dinh-Nguyen aff011;  Van Hieu Phan aff010;  Thanh-Thuy Thi Do aff004;  Kiet Truong Dinh aff002;  Han Ngoc Do aff001;  Minh-Duy Phan aff001;  Hoa Giang aff001;  Hoai-Nghia Nguyen aff004
Působiště autorů: Gene Solutions, Ho Chi Minh, Vietnam aff001;  Medical Genetics Institute, Ho Chi Minh City, Vietnam aff002;  Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam aff003;  University of Medicine and Pharmacy, Ho Chi Minh city, Vietnam aff004;  Pham Ngoc Thach Hospital, Ho Chi Minh city, Vietnam aff005;  Thu Duc Hospital, Ho Chi Minh city, Vietnam aff006;  Center for Standardization and QC in Medical Lab of Ho Chi Minh City, Ho Chi Minh City, Vietnam aff007;  Vietnam National Cancer Hospital, Ha Noi, Vietnam aff008;  Bach Mai Hospital, Ha Noi, Vietnam aff009;  Center for Forensic Science, Ho Chi Minh City, Vietnam aff010;  Tan Hung General Hospital, Ho Chi Minh City, Vietnam aff011;  School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia aff012
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article
doi: 10.1371/journal.pone.0226193

Souhrn

The identification and quantification of actionable mutations are of critical importance for effective genotype-directed therapies, prognosis and drug response monitoring in patients with non-small-cell lung cancer (NSCLC). Although tumor tissue biopsy remains the gold standard for diagnosis of NSCLC, the analysis of circulating tumor DNA (ctDNA) in plasma, known as liquid biopsy, has recently emerged as an alternative and noninvasive approach for exploring tumor genetic constitution. In this study, we developed a protocol for liquid biopsy using ultra-deep massively parallel sequencing (MPS) with unique molecular identifier tagging and evaluated its performance for the identification and quantification of tumor-derived mutations from plasma of patients with advanced NSCLC. Paired plasma and tumor tissue samples were used to evaluate mutation profiles detected by ultra-deep MPS, which showed 87.5% concordance. Cross-platform comparison with droplet digital PCR demonstrated comparable detection performance (91.4% concordance, Cohen’s kappa coefficient of 0.85 with 95% CI = 0.72–0.97) and great reliability in quantification of mutation allele frequency (Intraclass correlation coefficient of 0.96 with 95% CI = 0.90–0.98). Our results highlight the potential application of liquid biopsy using ultra-deep MPS as a routine assay in clinical practice for both detection and quantification of actionable mutation landscape in NSCLC patients.

Klíčová slova:

Amplification-refractory mutation system analysis – Biopsy – Blood plasma – Circulating tumor DNA – Mutation detection – Non-small cell lung cancer – Point mutation – Polymerase chain reaction


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2019 Číslo 12