Open AccessUltra-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
Author(s) -
Le Son Tran,
Hong-Anh Thi Pham,
Van Thi Thanh Tran,
Thuy Thi Thu Tran,
Anh-Thu Huynh Dang,
Dinh-Thong Vu Le,
Son-Lam Nguyen,
Ngoc-Vu Nguyen,
Tuan S. Nguyen,
Binh Thanh Vo,
Hong-Thuy Thi Dao,
Nguyen Huu Nguyen,
Thuy Tran,
Chu Van Nguyen,
Phuong Cam Pham,
Anh Tuan Dang-Mai,
Thien Kim Dinh-Nguyen,
Vu Hien Phan,
Thanh-Thuy Thi,
Kiet Truong Dinh,
Han Ngoc,
Minh-Duy Phan,
Hoa Giang,
HoaiNghia Nguyen
Publication year - 2019
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0226193
Subject(s) - digital polymerase chain reaction , concordance , liquid biopsy , massive parallel sequencing , biopsy , deep sequencing , lung cancer , cancer , medicine , mutation , dna sequencing , pathology , oncology , polymerase chain reaction , biology , cancer research , dna , gene , genetics , genome
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.