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

• Published in: PloS one 2019-12, Vol.14 (12), p.e0226193
• Main Authors: Tran, Le Son, Pham, Hong-Anh Thi, Tran, Vu-Uyen, Tran, Thanh-Truong, Dang, Anh-Thu Huynh, Le, Dinh-Thong, Nguyen, Son-Lam, Nguyen, Ngoc-Vu, Nguyen, Trieu-Vu, Vo, Binh Thanh, Dao, Hong-Thuy Thi, Nguyen, Nguyen Huu, Tran, Tam Huu, Nguyen, Chu Van, Pham, Phuong Cam, Dang-Mai, Anh Tuan, Dinh-Nguyen, Thien Kim, Phan, Van Hieu, Do, Thanh-Thuy Thi, Truong Dinh, Kiet, Do, Han Ngoc, Phan, Minh-Duy, Giang, Hoa, Nguyen, Hoai-Nghia
• Format: Article
• Language: English
• Subjects: Adult; Afatinib; Aged; Aged, 80 and over; Analysis; Biology and Life Sciences; Biopsy; Cancer genetics; Cancer patients; Carcinoma, Non-Small-Cell Lung - diagnosis; Carcinoma, Non-Small-Cell Lung - genetics; Carcinoma, Non-Small-Cell Lung - pathology; Care and treatment; Circulating Tumor DNA - analysis; Circulating Tumor DNA - genetics; Correlation coefficient; Correlation coefficients; Deoxyribonucleic acid; Depth profiling; DNA; DNA Barcoding, Taxonomic - methods; DNA Mutational Analysis - methods; DNA, Neoplasm - analysis; DNA, Neoplasm - genetics; DNA, Neoplasm - isolation & purification; Droplets; EDTA; ErbB Receptors - genetics; Female; Forensic sciences; Gene frequency; Genetic aspects; Genetic testing; Genetics; Genotypes; GTP Phosphohydrolases - genetics; High-Throughput Nucleotide Sequencing - methods; Hospitals; Humans; Limit of Detection; Liquid Biopsy; Lung cancer; Lung diseases; Lung Neoplasms - diagnosis; Lung Neoplasms - genetics; Lung Neoplasms - pathology; Male; Marking; Medical prognosis; Medical research; Medical schools; Medicine and Health Sciences; Membrane Proteins - genetics; Middle Aged; Multiprocessing; Mutation; Non-small cell lung cancer; Non-small cell lung carcinoma; Oncology; Osimertinib; Patient monitoring equipment; Performance evaluation; Pham, Vu; Pharmacy; Plasma; Polymerase chain reaction; Polymerase Chain Reaction - methods; Prognosis; Proto-Oncogene Proteins B-raf - genetics; Proto-Oncogene Proteins p21(ras) - genetics; Reproducibility of Results; Research and Analysis Methods; Sequence Tagged Sites; Small cell lung carcinoma; Son Tran; Tumors
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0226193

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.