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
| Autor: | Chu Van Nguyen, Anh-Thu Huynh Dang, Hong-Thuy Thi Dao, Son-Lam Vu Nguyen, Phuong Cam Pham, Le Son Tran, Thanh-Truong Tran, Hong-Anh Thi Pham, Dinh-Thong Vu Le, Thanh-Thuy Thi Do, Trieu-Vu Nguyen, Vu-Uyen Tran, Kiet Truong Dinh, Tam Tran, Thien Kim Dinh-Nguyen, Hoa Giang, Anh Tuan Dang-Mai, Nguyen Huu Nguyen, Binh Thanh Vo, Hoai-Nghia Nguyen, Van Hieu Phan, Minh-Duy Phan, Ngoc-Vu Vu Nguyen, Han Ngoc Do |
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| Rok vydání: | 2019 |
| Předmět: |
Male
0301 basic medicine Oncology Lung Neoplasms Physiology Biopsy DNA Mutational Analysis Gene Identification and Analysis Artificial Gene Amplification and Extension Polymerase Chain Reaction Biochemistry Lung and Intrathoracic Tumors Circulating Tumor DNA GTP Phosphohydrolases 0302 clinical medicine Limit of Detection Carcinoma Non-Small-Cell Lung Medicine and Health Sciences Medicine Digital polymerase chain reaction Sequence Tagged Sites Aged 80 and over Multidisciplinary Massive parallel sequencing medicine.diagnostic_test High-Throughput Nucleotide Sequencing DNA Neoplasm Middle Aged Body Fluids ErbB Receptors Blood 030220 oncology & carcinogenesis Female Anatomy Research Article Adult Proto-Oncogene Proteins B-raf medicine.medical_specialty Science Concordance Surgical and Invasive Medical Procedures Research and Analysis Methods Blood Plasma Proto-Oncogene Proteins p21(ras) 03 medical and health sciences Cancer detection and diagnosis Internal medicine Genetics Carcinoma DNA Barcoding Taxonomic Humans Point Mutation Liquid biopsy Molecular Biology Techniques Lung cancer Mutation Detection Molecular Biology Aged business.industry Liquid Biopsy Membrane Proteins Reproducibility of Results Biology and Life Sciences Cancers and Neoplasms Gold standard (test) medicine.disease Diagnostic medicine Non-Small Cell Lung Cancer 030104 developmental biology Mutation Amplification-Refractory Mutation System Analysis business Biomarkers |
| Zdroj: | PLoS ONE, Vol 14, Iss 12, p e0226193 (2019) PLoS ONE |
| ISSN: | 1932-6203 |
| DOI: | 10.1371/journal.pone.0226193 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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