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: Tran LS; Gene Solutions, Ho Chi Minh, Vietnam.; Medical Genetics Institute, Ho Chi Minh City, Vietnam., Pham HT; Gene Solutions, Ho Chi Minh, Vietnam.; Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam., Tran VU; Gene Solutions, Ho Chi Minh, Vietnam.; Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam., Tran TT; Gene Solutions, Ho Chi Minh, Vietnam.; Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam., Dang AH; University of Medicine and Pharmacy, Ho Chi Minh city, Vietnam., Le DT; Pham Ngoc Thach Hospital, Ho Chi Minh city, Vietnam., Nguyen SL; Pham Ngoc Thach Hospital, Ho Chi Minh city, Vietnam., Nguyen NV; Pham Ngoc Thach Hospital, Ho Chi Minh city, Vietnam., Nguyen TV; Thu Duc Hospital, Ho Chi Minh city, Vietnam., Vo BT; Gene Solutions, Ho Chi Minh, Vietnam.; Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam., Dao HT; Gene Solutions, Ho Chi Minh, Vietnam.; Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam., Nguyen NH; Gene Solutions, Ho Chi Minh, Vietnam., Tran TH; Center for Standardization and QC in Medical Lab of Ho Chi Minh City, Ho Chi Minh City, Vietnam., Nguyen CV; Vietnam National Cancer Hospital, Ha Noi, Vietnam., Pham PC; Bach Mai Hospital, Ha Noi, Vietnam., Dang-Mai AT; Center for Forensic Science, Ho Chi Minh City, Vietnam., Dinh-Nguyen TK; Tan Hung General Hospital, Ho Chi Minh City, Vietnam., Phan VH; Center for Forensic Science, Ho Chi Minh City, Vietnam., Do TT; University of Medicine and Pharmacy, Ho Chi Minh city, Vietnam., Truong Dinh K; Medical Genetics Institute, Ho Chi Minh City, Vietnam., Do HN; Gene Solutions, Ho Chi Minh, Vietnam., Phan MD; Gene Solutions, Ho Chi Minh, Vietnam.; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia., Giang H; Gene Solutions, Ho Chi Minh, Vietnam.; Medical Genetics Institute, Ho Chi Minh City, Vietnam., Nguyen HN; University of Medicine and Pharmacy, Ho Chi Minh city, Vietnam.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2019 Dec 16; Vol. 14 (12), pp. e0226193. Date of Electronic Publication: 2019 Dec 16 (Print Publication: 2019).
DOI: 10.1371/journal.pone.0226193
Abstrakt: 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.
Competing Interests: This research is funded by The Vietnam National Foundation for Science and Technology Development (NAFOSTED, https://nafosted.gov.vn/) under grant number 108.01-2017.306 (to HNN) and Ho Chi Minh city Department of Science and Technology under grant number 257/2017/HD-SKHCN (to HNN) and Gene Solutions (GS-003). We confirm that the funder Gene Solutions provided support in the form of salaries for authors LS Tran, HAT Pham, VU Tran, TT Tran, BT Vo, HTT Dao, NH Nguyen, HN Do, M-D Phan and H Giang but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section. We also confirm that this does not alter our adherence to PLOS ONE policies on sharing data and materials.
Databáze: MEDLINE
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