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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

PloS one, 2019-12, Vol.14 (12), p.e0226193-e0226193 [Peer Reviewed Journal]

COPYRIGHT 2019 Public Library of Science ;COPYRIGHT 2019 Public Library of Science ;2019 Tran et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;2019 Tran et al 2019 Tran et al ;ISSN: 1932-6203 ;EISSN: 1932-6203 ;DOI: 10.1371/journal.pone.0226193 ;PMID: 31841547

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Title:
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
Author: 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
Burns, Jorge S.
Subjects: Adult ; Afatinib ; Aged ; Aged, 80 and over ; Analysis ; Biology and Life Sciences ; Biopsy ; Cancer ; 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 ; Ethylenediaminetetraacetic acid ; 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 cancer, Non-small cell ; 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 ; Tagging ; Tumors
Is Part Of: PloS one, 2019-12, Vol.14 (12), p.e0226193-e0226193
Description: 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.
Publisher: United States: Public Library of Science
Language: English
Identifier: ISSN: 1932-6203
EISSN: 1932-6203
DOI: 10.1371/journal.pone.0226193
PMID: 31841547
Source: Public Library of Science (PLoS) Journals Open Access
Geneva Foundation Free Medical Journals at publisher websites
MEDLINE
PubMed Central
ProQuest Central
DOAJ Directory of Open Access Journals

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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

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