Next-generation sequencing for tumor mutation quantification using liquid biopsies.
Adult
Aged
Biomarkers, Tumor
/ genetics
Carcinoma, Non-Small-Cell Lung
/ diagnosis
Circulating Tumor DNA
/ chemistry
Female
Gene Frequency
High-Throughput Nucleotide Sequencing
/ methods
Humans
Liquid Biopsy
Lung Neoplasms
/ genetics
Male
Middle Aged
Mutation
Mutation, Missense
Neoplasm Staging
Polymerase Chain Reaction
Reagent Kits, Diagnostic
biomarker testing
cfDNA
ctDNA
digital PCR (dPCR)
liquid biopsy
next-generation sequencing (NGS)
non-small cell lung cancer (NSCLC)
Journal
Clinical chemistry and laboratory medicine
ISSN: 1437-4331
Titre abrégé: Clin Chem Lab Med
Pays: Germany
ID NLM: 9806306
Informations de publication
Date de publication:
28 01 2020
28 01 2020
Historique:
received:
21
07
2019
accepted:
05
08
2019
pubmed:
31
8
2019
medline:
7
4
2021
entrez:
31
8
2019
Statut:
ppublish
Résumé
Background Non-small cell lung cancer (NSCLC) patients benefit from targeted therapies both in first- and second-line treatment. Nevertheless, molecular profiling of lung cancer tumors after first disease progression is seldom performed. The analysis of circulating tumor DNA (ctDNA) enables not only non-invasive biomarker testing but also monitoring tumor response to treatment. Digital PCR (dPCR), although a robust approach, only enables the analysis of a limited number of mutations. Next-generation sequencing (NGS), on the other hand, enables the analysis of significantly greater numbers of mutations. Methods A total of 54 circulating free DNA (cfDNA) samples from 52 NSCLC patients and two healthy donors were analyzed by NGS using the Oncomine™ Lung cfDNA Assay kit and dPCR. Results Lin's concordance correlation coefficient and Pearson's correlation coefficient between mutant allele frequencies (MAFs) assessed by NGS and dPCR revealed a positive and linear relationship between the two data sets (ρc = 0.986; 95% confidence interval [CI] = 0.975-0.991; r = 0.987; p < 0.0001, respectively), indicating an excellent concordance between both measurements. Similarly, the agreement between NGS and dPCR for the detection of the resistance mutation p.T790M was almost perfect (K = 0.81; 95% CI = 0.62-0.99), with an excellent correlation in terms of MAFs (ρc = 0.991; 95% CI = 0.981-0.992 and Pearson's r = 0.998; p < 0.0001). Importantly, cfDNA sequencing was successful using as low as 10 ng cfDNA input. Conclusions MAFs assessed by NGS were highly correlated with MAFs assessed by dPCR, demonstrating that NGS is a robust technique for ctDNA quantification using clinical samples, thereby allowing for dynamic genomic surveillance in the era of precision medicine.
Identifiants
pubmed: 31469650
doi: 10.1515/cclm-2019-0745
pii: cclm-2019-0745
doi:
Substances chimiques
Biomarkers, Tumor
0
Circulating Tumor DNA
0
Reagent Kits, Diagnostic
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
306-313Références
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