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Next-generation sequencing for tumor mutation quantification using liquid biopsies.

Abstract：

: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.

journal_name

Clin Chem Lab Med

journal_title

Clinical chemistry and laboratory medicine

authors

Provencio M,Pérez-Barrios C,Barquin M,Calvo V,Franco F,Sánchez E,Sánchez R,Marsden D,Cristóbal Sánchez J,Martin Acosta P,Laza-Briviesca R,Cruz-Bermúdez A,Romero A

doi

10.1515/cclm-2019-0745

subject

Has Abstract

pub_date

2020-01-28 00:00:00

pages

306-313

issue

eissn

1434-6621

issn

1437-4331

pii

/j/cclm.ahead-of-print/cclm-2019-0745/cclm-2019-07

journal_volume

pub_type

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Next-generation sequencing for tumor mutation quantification using liquid biopsies.