Analysis of Base-Position Error Rate of Next-Generation Sequencing to Detect Tumor Mutations in Circulating DNA

Pécuchet, Nicolas; Rozenholc, Yves; Zonta, Eleonora; Pietrasz, Daniel; Didelot, Audrey; Combe, Pierre; Gibault, Laure; Bachet, Jean‐Baptiste; Taly, Valérie; Fabre, Elizabeth; Blons, Hélène; Laurent‐Puig, Pierre

doi:10.1373/clinchem.2016.258236

Cited by 73 publications

(54 citation statements)

References 41 publications

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“…A previous assessment of NGS performance in clinical samples showed a high level of agreement with dPCR for EGFR and KRAS mutations [27]. In the present study, double testing of 59 patients with EGFR -, KRAS -, or BRAF -mutated tumors confirmed these results (Fig 2).…”

Section: Resultssupporting

confidence: 88%

“…Droplets were loaded into the RainDrop Sense instrument and analyzed using RainDrop Analyst software. To calculate the percentage of mutations, a limit of blank was determined for each assay [29] and applied to all samples as previously described [27]. …”

Section: Methodsmentioning

confidence: 99%

“…This method detects high sensitivity mutations in circulating DNA at allele frequencies of as low as 0.001 for insertions or deletions >2 bp, and at 0.003 for single nucleotide variations. The BPER method is highly consistent with dPCR for EGFR and KRAS mutations, kappa 0.90 (0.73–1.06) [27]. It has been implemented within an R package entitled “PlasmaMutationDetector,” which is publicly available at https://cran.r-project.org/package=PlasmaMutationDetector.…”

Section: Methodsmentioning

confidence: 99%

“…Moreover, in some specific cases, it can be used to assess the relative disposition of different genetic alterations, such as the cis or trans positions of EGFR p.C797S and p.T790M [18]. For this purpose, we previously developed the base-position error rate (BPER) method, a bioinformatics analytical pipeline dedicated to routine ctDNA testing using ultra-deep targeted NGS at 10,000× (Ion Proton, Thermo Fisher Scientific) [27]. …”

Section: Introductionmentioning

confidence: 99%

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Base-Position Error Rate Analysis of Next-Generation Sequencing Applied to Circulating Tumor DNA in Non-Small Cell Lung Cancer: A Prospective Study

et al. 2016

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BackgroundCirculating tumor DNA (ctDNA) is an approved noninvasive biomarker to test for the presence of EGFR mutations at diagnosis or recurrence of lung cancer. However, studies evaluating ctDNA as a noninvasive “real-time” biomarker to provide prognostic and predictive information in treatment monitoring have given inconsistent results, mainly due to methodological differences. We have recently validated a next-generation sequencing (NGS) approach to detect ctDNA. Using this new approach, we evaluated the clinical usefulness of ctDNA monitoring in a prospective observational series of patients with non-small cell lung cancer (NSCLC).Methods and FindingsWe recruited 124 patients with newly diagnosed advanced NSCLC for ctDNA monitoring. The primary objective was to analyze the prognostic value of baseline ctDNA on overall survival. ctDNA was assessed by ultra-deep targeted NGS using our dedicated variant caller algorithm. Common mutations were validated by digital PCR. Out of the 109 patients with at least one follow-up marker mutation, plasma samples were contributive at baseline (n = 105), at first evaluation (n = 85), and at tumor progression (n = 66). We found that the presence of ctDNA at baseline was an independent marker of poor prognosis, with a median overall survival of 13.6 versus 21.5 mo (adjusted hazard ratio [HR] 1.82, 95% CI 1.01–3.55, p = 0.045) and a median progression-free survival of 4.9 versus 10.4 mo (adjusted HR 2.14, 95% CI 1.30–3.67, p = 0.002). It was also related to the presence of bone and liver metastasis. At first evaluation (E1) after treatment initiation, residual ctDNA was an early predictor of treatment benefit as judged by best radiological response and progression-free survival. Finally, negative ctDNA at E1 was associated with overall survival independently of Response Evaluation Criteria in Solid Tumors (RECIST) (HR 3.27, 95% CI 1.66–6.40, p < 0.001). Study population heterogeneity, over-representation of EGFR-mutated patients, and heterogeneous treatment types might limit the conclusions of this study, which require future validation in independent populations.ConclusionsIn this study of patients with newly diagnosed NSCLC, we found that ctDNA detection using targeted NGS was associated with poor prognosis. The heterogeneity of lung cancer molecular alterations, particularly at time of progression, impairs the ability of individual gene testing to accurately detect ctDNA in unselected patients. Further investigations are needed to evaluate the clinical impact of earlier evaluation times at 1 or 2 wk. Supporting clinical decisions, such as early treatment switching based on ctDNA positivity at first evaluation, will require dedicated interventional studies.

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Section: Resultssupporting

confidence: 88%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Base-Position Error Rate Analysis of Next-Generation Sequencing Applied to Circulating Tumor DNA in Non-Small Cell Lung Cancer: A Prospective Study

et al. 2016

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“…Another approach was to improve alteration detections using adapted statistical methods. Thus, determination of the base position-error rate (BPER) from control samples allowed detection of true mutations as low as 0.003% and 0.001% for indels after statistical computational [44]. …”

Section: Technical Approaches For Ctdna Detection and Analysismentioning

confidence: 99%

Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management

Vendrell

Mau-Them

Béganton

et al. 2017

IJMS

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Circulating tumoral DNA (ctDNA), commonly named “liquid biopsy”, has emerged as a new promising noninvasive tool to detect biomarker in several cancers including lung cancer. Applications involving molecular analysis of ctDNA in lung cancer have increased and encompass diagnosis, response to treatment, acquired resistance and prognosis prediction, while bypassing the problem of tumor heterogeneity. ctDNA may then help perform dynamic genetic surveillance in the era of precision medicine through indirect tumoral genomic information determination. The aims of this review were to examine the recent technical developments that allowed the detection of genetic alterations of ctDNA in lung cancer. Furthermore, we explored clinical applications in patients with lung cancer including treatment efficiency monitoring, acquired therapy resistance mechanisms and prognosis value.

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Liquid biopsy in pancreatic ductal adenocarcinoma: current status of circulating tumor cells and circulating tumor DNA

et al. 2019

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Reliable biomarkers are required to evaluate and manage pancreatic ductal adenocarcinoma. Circulating tumor cells and circulating tumor DNA are shed into blood and can be relatively easily obtained from minimally invasive liquid biopsies for serial assays and characterization, thereby providing a unique potential for early diagnosis, forecasting disease prognosis, and monitoring of therapeutic response. In this review, we provide an overview of current technologies used to detect circulating tumor cells and circulating tumor DNA and describe recent advances regarding the multiple clinical applications of liquid biopsy in pancreatic ductal adenocarcinoma.

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Analysis of Base-Position Error Rate of Next-Generation Sequencing to Detect Tumor Mutations in Circulating DNA

Abstract: Targeted next-generation sequencing analyzed with the base-PER method represents a robust and low cost method to detect circulating tumor DNA in patients with cancer.

Cited by 73 publications

References 41 publications

Base-Position Error Rate Analysis of Next-Generation Sequencing Applied to Circulating Tumor DNA in Non-Small Cell Lung Cancer: A Prospective Study

Base-Position Error Rate Analysis of Next-Generation Sequencing Applied to Circulating Tumor DNA in Non-Small Cell Lung Cancer: A Prospective Study

Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management

Liquid biopsy in pancreatic ductal adenocarcinoma: current status of circulating tumor cells and circulating tumor DNA

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