Detection of EGFR Mutations in cfDNA and CTCs, and Comparison to Tumor Tissue in Non-Small-Cell-Lung-Cancer (NSCLC) Patients

Liu, Haiyan E.; Vuppalapaty, Meghah; Wilkerson, Charles; Renier, Corinne; Chiu, Michael; Lemaire, Clementine A.; Che, James; Matsumoto, Melissa; Carroll, James M.; Crouse, Steve; Hanft, Violet R.; Jeffrey, Stefanie S.; Carlo, Dino Di; Garon, Edward B.; Goldman, Jonathan W.; Sollier, Elodie

doi:10.3389/fonc.2020.572895

Cited by 41 publications

(38 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Discordances between cfDNA in plasma and CTCs may be indicative of tumor heterogeneity that characterizes NSCLC [ 58 ] and also predictive for the resistance mechanisms that occur under selective therapy pressure due to the dominance of T790M wild type clones as it was previously described [ 59 ]. Comprehensive analysis of EGFR mutations in cfDNA and CTCs could be more informative regarding the treatment monitoring of NSCLC patients as it was recently demonstrated in studies that included both liquid biopsy biomarkers [ 60 , 61 ].…”

Section: Discussionmentioning

confidence: 99%

Detection of EGFR Mutations in Plasma cfDNA and Paired CTCs of NSCLC Patients before and after Osimertinib Therapy Using Crystal Digital PCR

Ntzifa

Κotsakis

Georgoulias

et al. 2021

Cancers

View full text Add to dashboard Cite

Circulating tumor DNA (ctDNA) analysis has clinical utility in EGFR mutant NSCLC. Circulating tumor cells (CTCs) consist a unique source of information at the cellular level. Digital PCR (dPCR) is a valuable tool for accurate and valid analysis of gene mutations in liquid biopsy analysis. In the present study we detected EGFR mutations in ctDNA and paired CTCs under osimertinib therapy at two time points using crystal dPCR and the naica® system (Stilla Technologies). We quantified mutation allele frequencies (MAF) of EGFR mutations in 91 plasma cfDNA samples of 48 EGFR mutant NSCLC patients and in 64 matched CTC-derived genomic DNA samples, and the FDA-cleared cobas® EGFR mutation test in 80 identical plasma samples. Direct comparison between crystal dPCR and the cobas EGFR assay revealed a high concordance for all EGFR mutations. Our comparison of crystal dPCR results in ctDNA with the corresponding primary tissue has shown a strong correlation. EGFR mutations analysis in paired CTC-derived gDNA revealed a high heterogeneity. Crystal dPCR offers the unique advantages of high analytical sensitivity, precision, and accuracy for detecting and quantifying multiple EGFR mutations in plasma cfDNA and CTCs of NSCLC patients.

show abstract

Section: Discussionmentioning

confidence: 99%

Detection of EGFR Mutations in Plasma cfDNA and Paired CTCs of NSCLC Patients before and after Osimertinib Therapy Using Crystal Digital PCR

Ntzifa

Κotsakis

Georgoulias

et al. 2021

Cancers

View full text Add to dashboard Cite

show abstract

“…To select the most appropriate mutation profiling specimens guiding clinical-decision making, it is necessary to perform a comparative study of CTC-derived DNA (CTC-DNA), ctDNA, and tumor tissue DNA (tumor DNA; Table 4). Sundaresan et al [148,149] believe the overall performance of ctDNA is superior to CTCs, but there is still a 20-30% blank that needs to be covered by combination analysis of ctDNA and CTC-DNA in non-small-cell lung cancer, a finding also corroborated in colorectal cancer [150], thoracic cancer [151], metastatic prostate cancer [152], and HCC [153].…”

Section: Limitations and Future Perspectivementioning

confidence: 99%

Current status of ctDNA in precision oncology for hepatocellular carcinoma

Zheng

et al. 2021

J Exp Clin Cancer Res

View full text Add to dashboard Cite

The conventional method used to obtain a tumor biopsy for hepatocellular carcinoma (HCC) is invasive and does not evaluate dynamic cancer progression or assess tumor heterogeneity. It is thus imperative to create a novel non-invasive diagnostic technique for improvement in cancer screening, diagnosis, treatment selection, response assessment, and predicting prognosis for HCC. Circulating tumor DNA (ctDNA) is a non-invasive liquid biopsy method that reveals cancer-specific genetic and epigenetic aberrations. Owing to the development of technology in next-generation sequencing and PCR-based assays, the detection and quantification of ctDNA have greatly improved. In this publication, we provide an overview of current technologies used to detect ctDNA, the ctDNA markers utilized, and recent advances regarding the multiple clinical applications in the field of precision medicine for HCC.

show abstract

“…A decrease in ctDNA and CTC levels from the baseline to the second cycle of paclitaxel and bevacizumab in HER2− MBC patients was independent prognostic markers, but with a stronger value for ctDNA when compared to CTCs [ 50 ]. The comprehensive mutational analysis of cfDNA and CTCs revealed the additive value of the analytes [ 14 , 51 ]. Variant analysis in CTCs was shown to be able to identify newly emerging resistance mutations in contrast to cfDNA, where resistance mutations might only be detected after apoptosis of the cells harboring new alterations [ 51 ], thereby highlighting the potential benefits of variant analysis in CTCs over cfDNA.…”

Section: Discussionmentioning

confidence: 99%

“…The comprehensive mutational analysis of cfDNA and CTCs revealed the additive value of the analytes [ 14 , 51 ]. Variant analysis in CTCs was shown to be able to identify newly emerging resistance mutations in contrast to cfDNA, where resistance mutations might only be detected after apoptosis of the cells harboring new alterations [ 51 ], thereby highlighting the potential benefits of variant analysis in CTCs over cfDNA. The case study of a HR+ MBC patient with serial liquid biopsies across treatment over 4 years showed the correlation of single CTC and cfDNA copy number variants and mutations, but the authors argued that only the analysis of variants in single CTCs deconvolutes the subclonal evolution in cellular resolution [ 52 ].…”

Section: Discussionmentioning

confidence: 99%

Integrative statistical analyses of multiple liquid biopsy analytes in metastatic breast cancer

et al. 2021

View full text Add to dashboard Cite

Background Single liquid biopsy analytes (LBAs) have been utilized for therapy selection in metastatic breast cancer (MBC). We performed integrative statistical analyses to examine the clinical relevance of using multiple LBAs: matched circulating tumor cell (CTC) mRNA, CTC genomic DNA (gDNA), extracellular vesicle (EV) mRNA, and cell-free DNA (cfDNA). Methods Blood was drawn from 26 hormone receptor-positive, HER2-negative MBC patients. CTC mRNA and EV mRNA were analyzed using a multi-marker qPCR. Plasma from CTC-depleted blood was utilized for cfDNA isolation. gDNA from CTCs was isolated from mRNA-depleted CTC lysates. CTC gDNA and cfDNA were analyzed by targeted sequencing. Hierarchical clustering was performed within each analyte, and its results were combined into a score termed Evaluation of multiple Liquid biopsy analytes In Metastatic breast cancer patients All from one blood sample (ELIMA.score), which calculates the contribution of each analyte to the overall survival prediction. Singular value decomposition (SVD), mutual information calculation, k-means clustering, and graph-theoretic analysis were conducted to elucidate the dependence between individual analytes. Results A combination of two/three/four LBAs increased the prevalence of patients with actionable signals. Aggregating the results of hierarchical clustering of individual LBAs into the ELIMA.score resulted in a highly significant correlation with overall survival, thereby bolstering evidence for the additive value of using multiple LBAs. Computation of mutual information indicated that none of the LBAs is independent of the others, but the ability of a single LBA to describe the others is rather limited—only CTC gDNA could partially describe the other three LBAs. SVD revealed that the strongest singular vectors originate from all four LBAs, but a majority originated from CTC gDNA. After k-means clustering of patients based on parameters of all four LBAs, the graph-theoretic analysis revealed CTC ERBB2 variants only in patients belonging to one particular cluster. Conclusions The additional benefits of using all four LBAs were objectively demonstrated in this pilot study, which also indicated a relative dominance of CTC gDNA over the other LBAs. Consequently, a multi-parametric liquid biopsy approach deconvolutes the genomic and transcriptomic complexity and should be considered in clinical practice.

show abstract

Detection of EGFR Mutations in cfDNA and CTCs, and Comparison to Tumor Tissue in Non-Small-Cell-Lung-Cancer (NSCLC) Patients

Cited by 41 publications

References 36 publications

Detection of EGFR Mutations in Plasma cfDNA and Paired CTCs of NSCLC Patients before and after Osimertinib Therapy Using Crystal Digital PCR

Detection of EGFR Mutations in Plasma cfDNA and Paired CTCs of NSCLC Patients before and after Osimertinib Therapy Using Crystal Digital PCR

Current status of ctDNA in precision oncology for hepatocellular carcinoma

Integrative statistical analyses of multiple liquid biopsy analytes in metastatic breast cancer

Contact Info

Product

Resources

About