scholarly journals Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling

Cancers ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1588 ◽  
Author(s):  
Sabrina Weber ◽  
Benjamin Spiegl ◽  
Samantha O. Perakis ◽  
Christine M. Ulz ◽  
Peter M. Abuja ◽  
...  
Keyword(s):  
Mutation Analysis ◽  
Reference Materials ◽  
Test Performance ◽  
Liquid Biopsy ◽  
Attractive Alternative ◽  
Routine Practice ◽  
Patients With Cancer ◽  
Technical Evaluation ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Molecular profiling from liquid biopsy, in particular cell-free DNA (cfDNA), represents an attractive alternative to tissue biopsies for the detection of actionable targets and tumor monitoring. In addition to PCR-based assays, Next Generation Sequencing (NGS)-based cfDNA assays are now commercially available and are being increasingly adopted in clinical practice. However, the validity of these products as well as the clinical utility of cfDNA in the management of patients with cancer has yet to be proven. Within framework of the Innovative Medicines Initiative (IMI) program CANCER-ID we evaluated the use of commercially available reference materials designed for ctDNA testing and cfDNA derived from Diagnostic Leukaphereses (DLA) for inter- and intra-assay as well as intra- and inter-laboratory comparisons. In three experimental setups, a broad range of assays including ddPCR, MassARRAY and various NGS-based assays were tested. We demonstrate that both reference materials with predetermined VAFs and DLA samples are extremely useful for the performance assessment of mutation analysis platforms. Moreover, our data indicate a substantial variability of NGS assays with respect to sensitivity and specificity highlighting the importance of extensive validation of the test performance before offering these tests in clinical routine practice.

scholarly journals Molecular Profiling of Malignant Pleural Effusions with Next Generation Sequencing (NGS): Evidence that Supports Its Role in Cancer Management

2020 ◽  
Vol 10 (4) ◽  
pp. 206
Author(s):  
Georgia Ι. Grigoriadou ◽  
Stepan M. Esagian ◽  
Han Suk Ryu ◽  
Ilias P. Nikas
Keyword(s):  
Next Generation Sequencing ◽  
Cancer Patients ◽  
Advanced Cancer ◽  
Liquid Biopsy ◽  
Molecular Profiling ◽  
Pleural Effusions ◽  
Advanced Cancer Patients ◽  
Cancer Management ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Malignant pleural effusions (MPEs) often develop in advanced cancer patients and confer significant morbidity and mortality. In this review, we evaluated whether molecular profiling of MPEs with next generation sequencing (NGS) could have a role in cancer management, focusing on lung cancer. We reviewed and compared the diagnostic performance of pleural fluid liquid biopsy with other types of samples. When applied in MPEs, NGS may have comparable performance with corresponding tissue biopsies, yield higher DNA amount, and detect more genetic aberrations than blood-derived liquid biopsies. NGS in MPEs may also be preferable to plasma liquid biopsy in advanced cancer patients with a MPE and a paucicellular or difficult to obtain tissue/fine-needle aspiration biopsy. Of interest, post-centrifuge supernatant NGS may exhibit superior results compared to cell pellet, cell block or other materials. NGS in MPEs can also guide clinicians in tailoring established therapies and identifying therapy resistance. Evidence is still premature regarding the role of NGS in MPEs from patients with cancers other than lung. We concluded that MPE processing could provide useful prognostic and theranostic information, besides its diagnostic role.

Highly accurate NGS-based multi-gene testing in the diagnosis of thyroid nodules with indeterminate cytology.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e13579-e13579
Author(s):  
Yuntao Song ◽  
Bin Zhang ◽  
Tonghui Ma
Keyword(s):  
Next Generation Sequencing ◽  
Mutation Analysis ◽  
Predictive Value ◽  
Thyroid Nodules ◽  
Braf V600e Mutation ◽  
Braf V600e ◽  
Gene Testing ◽  
Indeterminate Cytology ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

e13579 Background: Thyroid nodules are highly prevalent, Fine-needle aspiration (FNA) is the standard pre-operative tool for diagnosis. However, some of the samples are classified as indeterminate, which leads to unnecessary surgery. BRAF V600E mutation is often used as a diagnostic marker for thyroid cancer, and it is highly specific for papillary thyroid carcinoma (PTC). But BRAF mutation is rarely occurred in thyroid nodules with indeterminate cytology. To diagnose the indeterminate thyroid nodules precisely, some NGS-based multi-gene testing panel has been developed and clinically used in America and Europe, but rare research was reported in China. In this study, we evaluated the value of a next-generation sequencing (NGS) panel to cancer diagnosis in indeterminate thyroid nodules. Methods: From February 2018 to September 2018, 360 patients with thyroid nodules who underwent FNA at Peking University Cancer Hospital were enrolled. And the FNA samples with indeterminate cytology were evaluated using a next-generation sequencing (NGS) assay, including 16 genes analyzed for point mutations and 26 types of gene fusions. Diagnostic performance of this multi-gene testing panel was compared with BRAF V600E single gene mutation analysis. Results: 141 nodules were cytologically indeterminate among 360 patients on FNA biopsy, 72 of which were resected and analyzed by NGS successfully. Histologic analysis after surgery revealed 41 (56.9%) cancers in these 72 patients. The multi-gene testing assay could classify 30/41 cancers correctly, showing a sensitivity of 73.2%, specificity of 96.8%, positive predictive value of 96.8%, and negative predictive value of 73.2%. The diagnostic accuracy of the multi-gene testing was significantly higher than the BRAF V600E mutation analysis (83.3% vs 73.6%, x2= 31.588, p < 0.01). Conclusions: Our study demonstrated that the multi-gene testing provided both high sensitivity and high specificity for cancer detection in thyroid nodules with indeterminate cytology, and its accuracy was much higher than BRAF V600E mutation test.

scholarly journals Monitoring of RAS mutant clones in plasma of patients with RAS mutant metastatic colorectal cancer

2022 ◽  
Author(s):  
A. Fernández Montes ◽  
E. Élez ◽  
A. Vivancos ◽  
N. Martínez ◽  
P. González ◽  
...  
Keyword(s):  
Liquid Biopsy ◽  
Line Treatment ◽  
First Line ◽  
Liquid Biopsies ◽  
Therapeutic Implications ◽  
Next Generation Sequencing Ngs ◽  
Solid Liquid ◽  
Mutant Genes ◽  
Generation Sequencing ◽  
First Line Treatment

Abstract Purpose Some patients with histologically confirmed primary mCRC and mutated RAS reported undetectable RAS mutant clones in plasma after receiving anti-VEGF treatment. The aim was to prospectively assess it with its potential therapeutic implications. Methods RAS mutant genes in solid biopsy (before first-line treatment: FOLFOX/CAPOX + bevacizumab) were compared in liquid biopsy (before second-line treatment: panitumumab + FOLFIRI), using Idylla™ system. Discordant results between solid/liquid biopsies were assessed by the next-generation sequencing (NGS) test (solid/liquid biopsies). Results Twenty-three patients were assessed (seven had RAS mutant discrepancies between solid/liquid biopsies). The NGS test confirmed that 3/23 (13%) patients had undetectable RAS mutant clones in liquid biopsy and 3/23 (13%) presented discrepancies in solid biopsy (Idylla™ system vs. NGS test). Conclusion Thirteen percentage of patients had undetectable RAS mutant clones in liquid biopsy after first-line treatment. However, some discrepancies between solid and liquid biopsies have been observed. These results suggest a need to improve accuracy of RAS analyses, especially in solid biopsies.

scholarly journals Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC’s Analytical Variables Working Group

2020 ◽  
Vol 66 (9) ◽  
pp. 1156-1166 ◽  
Author(s):  
James H Godsey ◽  
Angela Silvestro ◽  
J Carl Barrett ◽  
Kelli Bramlett ◽  
Darya Chudova ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Liquid Biopsy ◽  
Working Group ◽  
Circulating Tumor Dna ◽  
Next Generation ◽  
Analytical Validation ◽  
Consensus Recommendation ◽  
Next Generation Sequencing Ngs ◽  
Development And Validation ◽  
Generation Sequencing

Abstract Liquid biopsy, particularly the analysis of circulating tumor DNA (ctDNA), has demonstrated considerable promise for numerous clinical intended uses. Successful validation and commercialization of novel ctDNA tests have the potential to improve the outcomes of patients with cancer. The goal of the Blood Profiling Atlas Consortium (BloodPAC) is to accelerate the development and validation of liquid biopsy assays that will be introduced into the clinic. To accomplish this goal, the BloodPAC conducts research in the following areas: Data Collection and Analysis within the BloodPAC Data Commons; Preanalytical Variables; Analytical Variables; Patient Context Variables; and Reimbursement. In this document, the BloodPAC’s Analytical Variables Working Group (AV WG) attempts to define a set of generic analytical validation protocols tailored for ctDNA-based Next-Generation Sequencing (NGS) assays. Analytical validation of ctDNA assays poses several unique challenges that primarily arise from the fact that very few tumor-derived DNA molecules may be present in circulation relative to the amount of nontumor-derived cell-free DNA (cfDNA). These challenges include the exquisite level of sensitivity and specificity needed to detect ctDNA, the potential for false negatives in detecting these rare molecules, and the increased reliance on contrived samples to attain sufficient ctDNA for analytical validation. By addressing these unique challenges, the BloodPAC hopes to expedite sponsors’ presubmission discussions with the Food and Drug Administration (FDA) with the protocols presented herein. By sharing best practices with the broader community, this work may also save the time and capacity of FDA reviewers through increased efficiency.

scholarly journals A DNA methylation-based liquid biopsy for triple-negative breast cancer

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Katrina Cristall ◽  
Francois-Clement Bidard ◽  
Jean-Yves Pierga ◽  
Michael J. Rauh ◽  
Tatiana Popova ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
Liquid Biopsy ◽  
Blood Test ◽  
Triple Negative ◽  
Superior Performance ◽  
Serum Samples ◽  
Clonal Hematopoiesis ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractHere, we present a next-generation sequencing (NGS) methylation-based blood test called methylation DETEction of Circulating Tumour DNA (mDETECT) designed for the optimal detection and monitoring of metastatic triple-negative breast cancer (TNBC). Based on a highly multiplexed targeted sequencing approach, this assay incorporates features that offer superior performance and included 53 amplicons from 47 regions. Analysis of a previously characterised cohort of women with metastatic TNBC with limited quantities of plasma (<2 ml) produced an AUC of 0.92 for detection of a tumour with a sensitivity of 76% for a specificity of 100%. mDETECTTNBC was quantitative and showed superior performance to an NGS TP53 mutation-based test carried out on the same patients and to the conventional CA15-3 biomarker. mDETECT also functioned well in serum samples from metastatic TNBC patients where it produced an AUC of 0.97 for detection of a tumour with a sensitivity of 93% for a specificity of 100%. An assay for BRCA1 promoter methylation was also incorporated into the mDETECT assay and functioned well but its clinical significance is currently unclear. Clonal Hematopoiesis of Indeterminate Potential was investigated as a source of background in control subjects but was not seen to be significant, though a link to adiposity may be relevant. The mDETECTTNBC assay is a liquid biopsy able to quantitatively detect all TNBC cancers and has the potential to improve the management of patients with this disease.

scholarly journals BRCA1/2 NGS Somatic Testing in Clinical Practice: A Short Report

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1917
Author(s):  
Francesco Pepe ◽  
Pasquale Pisapia ◽  
Gianluca Russo ◽  
Mariantonia Nacchio ◽  
Pierlorenzo Pallante ◽  
...  
Keyword(s):  
High Sensitivity ◽  
Adenosine Diphosphate ◽  
Routine Practice ◽  
Short Report ◽  
Ovarian Carcinomas ◽  
Thermo Fisher Scientific ◽  
Genetics And Genomics ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Fisher Scientific

High-grade serous ovarian carcinoma (HGSOC) is the most common subtype of all ovarian carcinomas. HGSOC harboring BRCA1/2 germline or somatic mutations are sensitive to the poly (adenosine diphosphate-ribose) polymerase inhibitors (PARPi). Therefore, detecting these mutations is crucial to identifying patients for PARPi-targeted treatment. In the clinical setting, next generation sequencing (NGS) has proven to be a reliable diagnostic approach BRCA1/2 molecular evaluation. Here, we review the results of our BRCA1/2 NGS analysis obtained in a year and a half of diagnostic routine practice. BRCA1/2 molecular NGS records of HGSOC patients were retrieved from our institutional archive covering the period from January 2020 to September 2021. NGS analysis was performed on the Ion S5™ System (Thermo Fisher Scientific, Waltham, MA, USA) with the Oncomine™ BRCA Research Assay panel (Thermo Fisher Scientific). Variants were classified as pathogenic or likely pathogenic according to the guidelines of the American College of Medical Genetics and Genomics by using the inspection of Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) and ClinVar (NCBI) databases. Sixty-five HGSOC patient samples were successfully analyzed. Overall, 11 (16.9%) out of 65 cases harbored a pathogenic alteration in BRCA1/2, in particular, six BRCA1 and five BRCA2 pathogenic variations. This study confirms the efficiency and high sensitivity of NGS analysis in detecting BRCA1/2 germline or somatic variations in patients with HGSOC.

Endometrial Liquid Biopsy Provides a miRNA Roadmap of the Secretory Phase of the Human Endometrium

2019 ◽  
Vol 105 (3) ◽  
pp. 877-889 ◽  
Author(s):  
Alessia Grasso ◽  
Roser Navarro ◽  
Nuria Balaguer ◽  
Inmaculada Moreno ◽  
Pilar Alama ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Ribonucleic Acid ◽  
Liquid Biopsy ◽  
Bioinformatic Analysis ◽  
Endometrial Receptivity ◽  
Mirna Signature ◽  
Secretory Phase ◽  
Messenger Ribonucleic Acid ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Context Endometrial liquid biopsy (ELB) is a minimally invasive alternative for research and diagnosis in endometrial biology. Objective We sought to establish an endometrial micro ribonucleic acid (miRNA) roadmap based on ELB during the secretory phase of the menstrual cycle in both natural and hormonal replacement therapy (HRT) cycles. Design Human ELB samples (n = 58) were obtained from healthy ovum donors undergoing a natural and an HRT cycle consecutively. miRNA profiles were identified using next-generation sequencing (NGS). For functional analysis, messenger ribonucleic acid targets were chosen among those reported in the endometrial receptivity analysis. Results The human endometrial secretory phase is characterized by a dynamic miRNA secretion pattern that varies from the prereceptive to the receptive stages. No differences in miRNA profiles were found among natural versus HRT cycles in the same women, reinforcing the similarities in functional and clinical outcomes in natural versus medicated cycles. Bioinformatic analysis revealed 62 validated interactions and 81 predicted interactions of miRNAs differentially expressed in the HRT cycle. Annotation of these genes linked them to 51 different pathways involved in endometrial receptivity. Conclusion This NGS-based study describes the miRNA signature in human ELB during the secretory phase of natural and HRT cycles. A consistent endometrial miRNA signature was observed in the acquisition of endometrial receptivity. Interestingly, no significant differences in miRNA expression were found in natural versus HRT cycles reinforcing the functional clinical similarities between both approaches.

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