scholarly journals Analytical validation of a next generation sequencing liquid biopsy assay for high sensitivity broad molecular profiling

PLoS ONE ◽  
2018 ◽  
Vol 13 (3) ◽  
pp. e0193802 ◽  
Author(s):  
Vincent Plagnol ◽  
Samuel Woodhouse ◽  
Karen Howarth ◽  
Stefanie Lensing ◽  
Matt Smith ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Liquid Biopsy ◽  
High Sensitivity ◽  
Molecular Profiling ◽  
Next Generation ◽  
Analytical Validation ◽  
Generation Sequencing

A Novel Method for Microsatellite Instability Detection by Liquid Biopsy Based on Next- Generation Sequencing

2020 ◽  
Vol 15 ◽  
Author(s):  
Zheng Jiang ◽  
Hui Liu ◽  
Siwen Zhang ◽  
Jia Liu ◽  
Weitao Wang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Instability ◽  
Liquid Biopsy ◽  
Tumor Tissue ◽  
High Sensitivity ◽  
Next Generation ◽  
Tissue Samples ◽  
Next Generation Sequencing Technology ◽  
Medication Selection ◽  
Generation Sequencing

Background: Microsatellite instability (MSI) is a prognostic biomarker used to guide medication selection in multiple cancers, such as colorectal cancer. Traditional PCR with capillary electrophoresis and next-generation sequencing using paired tumor tissue and leukocyte samples are the main approaches for MSI detection due to their high sensitivity and specificity. Currently, patient tissue samples are obtained through puncture or surgery, which causes injury and risk of concurrent disease, further illustrating the need for MSI detection by liquid biopsy. Methods: We propose an analytic method using paired plasma/leukocyte samples and MSI detection using next-generation sequencing technology. Based on the theoretical progress of oncogenesis, we hypothesized that the microsatellite site length in plasma equals the combination of the distribution of tumor tissue and leukocytes. Thus, we defined a window-judgement method to identify whether biomarkers were stable. Results: Compared to traditional PCR as the standard, we evaluated three methods in 20 samples (MSI-H:3/MSS:17): peak shifting method using tissue vs. leukocytes, peak shifting method using plasma vs. leukocytes, and our method using plasma vs. leukocytes. Compared to traditional PCR, we observed a sensitivity of 100%, 0%, and 100%, and a specificity of 100.00%, 94.12%, and 88.24%, respectively. Conclusion: Our method has the advantage of possibly detecting MSI in a liquid biopsy and provides a novel direction for future studies to increase the specificity of the method.

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.

Abstract 1286: Analytical validation of an integrated next-generation sequencing pan-cancer liquid biopsy approach for detection of microsatellite instability

2018 ◽  
Author(s):  
Andrew Georgiadis ◽  
Derrick Wood ◽  
Derek Murphy ◽  
Sonya Parpart-Li ◽  
David Riley ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Instability ◽  
Liquid Biopsy ◽  
Next Generation ◽  
Analytical Validation ◽  
Pan Cancer ◽  
Generation Sequencing

scholarly journals Targeted Next-Generation Sequencing of Liquid Biopsy Samples from Patients with NSCLC

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 155
Author(s):  
Hestia Mellert ◽  
Jordan Reese ◽  
Leisa Jackson ◽  
Victoria Maxwell ◽  
Chérie Tschida ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Liquid Biopsy ◽  
High Sensitivity ◽  
Next Generation ◽  
Small Cell Lung ◽  
Chain Reaction ◽  
Targeted Next Generation Sequencing ◽  
Polymerase Chain ◽  
Test Process ◽  
Generation Sequencing

Liquid biopsy tests have become an integral part of the molecular diagnosis of patients with non-small cell lung cancer (NSCLC). We describe a new test panel that uses very low input (20 ng) of cell-free nucleic acids extracted from human plasma, which is designed to yield results in less than 72 h. In this study, we performed novel amplicon-based targeted next-generation sequencing with a semiconductor-based system, the Ion GeneStudio S5 Prime. The analytic performance of the assay was evaluated using contrived and retrospectively collected clinical specimens. The cumulative percent coefficient of variation for the new test process was very precise at 8.4% for inter-day, 4.0% for inter-operator and 3.4% for inter-instrument. We also observed significant agreement (95.7–100%) with an orthogonal, high-sensitivity droplet digital™ Polymerase Chain Reaction (ddPCR) test. This method offers a valuable supplement to assessing targeted mutations from blood while conserving specimens and maintaining sensitivity, with rapid turn-around times to actionable results.

Non‐invasive epigenomic molecular phenotyping of the human brain via liquid biopsy of cerebrospinal fluid and next generation sequencing

2020 ◽  
Vol 52 (11) ◽  
pp. 4536-4545
Author(s):  
Lisa Pan ◽  
Lora McClain ◽  
Patricia Shaw ◽  
Nicole Donnellan ◽  
Tianjiao Chu ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Next Generation Sequencing ◽  
Human Brain ◽  
Liquid Biopsy ◽  
Next Generation ◽  
Non Invasive ◽  
Generation Sequencing ◽  
Molecular Phenotyping

scholarly journals P1.02-059 Evaluation of Plasma DNA Extraction, Droplet PCR and Droplet next Generation Sequencing Methods for Liquid Biopsy Analysis

2017 ◽  
Vol 12 (1) ◽  
pp. S523-S524
Author(s):  
Lina Salleh ◽  
Michelle Rozario ◽  
Xue Qing Koh ◽  
Ross Soo ◽  
Richie Soong
Keyword(s):  
Next Generation Sequencing ◽  
Dna Extraction ◽  
Liquid Biopsy ◽  
Next Generation ◽  
Plasma Dna ◽  
Droplet Pcr ◽  
Generation Sequencing

scholarly journals Detection of Coccidioides posadasii in a patient with meningitis using metagenomic next-generation sequencing: a case report

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yuqiao Mao ◽  
Xia Li ◽  
Haibo Lou ◽  
Xiaoyu Shang ◽  
Yanjun Mai ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Los Angeles ◽  
Systemic Infection ◽  
High Sensitivity ◽  
Pathological Examination ◽  
Next Generation ◽  
Coccidioides Posadasii ◽  
Dimorphic Fungi ◽  
Almost All ◽  
Generation Sequencing

Abstract Background Coccidioidomycosis is a systemic infection caused by dimorphic fungi Coccidioides spp. endemic to Southwestern United States and Central and South America. A history of residence and travel in these areas is essential for the diagnostic of coccidioidomycosis, which has highly variable symptoms ranging from asymptomatic to severe, disseminated infection, and even death. Immunocompromised patients of coccidioidomycosis experience a high risk of dissemination, chronic infection, and mortality. Meningitis is one of the most deleterious coccidioidomycosis and can cause various life-threatening complications. Case presentation Here we report a case of Coccidioides posadasii meningitis in a 49-year-old female who returned to China after one and a half years residence in Los Angeles, USA. The repeated routine cultures using CSF for bacteria or fungi were all negative. To hunt for an infectious etiology, the state-of-the-art technology metagenomic next-generation sequencing (mNGS) was then utilized, suggesting Coccidioides posadasii. Organizational pathological examination and polymerase-chain-reaction (PCR) results subsequently confirmed the mNGS detection. Conclusion To our knowledge, cases for coccidioidal meningitis have been rarely reported in China. While global travelling may spread this disease across continents and make the diagnosis more difficult. mNGS can detect almost all known pathogens with high sensitivity and specificity, especially for uncommon pathogen, such as Coccidioides posadasii in China.

Molecular profiling of osteosarcoma in children and adolescents from different age groups using a next-generation sequencing panel

2021 ◽  
Author(s):  
G.M. Guimarães ◽  
F. Tesser-Gamba ◽  
A.S. Petrilli ◽  
C.R.P. Donato-Macedo ◽  
M.T.S. Alves ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Children And Adolescents ◽  
Age Groups ◽  
Molecular Profiling ◽  
Next Generation ◽  
Generation Sequencing

Liquid Biopsy by Next-Generation Sequencing: a Multimodality Test for Management of Cancer

2019 ◽  
Vol 14 (5) ◽  
pp. 358-367 ◽  
Author(s):  
Hanadi El Achi ◽  
Joseph D. Khoury ◽  
Sanam Loghavi
Keyword(s):  
Next Generation Sequencing ◽  
Liquid Biopsy ◽  
Next Generation ◽  
Multimodality Test ◽  
Generation Sequencing

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.

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