scholarly journals Reproducibility challenges for biomarker detection with uncertain but informative experimental data

2020 ◽  
Vol 14 (13) ◽  
pp. 1255-1263
Author(s):  
Wei Zhuang ◽  
Luísa Camacho ◽  
Camila S Silva ◽  
Huixiao Hong
Keyword(s):  
Experimental Data ◽  
Biomarker Detection ◽  
Circulating Biomarkers ◽  
Chain Reaction ◽  
Liquid Biopsies ◽  
Circulating Micrornas ◽  
Incomplete Observations ◽  
Polymerase Chain ◽  
Observation Method ◽  
Complete Observation

Recent studies have revealed that circulating microRNAs are promising biomarkers for detecting toxicity or disease. Quantitative real-time polymerase chain reaction (qPCR) is often used to measure the levels of microRNAs. Besides complete and certain data, investigators inevitably have observed technically incomplete or uncertain qPCR data. Investigators usually set incomplete observations equal to the maximum quality number of qPCR cycles, apply the complete-observation method, or choose not to analyze targets with incomplete observations. Using biostatistical knowledge and published studies, we show that three commonly applied methods tend to cause biased inference and decrease reproducibility in biomarker detection. More efforts are needed to address the challenges to identify and detect reliable, novel circulating biomarkers in liquid biopsies.

scholarly journals Current quantitative polymerase chain reaction to detect severe acute respiratory syndrome coronavirus 2 may give positive results for other described coronavirus

2021 ◽  
Author(s):  
Antonio Martínez-Murcia ◽  
Adrián García-Sirera ◽  
Aaron Navarro ◽  
Patricia Ros-Tárraga ◽  
Laura Pérez
Keyword(s):  
Experimental Data ◽  
Polymerase Chain Reaction ◽  
Severe Acute Respiratory Syndrome ◽  
Environmental Samples ◽  
Quantitative Polymerase Chain Reaction ◽  
Epidemiological Surveillance ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Positive Results

SUMMARYSome weeks after the first CoVID-19 outbreak, the WHO published some qPCR protocol assays developed by different institutions worldwide. These qPCR designs are being used to detect the presence of SARS-CoV-2 in the population, which allow us to monitore the prevalence of the virus during the pandemic. Moreover, the use of these designs is wide spreading and nowadays they are used to detect SARS-CoV-2 in environmental samples to act as epidemiological surveillance tool. However, at the time of designing the published RT-qPCR assays, a lack of SARS-CoV-2 genomes available may explain a low exclusivity in some cases. In this study, we are reporting experimental data which demonstrate that some of the current qPCR used to detect SARS-CoV-2 may give positive results for other described coronavirus different from SARS-CoV-2.

scholarly journals Standardisierte mikroRNA-Analytik — die große Chance für Biomarkerstudien?

BIOspektrum ◽  
2020 ◽  
Vol 26 (6) ◽  
pp. 621-623
Author(s):  
Maria Fauth ◽  
Meike J. Saul
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Clinical Application ◽  
Reverse Transcription ◽  
Prognostic Biomarkers ◽  
Chain Reaction ◽  
Acceptance Criteria ◽  
Circulating Micrornas ◽  
Polymerase Chain

Abstract Circulating microRNAs (miRs) represent promising diagnostic and prognostic biomarkers for various diseases. Despite the high number of biomarker studies, the results of these studies are hardly reproducible. This makes it difficult to transfer the results into clinical application. In this context, acceptance criteria for the quantification of miRs by reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) may help to standardize miR analysis and improve reproducibility.

scholarly journals Simera: Modelling the PCR Process to Simulate Realistic Chimera Formation

2016 ◽  
Author(s):  
Ben Nichols ◽  
Christopher Quince
Keyword(s):  
Experimental Data ◽  
Polymerase Chain Reaction ◽  
Community Structure ◽  
Chain Reaction ◽  
Future Studies ◽  
Target Dna ◽  
Detection Software ◽  
Polymerase Chain ◽  
Diversity Studies ◽  
Principal Method

AbstractPolymerase Chain Reaction (PCR) is the principal method of amplifying target DNA regions and, as such, is of great importance when performing microbial diversity studies. An unfortunate side effect of PCR is the formation of unwanted byproducts such as chimeras. The main goal of the work covered in this article is the development of an algorithm that simulates realistic chimeras for use in the evaluation of chimera detection software and for investigations into the accuracy of community structure analyses. Experimental data has helped to identify factors which may cause the formation of chimeras and has provided evidence of how influential these factors can be. This article makes use of some of this evidence in order to build a model with which to simulate the PCR process. This model helps to better explain the formation of chimeras and is therefore able to provide aid to future studies that intend to use PCR.

scholarly journals Ultrasensitive melanoma biomarker detection using a microchip SERS immunoassay with anisotropic Au–Ag alloy nanoboxes

RSC Advances ◽  
2020 ◽  
Vol 10 (48) ◽  
pp. 28778-28785
Author(s):  
Aswin Raj Kumar ◽  
Karthik Balaji Shanmugasundaram ◽  
Junrong Li ◽  
Zhen Zhang ◽  
Abu Ali Ibn Sina ◽  
...  
Keyword(s):  
Cancer Diagnosis ◽  
Diagnosis And Treatment ◽  
Biomarker Detection ◽  
Circulating Biomarkers ◽  
Liquid Biopsies ◽  
Treatment Management ◽  
Non Invasive

The detection of circulating biomarkers in liquid biopsies has the potential to provide a non-invasive route for earlier cancer diagnosis and treatment management.

scholarly journals Heterogeneity and Coexistence of T790M and T790 Wild-Type Resistant Subclones Drive Mixed Response to Third-Generation Epidermal Growth Factor Receptor Inhibitors in Lung Cancer

2018 ◽  
pp. 1-15 ◽  
Author(s):  
Zofia Piotrowska ◽  
Mehlika Hazar-Rethinam ◽  
Coleen Rizzo ◽  
Brandon Nadres ◽  
Emily E. Van Seventer ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Epidermal Growth Factor Receptor ◽  
Growth Factor ◽  
Growth Factor Receptor ◽  
Third Generation ◽  
Chain Reaction ◽  
Liquid Biopsies ◽  
Epidermal Growth ◽  
Polymerase Chain ◽  
Digital Polymerase Chain Reaction

Purpose Third-generation epidermal growth factor receptor (EGFR) inhibitors like nazartinib are active against EGFR mutation–positive lung cancers with T790M-mediated acquired resistance to initial anti-EGFR treatment, but some patients have mixed responses. Methods Multiple serial tumor and liquid biopsies were obtained from two patients before, during, and after treatment with nazartinib. Next-generation sequencing and droplet digital polymerase chain reaction were performed to assess heterogeneity and clonal dynamics. Results We observed the simultaneous emergence of T790M-dependent and -independent clones in both patients. Serial plasma droplet digital polymerase chain reaction illustrated shifts in relative clonal abundance in response to various systemic therapies, confirming a molecular basis for the clinical mixed radiographic responses observed. Conclusion Heterogeneous responses to treatment targeting a solitary resistance mechanism can be explained by coexistent tumor subclones harboring distinct genetic signatures. Serial liquid biopsies offer an opportunity to monitor clonal dynamics and the emergence of resistance and may represent a useful tool to guide therapeutic strategies.

Sign in / Sign up

Export Citation Format

Share Document