scholarly journals Development and validation of a multigene variant profiling assay to guide targeted and immuno therapy selection in solid tumors

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246048
Author(s):  
Dadasaheb Akolkar ◽  
Darshana Patil ◽  
Navin Srivastava ◽  
Revati Patil ◽  
Vineet Datta ◽  
...  
Keyword(s):  
Solid Tumors ◽  
Clinical Performance ◽  
High Specificity ◽  
Clinical Samples ◽  
Solid Organ ◽  
Analytical Sensitivity ◽  
Mutation Burden ◽  
Validation Parameters ◽  
Sensitivity Specificity ◽  
Selection Of

We present data on analytical validation of the multigene variant profiling assay (CellDx) to provide actionable indications for selection of targeted and immune checkpoint inhibitor (ICI) therapy in solid tumors. CellDx includes Next Generation Sequencing (NGS) profiling of gene variants in a targeted 452-gene panel as well as status of total Tumor Mutation Burden (TMB), Microsatellite instability (MSI), Mismatch Repair (MMR) and Programmed Cell Death—Ligand 1 (PD-L1) respectively. Validation parameters included accuracy, sensitivity, specificity and reproducibility for detection of Single Nucleotide Alterations (SNAs), Copy Number Alterations (CNAs), Insertions and Deletions (Indels), Gene fusions, MSI and PDL1. Cumulative analytical sensitivity and specificity of the assay were 99.03 (95% CI: 96.54–99.88) and 99.23% (95% CI: 98.54% - 99.65%) respectively with 99.20% overall Accuracy (95% CI: 98.57% - 99.60%) and 99.7% Precision based on evaluation of 116 reference samples. The clinical performance of CellDx was evaluated in a subsequent analysis of 299 clinical samples where 861 unique mutations were detected of which 791 were oncogenic and 47 were actionable. Indications in MMR, MSI and TMB for selection of ICI therapies were also detected in the clinical samples. The high specificity, sensitivity, accuracy and reproducibility of the CellDx assay is suitable for clinical application for guiding selection of targeted and immunotherapy agents in patients with solid organ tumors.

scholarly journals Clinical Performance of the Spot Vision Photo Screener before and after Induction of Cycloplegia in Children

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Konuralp Yakar
Keyword(s):  
Positive Predictive Value ◽  
Negative Predictive Value ◽  
Predictive Value ◽  
Clinical Performance ◽  
High Specificity ◽  
Screening Criteria ◽  
Predictive Values ◽  
Before And After ◽  
Sensitivity Specificity ◽  
Vision Screener

Aim. To compare the clinical performance of the Spot Vision Screener used to detect amblyopia risk factors (ARFs) in children before and after induction of cycloplegia; the children were referred because they met the screening criteria of the American Association for Pediatric Ophthalmology and Strabismus (AAPOS). Methods. The Spot Vision Screener and a standard autorefractometer were used to examine 200 eyes of 100 children aged 3–10 years, before and after cycloplegia induction, in terms of ARFs. Sensitivity, specificity, and positive and negative predictive values for the detection of significant refractive errors were measured using the AAPOS referral criteria. It was explored that Spot Screener data were affected by cycloplegia. The extent of agreement between cycloplegic/noncycloplegic photoscreening data and cycloplegic autorefraction measurements was assessed using Wilcoxon and Spearman correlation analyses. Results. The Spot’s sensitivity was improved from 60.9% to 85.3% and specificity from 94.9% to 87.4% with cycloplegia compared to cycloplegic standard autorefractometer results. The positive predictive value of Spot was 75.7%, and the negative predictive value was 90.4% without cycloplegia. With cycloplegia, the positive predictive value of Spot was 63.6% and the negative predictive value was 95.8%. Conclusions. The Spot Screener afforded moderate sensitivity and high specificity prior to cycloplegia. The sensitivity and negative predictive value improved after induction of cycloplegia. Examiners should be aware of the effects of cycloplegia on their findings.

scholarly journals Design and Validation of Transcription-Mediated-Amplification Nucleic Acid Amplification Tests forMycoplasma genitalium

2019 ◽  
Vol 57 (8) ◽  
Author(s):  
Brett Kirkconnell ◽  
Barbara Weinbaum ◽  
Katherine Santos ◽  
Trisha Le Nguyen ◽  
Bryan Vinluan ◽  
...  
Keyword(s):  
Clinical Performance ◽  
Mycoplasma Genitalium ◽  
Vaginal Swab ◽  
Nucleic Acid Amplification ◽  
Clinical Validation ◽  
Analytical Sensitivity ◽  
Reference Standard ◽  
Content Type ◽  
Sensitivity Specificity

ABSTRACTMycoplasma genitaliumis a sexually transmitted bacterium linked to adverse sexual and reproductive health outcomes in women and men.M. genitaliumis difficult to culture, and in the absence of validated amplified molecular methods for diagnosis of infection, there is no reference standard available for use as a comparator for the validation of newM. genitaliumdiagnostic tests. We evaluated the analytical and clinical performance of three transcription-mediated amplification (TMA) tests forM. genitalium, each targeting unique rRNA sequences, for use as a composite comparator for clinical validation of the AptimaMycoplasma genitalium(AMG) assay, anin vitrodiagnostic (IVD) TMA test that targets 16 s rRNA ofM. genitalium. Analytical sensitivity, specificity, and strain inclusivity of all four TMA tests were determined using nine laboratory strains ofM. genitaliumand 56 nontarget bacteria, protozoa, and viruses. Analytical sensitivity of the tests forM. genitaliumranged from 0.017 to 0.040 genome equivalents/ml. None of the nontarget organisms evaluated cross-reacted with any test. A composite comparator reference standard consisting of the 3 alternate (Alt) TMA tests was used to evaluate the clinical performance of the AMG assay by testing residual vaginal swab, female urine, and male urine specimens obtained from 1,400 adult subjects from three U.S. clinical sites. Using this reference standard to establish infected specimen status, the sensitivity, specificity, and overall agreement of the AMG IVD assay were 100%, 99.9%, and 99.9%, respectively. These results demonstrate the utility of molecular composite reference standard methodology for the clinical validation of future IVD tests for this organism.

scholarly journals Polymethacrylate Sphere-Based Assay for Ultrasensitive miRNA Detection

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Samira Hosseini ◽  
Patricia Vázquez-Villegas ◽  
Richard C. Willson ◽  
Marco Rito-Palomares ◽  
Margarita Sanchez-Dominguez ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Breast Cancer Incidence ◽  
High Specific Surface Area ◽  
Clinical Samples ◽  
Analytical Sensitivity ◽  
Important Target ◽  
Target Analytes ◽  
High Sequence Homology ◽  
Mirna Detection ◽  
Sensitivity Specificity

Although microRNAs (miRNAs) have emerged as increasingly important target analytes, their biorecognition remains challenging due to their small size, high sequence homology, and low abundance in clinical samples. Nanospheres and microspheres have also gained increasing attention in biosensor applications due to their high specific surface area and the wide variety of compositions available. In this study, chemically designed and synthesized microspheres with active functional groups were used to promote effective miRNA immobilization resulting in better biorecognition. Upon conjugation with fluorescence-labeled complimentary probes, acylate-based spheres have indirectly detected MiR159, offering significantly enhanced analytical sensitivity, specificity, and accuracy while yielding a considerably low limit of detection (LOD) of 40 picomolar. Furthermore, MiR159 presence, which is known to be inversely correlated to breast cancer incidence and progression, was successfully detected in a competitive assay, which is promising for upgrading the current assay to clinical use.

scholarly journals Evaluation of a rapid bacteriophage-based method for the detection of Mycobacterium tuberculosis in clinical samples

2003 ◽  
Vol 52 (4) ◽  
pp. 331-335 ◽  
Author(s):  
Ayman Mohamed Marei ◽  
Eman Mohamed El-Behedy ◽  
Heba Ali Mohtady ◽  
Afify Fahmy Afify
Keyword(s):  
Developing Countries ◽  
Mycobacterium Tuberculosis ◽  
Clinical Performance ◽  
Low Cost ◽  
Urine Samples ◽  
Clinical Samples ◽  
Pcr Assay ◽  
Microbiological Culture ◽  
Time To Diagnosis ◽  
Sensitivity Specificity

Rapid, sensitive and low-cost methods are needed urgently for the detection of Mycobacterium tuberculosis in clinical samples, especially in developing countries. To this end, the clinical performance of FASTPlaqueTBTM (a bacteriophage-based method) has been studied in parallel with microscopy, standard microbiological culture and in-house IS6110-based PCR methods. A total of 64 samples, including 42 sputum samples and 22 urine samples, were tested in this study. The sensitivity, specificity and overall accuracy values for the FASTPlaqueTB assay relative to that of culture were respectively 76.5, 95 and 90 %. The corresponding values for the in-house IS6110-based PCR assay were 88, 91 and 90 % and, for Ziehl–Neelsen staining, were 59, 95 and 85 %. FASTPlaqueTB gave better clinical performance with urine samples than with sputum samples (sensitivity, specificity and overall accuracy were 100 % with urine samples and 64, 93 and 84 % with sputum samples). The 100 % sensitivity of FASTPlaqueTB was higher than that of the corresponding values for PCR (67 %) with urine samples. In conclusion, FASTPlaqueTB proved to be sensitive, cheap relative to the PCR and rapid. It is able to detect M. tuberculosis in clinical samples within 1 day, reducing the time to diagnosis in comparison with culture.

scholarly journals MicroRNA In Vitro Diagnostics Using Immunoassay Analyzers

2015 ◽  
Vol 61 (4) ◽  
pp. 600-607 ◽  
Author(s):  
Andreas Kappel ◽  
Christina Backes ◽  
Yiwei Huang ◽  
Sachli Zafari ◽  
Petra Leidinger ◽  
...  
Keyword(s):  
Alzheimer Disease ◽  
Clinical Performance ◽  
Pearson Correlation ◽  
High Specificity ◽  
Substantial Effect ◽  
Analytical Sensitivity ◽  
Laboratory Equipment ◽  
Novel Approach ◽  
New Biomarkers

Abstract BACKGROUND The implementation of new biomarkers into clinical practice is one of the most important areas in medical research. Besides their clinical impact, novel in vitro diagnostic markers promise to have a substantial effect on healthcare costs. Although numerous publications report the discovery of biomarkers, only a fraction of those markers are routinely used. One key challenge is a measurement system that is compatible with clinical workflows. METHODS We designed a new immunoassay for microRNA (miRNA) quantification. The assay combines streptavidin-linked microparticles, a biotinylated catcher oligonucleotide complementary to a single miRNA species, and finally, a monoclonal antibody to DNA/RNA heterohybrids labeled with acridinium ester. Importantly, our assay runs on standard immunoassay analyzers. After a technical validation of the assay, we evaluated the clinical performance on 4 Alzheimer disease miRNAs. RESULTS Our assay has an analytical specificity of 99.4% and is at the same time sensitive (concentrations in the range of 1 pmol/L miRNA can be reliably profiled). Because the novel approach did not require amplification steps, we obtained high reproducibility for up to 40 biological replicates. Importantly, our assay prototype exhibited a time to result of <3 h. With human blood samples, the assay was able to measure 4 miRNAs that can detect Alzheimer disease with a diagnostic accuracy of 82% and showed a Pearson correlation >0.994 with the gold standard qRT-PCR. CONCLUSIONS Our miRNA immunoassay allowed the measurement of miRNA signatures with sufficient analytical sensitivity and high specificity on commonly available laboratory equipment.

scholarly journals An isothermal method for sensitive detection of Mycobacterium tuberculosis complexes using CRISPR/Cas12a cis- and trans-cleavage

2020 ◽  
Author(s):  
Haipo Xu ◽  
Xiaolong Zhang ◽  
Zhixiong Cai ◽  
Xiuqing Dong ◽  
Geng Chen ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Limit Of Detection ◽  
Clinical Performance ◽  
High Specificity ◽  
Culture Method ◽  
Sensitive Detection ◽  
Clinical Samples ◽  
Target Sequence ◽  
Guide Rna ◽  
Specificity And Sensitivity

AbstractTuberculosis is still one of the most serious infectious diseases resulting in lethal death worldwide. The traditional method is still not enough to meet the clinical requirements of rapid diagnosis, high specificity and sensitivity. Fast, sensitive and accurate detection of mycobacterium tuberculosis (MTB) is an urgent need for the treatment and control of tuberculosis disease. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated proteins (Cas12a) exhibits strongly nonspecific degradation ability of exogenous single-strand nucleic acid (trans-cleavage) after specific recognition of target sequence. We purified Cas12a protein and selected a proper guide RNA (gRNA) based on conserved sequences of MTB from gRNA library we designed. Then, we proposed a novel method based on recombinase polymerase amplification (RPA) and CRISPR/Cas12a nuclease system for specific and sensitive detection of MTB DNA. The assay based on fluorescence detection pattern showed 4.48 fM of limit of detection (LOD) and good linear correlation of concentration and fluorescence value (R2=0.9775). Also, it showed good performance in distinguishing other bacteria. Furthermore, its clinical performance was evaluated by 193 samples and showed sensitivity of 99.29% (139/140) and specificity of 100% (53/53) at 99% confidence interval, respectively, compared with culture method. The CRISPR/Cas12a system showed good specificity, excellent sensitivity and accuracy for MTB detection, and it meets requirements of MTB detection in clinical samples and has great potential for clinical translation.

A novel xenonucleic acid mediated molecular clamping technology for early colorectal cancer diagnostics.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e16106-e16106
Author(s):  
Qing Sun ◽  
Larry Pastor ◽  
Jinwei Du ◽  
Michael Joseph Powell ◽  
Aiguo Zhang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Clinical Performance ◽  
Cancer Diagnostics ◽  
Clinical Samples ◽  
Early Colorectal Cancer ◽  
Analytical Sensitivity ◽  
Assay Sensitivity ◽  
Specificity And Sensitivity ◽  
Ffpe Samples ◽  
Performance Results

e16106 Background: Colorectal cancer (CRC) is one of the leading causes of cancer-related death. Early detection is critical to reduce CRC morbidity and mortality. In order to meet this need, we developed a molecular clamping assay called ColoScape for early colorectal cancer diagnostics. Methods: Nineteen mutations in four genes APC, KRAS, BRAF and CTNNB1 associated with early events in CRC pathogenesis are targeted in the ColoScape assay. Xenonucleic Acid (XNA) mediated qPCR clamping technology was applied to minimize the wild-type background amplification in order to improve assay sensitivity of CRC mutation detection. The assay analytical performance was verified and validated, cfDNA and FFPE CRC patient samples were assessed for clinical performance, and a ROC curve was applied to evaluate its performance. Results: The data showed that the assay analytical sensitivity is 0.5% Variant Allele Frequency, corresponding to ~7-8 copies of mutant DNA with 5ng total DNA input per test. This assay is highly reproducible with intra-assay CV < 3% and inter-assay CV < 5%. We have investigated 380 clinical samples including plasma cfDNA and FFPE samples from patients with different stages of CRC. The preliminary assay clinical specificity and sensitivity for cfDNA were 100% (95% CI, 80.3-97.5%) and 92.2% (95% CI, 94.7-100%) respectively with AUC being about 0.96; and 96% (95% CI, 77.6-99.7%) specificity and 92% (95% CI, 86.1-95.6%) sensitivity with AUC 0.94 for FFPE. Conclusions: XNA mediated molecular clamping assay is a rapid, precise, and sensitive assay for the detection of CRC mutations in cfDNA or FFPE samples.

scholarly journals Analytical and clinical evaluation of antibody tests for SARS-CoV-2 serosurveillance studies used in Finland in 2020

2021 ◽  
Author(s):  
Nina Ekström ◽  
Camilla Virta ◽  
Anu Haveri ◽  
Timothée Dub ◽  
Lotta Hagberg ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Clinical Performance ◽  
High Specificity ◽  
Target Population ◽  
Analytical Performance ◽  
Analytical Sensitivity ◽  
Set Up ◽  
Antibody Tests ◽  
Microneutralization Test ◽  
Microsphere Immunoassay

AbstractBackgroundSensitive and highly specific antibody tests are critical for detection of SARS-CoV-2 antibodies especially in populations where seroprevalence is low.AimTo set up, optimize and evaluate the analytical and clinical performance of a new in-house microsphere immunoassay for measurement of IgG antibodies to SARS-CoV-2 nucleoprotein for assessment of population seroprevalence in Finland.MethodsWe set up a new in-house microsphere immunoassay (FMIA) with SARS-CoV-2 nucleoprotein and optimized its analytical performance. For evaluation of clinical performance, we tested sera collected in a well-characterized cohort of PCR positive-confirmed SARS-CoV-2 patients (n=89) with mostly mild symptoms, and before the COVID-19 pandemic (n=402), for nucleoprotein specific IgG concentrations by FMIA and a commercial chemiluminescent immunoassay and for neutralizing antibodies by the microneutralization test.ResultsThe analytical performance of FMIA was established in terms of sensitivity, linearity and precision. FMIA discriminated between COVID-19 patient and control samples with high specificity (100%) and sensitivity (100%). We generated FMIA seropositivity cut-offs, 0.46 and 1.71 U/ml, for low- and high-seroprevalence settings, respectively. In addition, we obtained high level of agreement between FMIA results and results by the microneutralization test.ConclusionThe fluorescent microsphere immunoassay showed excellent analytical and clinical performance and is well suited for serosurveillance studies of SARS-CoV-2. However, to optimize analytical sensitivity and clinical specificity of the assay, different seropositivity thresholds depending on the intended use of the assay and the target population, may be needed.

scholarly journals Comparative evaluation of six nucleic acid amplification kits for SARS-CoV-2 RNA detection

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Shuang Wu ◽  
Xiaolu Shi ◽  
Qiongcheng Chen ◽  
Yixiang Jiang ◽  
Le Zuo ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Comparative Study ◽  
Clinical Performance ◽  
Positive Sample ◽  
Nucleic Acid Amplification ◽  
Clinical Samples ◽  
Predictive Values ◽  
Health Crisis ◽  
Specificity And Sensitivity ◽  
Sensitivity Specificity

Abstract Background SARS-CoV-2 is a newly emerged coronavirus, causing the coronavirus disease 2019 (COVID-19) outbreak in December, 2019. As drugs and vaccines of COVID-19 remain in development, accurate virus detection plays a crucial role in the current public health crisis. Quantitative real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) kits have been reliably used for detection of SARS-CoV-2 RNA since the beginning of the COVID-19 outbreak, whereas isothermal nucleic acid amplification-based point-of-care automated kits have also been considered as a simpler and rapid alternative. However, as these kits have only been developed and applied clinically within a short timeframe, their clinical performance has not been adequately evaluated to date. We describe a comparative study between a newly developed cross-priming isothermal amplification (CPA) kit (Kit A) and five RT-qPCR kits (Kits B–F) to evaluate their sensitivity, specificity, predictive values and accuracy. Methods Fifty-two clinical samples were used including throat swabs (n = 30), nasal swabs (n = 7), nasopharyngeal swabs (n = 7) and sputum specimens (n = 8), comprising confirmed (n = 26) and negative cases (n = 26). SARS-CoV-2 detection was simultaneously performed on each sample using six nucleic acid amplification kits. The sensitivity, specificity, positive/negative predictive values (PPV/NPV) and the accuracy for each kit were assessed using clinical manifestation and molecular diagnoses as the reference standard. Reproducibility for RT-qPCR kits was evaluated in triplicate by three different operators using a SARS-CoV-2 RNA-positive sample. On the basis of the six kits’ evaluation results, CPA kit (Kit A) and two RT-qPCR Kits (Kit B and F) were applied to the SARS-CoV-2 detection in close-contacts of COVID-19 patients. Results For Kit A, the sensitivity, specificity, PPV/NPV and accuracy were 100%. Among the five RT-qPCR kits, Kits B, C and F had good agreement with the clinical diagnostic reports (Kappa ≥ 0.75); Kits D and E were less congruent (0.4 ≤ Kappa < 0.75). Differences between all kits were statistically significant (P < 0.001). The reproducibility of RT-qPCR kits was determined using a coefficients of variation (CV) between 0.95% and 2.57%, indicating good reproducibility. Conclusions This is the first comparative study to evaluate CPA and RT-qPCR kits’ specificity and sensitivity for SARS-CoV-2 detection, and could serve as a reference for clinical laboratories, thus informing testing protocols amid the rapidly progressing COVID-19 pandemic.

scholarly journals Comparative performance of four nucleic acid amplification tests for SARS-CoV-2 virus

2020 ◽  
Author(s):  
Yujuan Xiong ◽  
Zhen-Zhen Li ◽  
Qi-Zhen Zhuang ◽  
Yan Chao ◽  
Fei Li ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Limit Of Detection ◽  
High Specificity ◽  
Nucleic Acid Amplification ◽  
Virus Concentration ◽  
Analytical Sensitivity ◽  
Comparative Performance ◽  
Consistency Test ◽  
Nucleic Acid Amplification Tests ◽  
Selection Of

AbstractCoronavirus disease 2019 (COVID-19) can be screened and diagnosed through the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction. SARS-CoV-2 nucleic acid amplification tests (NAATs) have been rapidly developed and quickly applied to clinical testing during the pandemic. However, studies evaluating the performance of these NAAT assays are limited. We evaluated the performance of four NAATs, which were marked by the Conformité Européenne and widely used in China during the pandemic. Results showed that the analytical sensitivity of the four assays was significantly lower than that claimed by the NAAT manufacturers. The limit of detection (LOD) of Daan, Sansure, and Hybribio NAATs was 3000 copies/mL, whereas the LOD of Bioperfectus NAATs was 4000 copies/mL. The results of the consistency test using 46 samples showed that Daan, Sansure, and Hybribio NAATs could detect the samples with a specificity of 100% (30/30) and a sensitivity of 100% (16 /16), whereas Bioperfectus NAAT detected the samples with a specificity of 100% (30/30) and a sensitivity 81.25% (13/16). The sensitivity of Bioperfectus NAAT was lower than that of the three other NAATs; this finding was consistent with the result that Bioperfectus NAAT had a higher LOD than the three other kinds of NAATs. The four above mentioned reagents presented high specificity; however, for the detection of the samples with low virus concentration, Bioperfectus reagent had the risk of missing detection. Therefore, the LOD should be considered in the selection of SARS-CoV-2 NAATs.

Sign in / Sign up

Export Citation Format

Share Document