Clinical Validation of Novel Chip-Based Digital PCR Platform for Fetal Aneuploidies Screening

Fetal aneuploidy is routinely diagnosed by karyotyping. The development of techniques for rapid aneuploidy detection based on the amplification reaction allows cheaper and rapid diagnosis. However, the currently available solutions have limitations. We tested a novel approach as a diagnostic tool in clinical practice. The objective of this study was to provide a clinical performance of the sensitivity and specificity of a novel chip-based digital PCR approach for fetal aneuploidy screening. The study was conducted in 505 pregnant women with increased risk for fetal aneuploidy undergoing invasive prenatal diagnostics. DNA extracted from amniotic fluid or CVS was analyzed for the copy number of chromosomes 13, 18, 21, X, and Y using a new chip-based solution. Performance was assessed by comparing results with findings from karyotyping. Aneuploidy was confirmed in 65/505 cases positive for trisomy 21, 30/505 cases positive for trisomy 18, 14/505 cases positive for trisomy 13 and 21/505 with SCAs. Moreover, 2 cases with triploidy and 2 cases with confirmed mosaicisms of 21 and X chromosomes were detected. Clinical sensitivity and specificity within this study was determined at 100% for T21 (95% CI, 99.26–100%), T18 (95% CI, 99.26–100%), and T13 (95% CI, 99.26–100%). Chip-based digital PCR provides equally high sensitivity and specificity in rapid aneuploidy screening and can be implemented into routine prenatal diagnostics.

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Blood amyloid β oligomerization as a biomarker of Alzheimer’s disease: a blinded validation study

10.21203/rs.2.19960/v1 ◽

2020 ◽

Author(s):

Young Chul Youn ◽

Byoung Sub Lee ◽

Gwang Je Kim ◽

Ji Sun Ryu ◽

Kuntaek Lim ◽

...

Keyword(s):

Clinical Diagnosis ◽

Sensitivity And Specificity ◽

Detection System ◽

Amyloid Β ◽

High Sensitivity ◽

Community Based ◽

Clinical Sensitivity ◽

Aβ Oligomerization ◽

Normal Cognition

Abstract INTRODUCTION: Oligomeric amyloid ß (Aß) is one of the major contributors to the pathomechanism of AD; Aß oligomerization in plasma can be measured using a Multimer Detection System-Oligomeric Aß (MDS-OAß) after incubation with spiked synthetic Aß. METHODS: We evaluated the clinical sensitivity and specificity of the MDS-OAß values by inBlood TM OAß test using heparin-treated plasma samples from 52 AD patients in comparison with 52 community-based subjects with normal cognition (NC). The inclusion criterion was proposed by the NINCDS-ADRDA and additionally required for the least 6 months of follow-up from the initial clinical diagnosis in the course of AD. RESULTS: The MDS-OAβ values were 1.43 ± 0.30 ng/ml in AD and 0.45 ± 0.19 ( p <0.001) in NC, respectively. Using a cut-off value of 0.78 ng/ml, the results revealed that 100% sensitivity 92.31% specificity. DISCUSSION: MDS-OAß to measure plasma Aβ oligomerization is a valuable blood-based biomarker for clinical diagnosis of AD, with high sensitivity and specificity.

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P6578Development of the novel program to diagnose atrial fibrillation using automated blood pressure monitor

European Heart Journal ◽

10.1093/eurheartj/ehz746.1166 ◽

2019 ◽

Vol 40 (Supplement_1) ◽

Author(s):

M Ishizawa ◽

T Noma ◽

S Ishikawa ◽

K Matsunaga ◽

R Kawakami ◽

...

Keyword(s):

Atrial Fibrillation ◽

Blood Pressure ◽

Sensitivity And Specificity ◽

Pressure Pulse ◽

High Sensitivity ◽

Cardiac Patients ◽

The Novel ◽

Waveform Data ◽

Medical Needs ◽

Increased Risk

Abstract Background Atrial fibrillation (AF) is often asymptomatic and contributes to an increased risk of strokes. The development of proper screening device of AF is unmet medical needs worldwide. Recently, we had reported that multiple measurements using Omron automated blood pressure (BP) monitor with irregular heartbeat detection showed high sensitivity and specificity for AF detection in general cardiac patients, however, this method had limitations in discriminating between AF and other arrhythmias. Purpose The aim of this study is to develop a novel program that can accurately diagnose AF by discriminating it from other arrhythmias using the pressure pulse waveform data outputted from Omron automated BP monitor. Methods In our previous clinical research, BP measurements were performed 3 times each for 303 general cardiac patients (mean age: 72.2 years, 69.8% male) with recording the real-time single lead ECG, and a total of 909 pressure pulse waveforms were obtained. Among them, 840 pressure pulse waveforms from 280 patients (include 40 AF patients) used for further analysis. We developed a program to analyze and visualize uniquely the characteristics of AF waveform through the autocorrelation-based waveform processing system produced by Melody International Ltd, Kagawa, Japan. All visualized results were judged and classified into Sinus, Non-AF and AF by two individuals blinded to the results. For each patient who obtained 3 results, a two by two contingency table was created and sensitivity, specificity, and accuracy for diagnosing AF were calculated. Results Among 840 pressure pulse waveforms, only 21 (2 Sinus and 19 Non-AF) out of 720 Sinus and Non-AF waveforms were judged as AF, and 7 out of 120 AF waveforms were judged as Non-AF. None of AF waveforms was absolutely misjudged as Sinus. In analysis for each patient, when one or more AF judgements were found in 3 waveforms, the diagnosis of AF has sensitivity and specificity of 100% and 95.8%, respectively. When two or more AF judgements were found in 3 waveforms, the diagnosis of AF has sensitivity and specificity of 100% and 97.9%, respectively. In this rule, the diagnostic accuracy of AF reached up to 98.8%, and no sinus patients were misjudged as AF. Conclusion The novel program, which applied autocorrelation methods uniquely to analysis of the pressure pulse waveforms recorded by automated BP monitor, showed high sensitivity and high specificity for AF diagnosis in general cardiac patients. This program is expected to be useful for early diagnosis for asymptomatic AF patients. Acknowledgement/Funding The present research is supported by a grant through the SCOPE from the Ministry of Internal Affairs and Communications, Japan.

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Sensitive detection of multiple islet autoantibodies in type 1 diabetes using small sample volumes by agglutination-PCR

PLoS ONE ◽

10.1371/journal.pone.0242049 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242049

Author(s):

Felipe de Jesus Cortez ◽

David Gebhart ◽

Peter V. Robinson ◽

David Seftel ◽

Narges Pourmandi ◽

...

Keyword(s):

Type 1 Diabetes ◽

Sensitivity And Specificity ◽

High Sensitivity ◽

Small Sample ◽

Insulin Autoantibodies ◽

Islet Autoantibodies ◽

Antibody Detection ◽

Clinical Sensitivity ◽

Analysis Platform

Islet autoantibodies are predominantly measured by radioassay to facilitate risk assessment and diagnosis of type 1 diabetes. However, the reliance on radioactive components, large sample volumes and limited throughput renders radioassay testing costly and challenging. We developed a multiplex analysis platform based on antibody detection by agglutination-PCR (ADAP) for the sample-sparing measurement of GAD, IA-2 and insulin autoantibodies/antibodies in 1 μL serum. The assay was developed and validated in 7 distinct cohorts (n = 858) with the majority of the cohorts blinded prior to analysis. Measurements from the ADAP assay were compared to radioassay to determine correlation, concordance, agreement, clinical sensitivity and specificity. The average overall agreement between ADAP and radioassay was above 91%. The average clinical sensitivity and specificity were 96% and 97%. In the IASP 2018 workshop, ADAP achieved the highest sensitivity of all assays tested at 95% specificity (AS95) rating for GAD and IA-2 autoantibodies and top-tier performance for insulin autoantibodies. Furthermore, ADAP correctly identified 95% high-risk individuals with two or more autoantibodies by radioassay amongst 39 relatives of T1D patients tested. In conclusion, the new ADAP assay can reliably detect the three cardinal islet autoantibodies/antibodies in 1μL serum with high sensitivity. This novel assay may improve pediatric testing compliance and facilitate easier community-wide screening for islet autoantibodies.

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Cell-free DNA screening for aneuploidies in 7113 pregnancies: single Italian centre study

Genetics Research ◽

10.1017/s001667232000004x ◽

2020 ◽

Vol 102 ◽

Cited By ~ 1

Author(s):

Alvaro Mesoraca ◽

Katia Margiotti ◽

Claudio Dello Russo ◽

Anthony Cesta ◽

Antonella Cima ◽

...

Keyword(s):

Sex Chromosome ◽

Clinical Performance ◽

False Negative ◽

Prenatal Testing ◽

High Sensitivity ◽

Trisomy 13 ◽

Sequencing Platform ◽

Non Invasive ◽

Negative Results ◽

False Negative Results

Abstract Introduction Non-invasive prenatal testing (NIPT) using cell-free foetal DNA has been widely accepted in recent years for detecting common foetal chromosome aneuploidies, such as trisomies 13, 18 and 21, and sex chromosome aneuploidies. In this study, the practical clinical performance of our foetal DNA testing was evaluated for analysing all chromosome aberrations among 7113 pregnancies in Italy. Methods This study was a retrospective analysis of collected NIPT data from the Ion S5 next-generation sequencing platform obtained from Altamedica Medical Centre in Rome, Italy. Results In this study, NIPT showed 100% sensitivity and 99.9% specificity for trisomies 13, 18 and 21. Out of the 7113 samples analysed, 74 cases (1%) were positive by NIPT testing; foetal karyotyping and follow-up results validated 2 trisomy 13 cases, 5 trisomy 18 cases, 58 trisomy 21 cases and 10 sex chromosome aneuploidy cases. There were no false-negative results. Conclusion In our hands, NIPT had high sensitivity and specificity for common chromosomal aneuploidies such as trisomies 13, 18 and 21.

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Clinical Validation of Automated and Rapid mariPOC SARS-CoV-2 Antigen Test

10.1101/2021.02.08.21250086 ◽

2021 ◽

Author(s):

Juha M. Koskinen ◽

Petri Antikainen ◽

Kristina Hotakainen ◽

Anu Haveri ◽

Niina Ikonen ◽

...

Keyword(s):

Sensitivity And Specificity ◽

Limit Of Detection ◽

Clinical Performance ◽

High Capacity ◽

Nasopharyngeal Swab ◽

Analytical Sensitivity ◽

Clinical Sensitivity ◽

Qrt Pcr ◽

Antigen Tests ◽

Novel Coronavirus

ABSTRACTNovel SARS coronavirus causing COVID-19 was recognized in late 2019. Diagnostics was quickly ramped up worldwide based on the detection of viral RNA. Based on the scientific knowledge for pre-existing coronaviruses, it was expected that the RNA of this novel coronavirus will be detected at significant rates from symptomatic and asymptomatic individuals due to existence of non-infectious RNA. To increase the efficacy of diagnostics, surveillance, screening and pandemic control, rapid methods, such as antigen tests, are needed for decentralized testing and to assess infectiousness. The objectives were to verify analytical sensitivity and specificity, and assess the clinical sensitivity, specificity and usability of a novel automated mariPOC SARS-CoV-2 test based on sophisticated optical laser technology detecting viral structure proteins. Analytical performance was verified using bacterial and viral preparations. Clinical performance of the test was evaluated against qRT-PCR in a retrospective study with nasopharyngeal swab specimens (N=211) collected from symptomatic patients suspected of acute SARS-CoV-2 infections. Sensitivity and specificity of the mariPOC test were 92.3% (12/13) and 100.0% (198/198), respectively. The test’s limit of detection was 22 PFU/test and it had no cross-reactions with the tested respiratory microbes. Our study shows that the mariPOC can detect infectious individuals already in 20 minutes while clinical sensitivity close to qRT-PCR is achieved in two hours or less. The test targets conserved epitopes of SARS-CoV-2 nucleoprotein, making it robust against strain variations. The new test is a promising and versatile tool for syndromic testing of symptomatic cases and for high capacity infection control screening.

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Clinical Performance of the Xpert® CT/NG Test for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae: A Multicenter Evaluation in Chinese Urban Hospitals

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.784610 ◽

2022 ◽

Vol 11 ◽

Author(s):

Yan Han ◽

Mei-Qin Shi ◽

Qing-Ping Jiang ◽

Wen-Jing Le ◽

Xiao-Lin Qin ◽

...

Keyword(s):

Chlamydia Trachomatis ◽

Neisseria Gonorrhoeae ◽

Sensitivity And Specificity ◽

Clinical Performance ◽

Point Of Care ◽

High Sensitivity ◽

Turnaround Time ◽

Urine Samples ◽

Urban Hospitals ◽

Receive Treatment

BackgroundWe aimed to evaluate the clinical performance of the GeneXpert® (Xpert) CT/NG assay for the detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) using urine and cervical swabs collected from patients in China.MethodsThis study was conducted from September 2016 to September 2018 in three Chinese urban hospitals. The results from the Xpert CT/NG test were compared to those from the Roche cobas® 4800 CT/NG test. Discordant results were confirmed by DNA sequence analysis.ResultsIn this study, 619 first void urine (FVU) specimens and 1,042 cervical swab specimens were included in the final dataset. There were no statistical differences between the results of the two tests for the detection of CT/NG in urine samples (p > 0.05), while a statistical difference was found in cervical swabs (p < 0.05). For CT detection, the sensitivity and specificity of the Xpert test were 100.0% (95%CI = 96.8–99.9) and 98.3% (95%CI = 96.6–99.2) for urine samples and 99.4% (95%CI = 96.5–100.0) and 98.6% (95%CI 97.5–99.2) for cervical swabs, respectively. For NG detection, the sensitivity and specificity of the Xpert test were 99.2% (95%CI = 94.9–100.0) and 100.0% (95%CI = 99.0–100.0) for urine and 100% (95%CI = 92.8–100.0) and 99.7% (95%CI = 99.0–99.9) for cervical swabs, respectively.ConclusionThe Xpert CT/NG test exhibited high sensitivity and specificity in the detection of CT and NG in both urine and cervical samples when compared to the reference results. The 90-min turnaround time for CT and NG detection at the point of care using Xpert may enable patients to receive treatment promptly.

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Value of Electrical Impedance Scanning (EIS) in the Evaluation of BI-RADS™ III/IV/V-Lesions

Technology in Cancer Research & Treatment ◽

10.1177/153303460500400112 ◽

2005 ◽

Vol 4 (1) ◽

pp. 93-97 ◽

Cited By ~ 13

Author(s):

Thomas Diebold ◽

Volkmar Jacobi ◽

Bernhard Scholz ◽

Conny Hensel ◽

Christine Solbach ◽

...

Keyword(s):

Sensitivity And Specificity ◽

Predictive Value ◽

Clinical Performance ◽

False Negative ◽

High Sensitivity ◽

Mucinous Carcinoma ◽

Patient Acceptance ◽

Electrical Impedance Scanning ◽

Movement Artifacts ◽

Development Center

Two hundred and fifty-six (256) patients (72% preoperative, 28% pre-Mammotome) were prospectively examined with EIS using the TS 2000 (TransScan Research and Development Center, Israel; temporarily distributed by Siemens, Erlangen) with the “LOS”-software (level of suspicion). All exams were performed with the targeted scan probe, the observer knowing all clinical and imaging facts. The area of the lesions was examined with EIS at least with 5 single scans. The evaluation included a scaling of lesions from 1 (surely benign) up to 5 (highly suggestive for malignancy) as well as the additional notification of spots. Results of EIS were based upon the automatic scaling which is provided by the software and were compared with mammography and histology. Furthermore the influence of the histology, size of lesions, and presence/absence of spots on the EIS results were analyzed. Histology revealed benign results in 138 lesions and malignant results in 118 lesions (DCIS=61, ID-Ca=51, IL-Ca=5, mucinous Ca=1). Mammography as expected yielded high values with 91% sensitivity and 62% specificity. Overall sensitivity of EIS was 75.4%, specificity 42.03%, negative predictive value 66.7% and positive predictive value 52.7% (89 TP, 58 TN, 80 FP, 29 FN). EIS was false negative in 20 ID-Ca, 3 IL-Ca, 1 IDL-Ca, 4 DCIS, and 1 mucinous carcinoma. Sensitivity and specificity of EIS did not differ for the different histological differentiations neither for the degree of invasion. Also the additional notification of “spots” didn't show a correlation to malignancy. There were significant differences of the sensitivity of EIS regarding the tumor size. While EIS correctly diagnosed 85% of lesions <10 mm in size, only 64% of lesions >10 mm were detected. Most frequent lesion types for false positives were mastopathy (55/80 FP) and fibroadenoma (21/80 FP). Patient acceptance of EIS was perfect and there were no drop outs because of movement artifacts. In conclusion the “LOS”-software clearly improved the clinical performance of the TS 2000 as compared to the initial software. The high sensitivity of EIS in small cancers which was found in our study may indicate an advantage of this method. However, the overall sensitivity and specificity with this setup of EIS is still far too low. Further improvements especially including the measurement of higher frequencies should be realized.

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Designing and Interpreting COVID-19 Diagnostics: Mathematics, Visual Logistics, and Low Prevalence

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2020-0443-sa ◽

2020 ◽

Author(s):

Gerald J. Kost

Keyword(s):

Sensitivity And Specificity ◽

Predictive Value ◽

Clinical Performance ◽

Geometric Mean ◽

High Sensitivity ◽

False Positives ◽

Predictive Values ◽

Minimum Requirements ◽

Sensitivity Specificity ◽

Low Prevalence

ABSTRACT Context. Coronavirus infectious disease-19 (COVID-19) diagnostics require understanding of how predictive values depend on sensitivity, specificity, and especially, low prevalence. Clear expectations, high sensitivity and specificity, and manufacturer disclosure will facilitate excellence of tests. Objectives. To derive mathematical equations for designing and interpreting COVID-19 tests, assess Food and Drug Administration (FDA) Emergency Use Authorization and Health Canada minimum requirements, establish sensitivity and specificity tiers, and enhance clinical performance in low prevalence settings. Design. PubMed and other sources generated articles on COVID-19 testing and prevalence. EndNote X9.1 consolidated references. Mathematica and open access software helped prove equations, perform recursive calculations, graph multivariate relationships, and visualize patterns, including a new relationship, predictive value geometric mean-squared. Results. Derived equations were used to illustrate shortcomings of COVID-19 diagnostics in low prevalence. Visual logistics helped establish sensitivity/specificity tiers. FDA/Canada's 90% sensitivity, 95% specificity minimum requirements generate excessive false positives at low prevalence. False positives exceed true positives at <5.3% prevalence, or if sensitivity is improved to 100% and specificity to 98%, at <2% prevalence. Recursive testing improves predictive value. Three tiers emerged from these results. With 100% sensitivity, physicians can select desired predictive values, then input local prevalence, to determine suitable specificity. Conclusions. Understanding low prevalence impact will help healthcare providers meet COVID-19 needs for effective testing. Laypersons should receive clinical performance disclosure when submitting specimens. Home testing needs to meet the same high standards as other tests. In the long run, it will be more cost-effective to improve COVID-19 POC tests rather than repeat testing multiple times.

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Novel DNA methylation biomarkers show high sensitivity and specificity for blood-based detection of colorectal cancer—a clinical biomarker discovery and validation study

Clinical Epigenetics ◽

10.1186/s13148-019-0757-3 ◽

2019 ◽

Vol 11 (1) ◽

Cited By ~ 11

Author(s):

Sarah Østrup Jensen ◽

Nadia Øgaard ◽

Mai-Britt Worm Ørntoft ◽

Mads Heilskov Rasmussen ◽

Jesper Bertram Bramsen ◽

...

Keyword(s):

Colorectal Cancer ◽

Dna Methylation ◽

Sensitivity And Specificity ◽

Biomarker Discovery ◽

Early Stage ◽

Stage Iv ◽

High Sensitivity ◽

Digital Pcr ◽

Minimal Invasive ◽

Screening Methods

Abstract Background Early detection plays an essential role to reduce colorectal cancer (CRC) mortality. While current screening methods suffer from poor compliance, liquid biopsy-based strategies for cancer detection is rapidly gaining promise. Here, we describe the development of TriMeth, a minimal-invasive blood-based test for detection of early-stage colorectal cancer. The test is based on assessment of three tumour-specific DNA methylation markers in circulating cell-free DNA. Results A thorough multi-step biomarker discovery study based on DNA methylation profiles of more than 5000 tumours and blood cell populations identified CRC-specific DNA methylation markers. The DNA methylation patterns of biomarker candidates were validated by bisulfite sequencing and methylation-specific droplet digital PCR in CRC tumour tissue and peripheral blood leucocytes. The three best performing markers were first applied to plasma from 113 primarily early-stage CRC patients and 87 age- and gender-matched colonoscopy-verified controls. Based on this, the test scoring algorithm was locked, and then TriMeth was validated in an independent cohort comprising 143 CRC patients and 91 controls. Three DNA methylation markers, C9orf50, KCNQ5, and CLIP4, were identified, each capable of discriminating plasma from colorectal cancer patients and healthy individuals (areas under the curve 0.86, 0.91, and 0.88). When combined in the TriMeth test, an average sensitivity of 85% (218/256) was observed (stage I: 80% (33/41), stage II: 85% (121/143), stage III: 89% (49/55), and stage IV: 88% (15/17)) at 99% (176/178) specificity in two independent plasma cohorts. Conclusion TriMeth enables detection of early-stage colorectal cancer with high sensitivity and specificity. The reported results underline the potential utility of DNA methylation-based detection of circulating tumour DNA in the clinical management of colorectal cancer.

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