scholarly journals Evaluation of Bias in Diagnostic-Test Sensitivity and Specificity Estimates Computed by Discrepant Analysis

1998 ◽  
Vol 36 (2) ◽  
pp. 375-381 ◽  
Author(s):  
Timothy A. Green ◽  
Carolyn M. Black ◽  
Robert E. Johnson
Keyword(s):  
Cell Culture ◽  
Nucleic Acid ◽  
Diagnostic Test ◽  
Sensitivity And Specificity ◽  
Nucleic Acid Amplification ◽  
Reference Test ◽  
Test Sensitivity ◽  
Test Specificity ◽  
Positive Results

When a new diagnostic test is potentially more sensitive than the reference test used to classify persons as infected or uninfected, a substantial number of specimens from infected persons may be reference-test negative but new-test positive. Discrepant analysis involves the performance of one or more additional tests with these specimens, reclassification as infected those persons for whom the new-test-positive results are confirmed, and recalculation of the estimates of new-test sensitivity and specificity by using the revised classification. This approach has been criticized because of the bias introduced by the selective use of confirmation testing. Under conditions appropriate for evaluating a nucleic acid amplification (NAA) test for Chlamydia trachomatis infection with cell culture as the reference test, we compared the bias in estimates based on the discrepant-analysis classification of persons as infected or uninfected with that in estimates based on the culture classification. We concluded that the bias in estimates of NAA-test specificity based on discrepant analysis is small and generally less than that in estimates based on culture. However, the accuracy of discrepant-analysis-based estimates of NAA-test sensitivity depends critically on whether culture specificity is equal to or is slightly less than 100%, and it is affected by competing biases that are not fully taken into account by discrepant analysis.

scholarly journals Evaluation of Fast Molecular Detection of Lymph Node Metastases in Prostate Cancer Patients Using One-Step Nucleic Acid Amplification (OSNA)

Cancers ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 1117
Author(s):  
Svenja Engels ◽  
Lutz Brautmeier ◽  
Lena Reinhardt ◽  
Clara Wasylow ◽  
Friederike Hasselmann ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Nucleic Acid ◽  
Sensitivity And Specificity ◽  
Nucleic Acid Amplification ◽  
Cytokeratin 19 ◽  
High Concordance ◽  
One Step ◽  
Node Metastases ◽  
Positive Results ◽  
Level Of Agreement

Background: In clinical routine, only fractions of lymph nodes (LNs) are examined histopathologically, often resulting in missed (micro-)metastases and incorrect staging of prostate cancer (PCa). One-step nucleic acid amplification (OSNA) analyzes the entire LN by detecting cytokeratin 19 (CK19) mRNA as a surrogate for LN metastases requiring less effort than conventional biomolecular techniques. We aimed to evaluate performance of OSNA in detecting sentinel LN (SLN) metastases in PCa. Methods: SLNs (n = 534) of 64 intermediate- or high-risk PCa patients undergoing radical prostatectomy with extended and sentinel-guided lymphadenectomy were cut into slices and alternatingly assigned to OSNA and histopathology (hematoxylin-eosin staining, CK19, and CK AE1/AE3 immunohistochemistry). Sensitivity and specificity of OSNA and concordance and measure of agreement (Cohen’s kappa (κ)) between OSNA and histopathology were assessed. Results: Histopathology revealed metastases in 76 SLNs. Sensitivity and specificity of OSNA were 84.2% and 96.1%, respectively. Discordant results were recorded for 30 of 534 SLNs, revealing high concordance (94.4%). Twenty-four discordant cases were classified as micrometastases, indicating a possible allocation bias. In 18 cases, positive results were conferred only by OSNA resulting in seven LN-positive patients who were missed by histopathology. Overall, the level of agreement was high (κ = 0.78). Conclusions: OSNA provided a diagnosis that was as least as accurate as detailed histological examination and might improve LN staging in PCa.

scholarly journals Observed Differences in Diagnostic Test Accuracy between Patient Subgroups: Is It Real or Due to Reference Standard Misclassification?

2007 ◽  
Vol 53 (10) ◽  
pp. 1725-1729 ◽  
Author(s):  
Corné Biesheuvel ◽  
Les Irwig ◽  
Patrick Bossuyt
Keyword(s):  
Clinical Practice ◽  
Diagnostic Test ◽  
Sensitivity And Specificity ◽  
Diagnostic Test Accuracy ◽  
Test Accuracy ◽  
Reference Standard ◽  
Target Condition ◽  
Test Sensitivity ◽  
The Past ◽  
Patient Subgroups

Abstract Before a new test is introduced in clinical practice, its accuracy should be assessed. In the past decade, researchers have put an increased emphasis on exploring differences in test sensitivity and specificity between patient subgroups. If the reference standard is imperfect and the prevalence of the target condition differs among subgroups, apparent differences in test sensitivity and specificity between subgroups may be caused by reference standard misclassification. We provide guidance on how to determine whether observed differences may be explained by reference standard misclassification. Such misclassification may be ascertained by examining how the apparent sensitivity and specificity change with the prevalence of the target condition in the subgroups.

scholarly journals Comparative performance and cycle threshold values of 10 nucleic acid amplification tests for SARS-CoV-2 on clinical samples

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252757
Author(s):  
Miyuki Mizoguchi ◽  
Sohei Harada ◽  
Koh Okamoto ◽  
Yoshimi Higurashi ◽  
Mahoko Ikeda ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Diagnostic Performance ◽  
Nucleic Acid Amplification ◽  
Clinical Samples ◽  
Nucleic Acid Amplification Tests ◽  
Cycle Threshold ◽  
E Gene ◽  
Viral Copy Number ◽  
Gene Test ◽  
Positive Results

Background A number of nucleic acid amplification tests (NAATs) for SARS-CoV-2 with different reagents have been approved for clinical use in Japan. These include research kits approved under emergency use authorization through simplified process to stabilize the supply of the reagents. Although these research kits have been increasingly used in clinical practice, limited data is available for the diagnostic performance in clinical settings. Methods We compared sensitivity, specificity, and cycle threshold (Ct) values obtained by NAATs using 10 kits approved in Japan including eight kits those receiving emergency use authorization using 69 frozen-stored clinical samples including 23 positive samples with various Ct values and 46 negative samples. Results Viral copy number of the frozen-stored samples determined with LightMix E-gene test ranged from 0.6 to 84521.1 copies/μL. While no false-positive results were obtained by any of these tests (specificity: 100% [95% CI, 88.9%-100%]), sensitivity of the nine tests ranged from 68.2% [95% CI, 45.1%-86.1%] to 95.5% [95% CI, 77.2%-99.9%] using LightMix E-gene test as the gold standard. All tests showed positive results for all samples with ≥100 copies/μL. Significant difference of Ct values even among tests amplifying the same genetic region (N1-CDC, N2) was also observed. Conclusion Difference in the diagnostic performance was observed among NAATs approved in Japan. Regarding diagnostic kits for emerging infectious diseases, a system is needed to ensure both rapidity of reagent supply and accuracy of diagnosis. Ct values, which are sometimes regarded as a marker of infectivity, are not interchangeable when obtained by different assays.

Development of a Molecular Method for the Detection of Enteric Viruses in Oysters

1995 ◽  
Vol 58 (12) ◽  
pp. 1357-1362 ◽  
Author(s):  
LEE-ANN JAYKUS ◽  
RICARDO DE LEON ◽  
MARK D. SOBSEY
Keyword(s):  
Cell Culture ◽  
Nucleic Acid ◽  
Hepatitis A Virus ◽  
Enteric Virus ◽  
Nucleic Acid Amplification ◽  
Detection Methods ◽  
Ammonium Bromide ◽  
Rt Pcr ◽  
Initial Inoculum ◽  
Ctab Precipitation

Detection of enteric virus contamination of shellfish is limited by current methodology, which is time-consuming, tedious, and lacking in sensitivity due to reliance on cell culture infectivity. Alternative detection methods based on nucleic acid amplification have been hampered by high sample volumes and the presence of enzymatic inhibitors. The goal of this study was to develop methods to purify and concentrate intact virions from oyster extracts to a volume and quality compatible with viral genomic nucleic acid amplification by reverse transcriptase-polymerase chain reaction (RT-PCR). Fifty-gram oyster samples were homogenized and processed by standard adsorption-elution precipitation methodology and then seeded with 105 PFU of poliovirus 1 (PV1) or hepatitis A virus (HAV). Seeded viruses were concentrated by fluorocarbon extraction, polyethylene glycol (PEG) precipitation, chloroform extraction, and cetyltrimethyl ammonium bromide (CTAB) precipitation to a volume of 100 μl with removal of RT-PCR inhibitors. Virus recovery after elution of PEG precipitates was 50% for PVI and IS to 20% for HAV as evaluted by cell culture infectivity. The CTAB precipitation step yielded a concentrated sample which was directly compatible with RT-PCR reactions and capable of detecting about 100 placque=forming units (PFU) of PVl or HAV. When 50-g oyster extracts were seeded and processed by the entire concentration and purification scheme, direct RT-PCR detection of viral genomic RNA was possible at initial inoculum levels of 104 PFU of HAV and 103 PFU of PV1, with recoveries of 1 to 5% of seeded viruses.

scholarly journals Keeping up with new technology: new approaches to diagnosis of Chlamydia infection

1996 ◽  
Vol 42 (5) ◽  
pp. 809-812 ◽  
Author(s):  
W D LeBar
Keyword(s):  
Cell Culture ◽  
Nucleic Acid ◽  
Clinical Utility ◽  
New Technology ◽  
Nucleic Acid Amplification ◽  
Chlamydia Infection ◽  
Chain Reaction ◽  
Sexually Transmitted ◽  
The Us ◽  
Infected Sample

Abstract Chlamydia trachomatis infections are among the most common sexually transmitted infections in the US today. One of the keys to the prevention of C. trachomatis infection rests on the ability to make this diagnosis on the basis of accurate laboratory testing. For many years the standard for diagnosis of C. trachomatis infections has been isolation in tissue culture. Numerous nonculture methods, including enzyme immunoassay, have been used as an alternative to cell culture. The performance characteristics of these tests have all been compared with a standard, cell culture, which at best will detect 90% of positive specimens. Nucleic acid amplification techniques, including PCR and ligase chain reaction, have been recently introduced. The advantage of these tests is their ability to detect 10-20% more positive specimens when compared with culture or confirmed nonculture methods performed with a single specimen. The sensitivity of amplified tests also allows us to test specimens from multiple sites (endocervix, urethra, urine), which expands our standard from an infected sample to detection of an infected patient. Tests based on amplified nucleic acid technology have greatly improved our ability to diagnose urogenital C. trachomatis infection. The use of an expanded standard will help us accurately define the true performance and clinical utility of nonculture Chlamydia diagnostic tests.

scholarly journals Use of Microfluidic Assays to Develop Reliable and Economic Nucleic Acid Application Technologies, Employing MicroRNAs for the Diagnostic Screening of Colon Cancer in Human Stool in Low-Resource Settings

2020 ◽  
Vol 5 (4) ◽  
pp. 1-29
Author(s):  
Farid E. Ahmed ◽  
Mostafa M. Gouda ◽  
Nancy C. Ahmed
Keyword(s):  
Colon Cancer ◽  
Nucleic Acid ◽  
Sensitivity And Specificity ◽  
Rolling Circle Amplification ◽  
Nucleic Acid Amplification ◽  
Performance Criteria ◽  
Quantitative Detection ◽  
Diagnostic Screening ◽  
Low Resource ◽  
Microfluidic Technology

Isolation methods that employ readily-available inexpensive supplies on the open market, which are reliable, as well as economical, such as nucleic acid amplification techniques (NAAT) based on microfluidic technology in low-resource research settings (LRRS) that meets the ASSURED guidelines are essential to develop a noninvasive diagnostic colon cancer screen in stool using micro(mi)RNA molecules. A combination of a microfluidic-based MiRNA stool test with a reliable rolling circle amplification/detection method applied to the quantification of miRNA molecules, result in an affordable sensitive and specific isothermal method for the noninvasive quantitative detection of miRNAs in LRRS. Scientists and engineers have become interested in miRNAs, and they have intensified their efforts to apply emerging simple detection tools to the important bioanalytical challenge of quantifying these small 18-26 nt long molecules. Some of the proposed approaches incorporate novel material, such as simple centrifuges and methods based on microfluidic technology, while others utilize the interesting biological properties of these molecules, such as forming branched RCA structures, allowing for the detection of these biomarker molecules at an attomolar "aM" concentration level, using low cost extraction and isothermal amplification methods in LRRS. We have been interested in studying colorectal cancer (CRC) because it is the 3rd most common malignancy worldwide, and stool can be obtained noninvasively from the patients. We have focused in this research on colon cancer (CC) because it is more common in the USA than rectal cancer (RC). The innovation of our approach lies in the exploratory use of an affordable, quantitative miRNA profiling in noninvasive stool samples in LRRS, whose extracted fragile total RNA is stabilized shortly after excretion from stool by commercially available kits, so it does not ever fragment, followed by quantitative standardized analytical tests that are neither labor intensive, nor require expensive instrumentation, in order to develop apanel of novel miRNA genes for the noninvasive diagnostic screening of early left and right sporadic colon cancers, more economically, and with higher sensitivity and specificity than any other colon cancer screening test currently available on the market. To show the clinical sensitivity and specificity of the proposed quantitative miRNA test using simple methodologies in LRRS,the miRNA results are to be correlated with FOBT, colonoscopy, and pathology data. Standardization establishes test’s performance criteria (sample selection, optimal sample running conditions, preservation and storage), in order to ensure that the assay will perform the same way in any laboratory, by any trained personnel, anywhere in low-resource laboratory settings worldwide.

Sign in / Sign up

Export Citation Format

Share Document