Investigation of sensitivity, specificity and accuracy of Tetra primer ARMS PCR method in comparison with conventional ARMS PCR, based on sequencing technique outcomes in IVS-II-I genotyping of beta thalassemia patients

In January 2021, the Chilean city of Concepción experienced a second wave of coronavirus 2019 (COVID-19) while in early April 2021, the entire country faced the same situation. This outbreak generated the need to modify and validate a method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in saliva, thereby expanding the capacity and versatility of testing for COVID-19. This study was conducted in February 2021 in the Chilean city of Concepción during which time, the town was under total quarantine. The study participants were mostly symptomatic (87.4%), not hospitalized, and attended care centers because of their health status rather than being asked by the researchers. People coming to the health center in Concepción to be tested for COVID-19 (via reverse transcriptase polymerase chain reaction [RT-PCR]) from a specimen of nasopharyngeal swab (NPS) were then invited to participate in this study. A total of 131 participants agreed to sign an informed consent and to provide saliva and NPS specimens to validate a method in terms of sensitivity, specificity, and statistical analysis of the cycle threshold (Ct) values from the RT-PCR. Calculations pertaining to the 127 participants who were ultimately included in the analysis showed sensitivity and specificity at 94.34% (95% CI: 84.34–98.82%) and 98.65% (95% CI: 92.70–99.97%), respectively. The saliva specimen showed a performance comparable to NPS as demonstrated by the diagnostic parameters. This RT-PCR method from the saliva specimen is a highly sensitive and specific alternative compared to the reference methodology, which uses the NPS specimen. This modified and validated method is intended for use in the in vitro diagnosis of SARS-CoV-2, which provides health authorities in Chile and local laboratories with a real testing alternative to RT-PCR from NPS.

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A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades

10.22541/au.160253855.53010053/v1 ◽

2020 ◽

Author(s):

Md. Tanvir Islam ◽

A. S. M. Alam ◽

Najmuj Sakib ◽

Md. Hasan ◽

Tanay Chakrovarty ◽

...

Keyword(s):

Cost Effective ◽

Arms Pcr ◽

Pcr Method

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Diagnostic Test Validity of MCV for Determination of Thalassaemia Carrier in Bangladesh

Journal of National Institute of Neurosciences Bangladesh ◽

10.3329/jninb.v2i2.34103 ◽

2017 ◽

Vol 2 (2) ◽

pp. 94-97

Author(s):

Nazmul Haque ◽

Narayan Chandra Saha ◽

Mohammad Ekhlasur Rahman ◽

Tahmina Ahmed

Keyword(s):

Diagnostic Test ◽

Test Validity ◽

Area Under The Curve ◽

Thalassemia Major ◽

Cross Sectional Study ◽

Beta Thalassemia ◽

College Hospital ◽

Cross Sectional ◽

Sensitivity Specificity

Background: Mean corpuscular volume (MCV) and mean corpuscular haemoglobin (MCH) of red blood cell is the useful diagnostic test which is performed during routine blood examination.Objective: The purpose of the present study was to measure the diagnostic test validity of MCV for the determination of thalassaemia carrier. Methodology: This analytic cross-sectional study was carried out in the Department of Pediatrics and Department of Medicine at MAG Osmani Medical College Hospital, Sylhet, Bangladesh from September 2007 to January 2009 for a period of one year and five months. Siblings and cousins of beta Thalassemia major and Hb- E -beta Thalassemia satisfying the selection criteria were enrolled. The detailed history and thorough physical examination were done meticulously. Five (5) mL blood was drawn from each case and control for determination of MCV and Hb-Electrophoresis. Result: Total 63 were enrolled as cases and total 65 were enrolled as controls. Sensitivity, specificity, positive and negative predictive value of MCV in determination of thalassemic carriers were 92%, 89.2%, 89.2% and 92% respectively. The area under the curve value was 0.094 (0.035 to 0.152). Conclusion: In conclusion the diagnostic test validity of MCH and MCH is high in determination of Thalassemic carrier. Journal of National Institute of Neurosciences Bangladesh, 2016;2(2): 94-97]

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Association of the Risk of Dental Caries and Polymorphism of MBL2 rs11003125 Gene in Iranian Adults

Caries Research ◽

10.1159/000489572 ◽

2018 ◽

Vol 53 (1) ◽

pp. 60-64 ◽

Cited By ~ 4

Author(s):

Mohammad Javad Mokhtari ◽

Fatemeh Koohpeima ◽

Feyzollah Hashemi-Gorji

Keyword(s):

Dental Caries ◽

Control Group ◽

Amplification Refractory Mutation System ◽

Fars Province ◽

Arms Pcr ◽

Genotype Frequencies ◽

Mutation System ◽

Pcr Method ◽

Larger Sample ◽

Control Study

This case-control study aimed to investigate the effect of rs11003125 in dental caries. For this purpose, a total number of 404 individuals – from Fars Province in Iran – were studied. The technique of this research was the tetra-primer amplification-refractory mutation system (ARMS)-PCR. Dental caries prevalence among the 404 individuals was assessed by counting the number of decayed, missing, and filled teeth. In this research, individuals were divided into two groups: cases (n = 238) and controls (n = 166), and the peripheral blood samples were used to extract the genomic DNA. For genotyping of DNA, the tetra-primer ARMS-PCR method was conducted using specific primer pairs. While examining MBL2 rs11003125 polymorphism, we found significant differences in the genotype frequencies between the case and the control group. The pooled estimates indicated that the GG and GC genotypes of MBL2 rs11003125 polymorphism significantly increased, and therefore caries risk (OR = 2.40, 95% CI = 1.31–4.40, p = 0.004) under the dominant model. These findings suggested that polymorphism in MBL2 gene was associated with dental caries in Iranian adults. Further verification is needed with more ethnic groups and larger sample sizes to determine whether rs11003125 polymorphism is related to dental caries in other regions or not.

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Threshold value of the anti-HCV test in the diagnosis of HCV infection

The Journal of Infection in Developing Countries ◽

10.3855/jidc.11657 ◽

2019 ◽

Vol 13 (10) ◽

pp. 914-919

Author(s):

Özlem Kirişci ◽

Ahmet Calıskan

Keyword(s):

Roc Analysis ◽

Threshold Value ◽

Hcv Infection ◽

Nucleic Acid Amplification ◽

High Rate ◽

Hcv Rna ◽

Serum Samples ◽

Predictive Values ◽

Pcr Method ◽

Sensitivity Specificity

Introduction: In the diagnosis of hepatitis C virus (HCV) infection, the first step is screening for anti-HCV antibodies, and positive results are generally confirmed with nucleic acid amplification tests. Recent studies have reported that more compatible results have been obtained with the HCV RNA test using signal to cut-off (S/Co) values >1, which are the routine reactivity threshold for the anti-HCV enzyme immunoassay (EIA) test. The aim of this study was to determine the most appropriate S/Co value for the anti-HCV test, predicting HCV infection. Methodology: Comparisons were made between results of 559 patients who underwent anti-HCV with ECLIA method and HCV RNA tests with real-time polymerase chain reaction (PCR) method. By accepting the HCV-RNA test as the gold standard for HCV infection, the sensitivity, specificity and predictive values of the ECLIA test were determined and statistical “receiver operating characteristic” (ROC) analysis was applied to determine the most appropriate threshold. Results: Between January 2013 and April 2018, a total of 81,203 serum samples were examined. Of 559 anti-HCV positive patients, HCV RNA positivity was determined in 214 (38.2 %). According to the ROC analysis results, the most appropriate S/Co value was determined as 12.27, at which sensitivity was 94.4 %, and specificity 97.4 %. The positive and negative predictive values were calculated at the high rate of 95.7% and 96.6% respectively. Conclusions: The results of this study investigating the anti-HCV reactivity values which could be used in the diagnosis of HCV infection determined the most appropriate value to be 12.27.

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