Analytical Specificity Research Articles

Performance evaluation of the SMG HHV-6 Q Real-Time PCR Kit for quantitative detection and differentiation of human herpesvirus 6A and 6B.

The aim of this study was to compare the performance of the newly developed SMG HHV-6 Q Real-Time PCR Kit (SMG assay) with the RealStar HHV-6 PCR Kit (RealStar assay). The analytical sensitivity and specificity, linearity, and precision of the SMG assay were evaluated. The clinical performance of the SMG assay was assessed and compared with that of the RealStar assay using 207 clinical specimens (HHV-6A positive, n = 51; HHV-6B positive, n = 64; HHV-6A/B negative, n = 92). The limit of detection of the SMG assay was 2.92 log10 copies/mL for HHV-6A DNA and 2.88 log10 copies/mL for HHV-6B DNA. The linear range was determined to be 3.40-9.00 log10 copies/mL for both viruses. Intra- and inter-assay variability were below 5% at concentrations ranging from 4 to 9 log10 copies/mL. No cross-reactivity was observed with the 25 microorganisms included in the specificity panel. The clinical sensitivity and specificity of the SMG and RealStar assays compared to in-house polymerase chain reaction and sequencing were as follows: SMG assay, 98.0% and 100% for HHV-6A DNA, respectively, and 96.9% and 100% for HHV-6B DNA, respectively; RealStar assay, 98.0% and 100% for HHV-6A DNA, respectively, and 90.6% and 100% for HHV-6B DNA, respectively. The correlation coefficients between viral loads measured by the two assays were 0.948 and 0.975, with mean differences of 0.62 and 0.32 log10 copies/mL for HHV-6A and HHV-6B DNA, respectively. These results demonstrate that the SMG assay is a sensitive and reliable tool for the quantitative detection and differentiation of HHV-6A and HHV-6B DNA.IMPORTANCEQuantitative real-time PCR (qPCR) that can distinguish between HHV-6A and HHV-6B DNA is recommended for diagnosis of active infection. The SMG HHV-6 Q Real-Time PCR Kit (SMG assay) is a newly developed qPCR assay that can differentiate between HHV-6A and HHV-6B DNA; however, little is known about its performance. In this study, we assessed the performance of the SMG assay and compared it with that of a commercially available qPCR assay, the RealStar HHV-6 PCR Kit (RealStar assay). The SMG assay demonstrated excellent analytical sensitivity and specificity, precision, and linearity. Furthermore, the viral loads measured by the SMG assay were highly correlated with those measured by the RealStar assay. Our results suggest that the SMG assay is a useful diagnostic tool for quantitative detection and differentiation of HHV-6A and HHV-6B DNA.

Analytical Validation of a Telomerase Reverse Transcriptase (TERT) Promoter Mutation Assay.

Telomerase reverse transcriptase (TERT) promoter-mutated thyroid cancers are associated with a decreased rate of disease-free and disease-specific survival. High-quality analytical validation of a diagnostic test promotes confidence in the results that inform clinical decision-making. This work aimed to demonstrate the analytical validation of the Afirma TERT promoter mutation assay. TERT promoter C228T and C250T variant detection in genomic DNA (gDNA) was analyzed by assessing variable DNA input and the limit of detection (LOD) of variant allele frequency (VAF). The negative and positive percentage agreement (NPA and PPA) of the Afirma TERT test was examined against a reference primer pair as was the analytical specificity from potential interfering substances (RNA and blood gDNA). Further, the intrarun, interrun, and interlaboratory reproducibility of the assay were tested. The Afirma TERT test is tolerant to variation in DNA input amount (7-13 ng) and can detect expected positive TERT promoter variants down to 5% VAF LOD at 7 ng DNA input with greater than 95% sensitivity. Both NPA and PPA were 100% against the reference primer pair. The test remains accurate in the presence of 20% RNA or 80% blood gDNA for an average patient sample that typically has 30% VAF. The test also demonstrated a 100% confirmation rate when compared with an external next-generation sequencing-based reference assay executed in a non-Veracyte laboratory. The analytical robustness and reproducibility of the Afirma TERT test support its routine clinical use among thyroid nodules with indeterminate cytology that are Afirma Genomic Sequencing Classifier suspicious or among Bethesda V/VI nodules.

Validation of a real-time polymerase chain reaction for the detection and quantification of the nucleic acid of Histoplasma from equine clinical samples.

Histoplasmosis is a neglected yet major cause of morbidity and mortality in both equids and people in resource-scarce settings. One of the major hindrances to the control of histoplasmosis is a lack of readily available diagnostic tests. Tests are needed to support clinical decision-making and to be applied in population-based research to further understand this disease in situ. This paper reports, for the first time, the validation and application of a qPCR to detect Histoplasma directly from equine clinical samples, bypassing the need to culture this notoriously difficult organism. We report and comment on the performance of the qPCR in comparison with our previously developed nested PCR.

Detection of PSMA expression on circulating tumor cells by blood-based liquid biopsy in prostate cancer.

For patients with mCRPC, PSMA-targeted radioligand treatment has significantly improved the clinical outcome. A blood-based liquid biopsy assay for recognizing PSMA protein expression on circulating tumor cells may be beneficial for better informing therapeutic decision-making and identifying the patients most likely to benefit from PSMA-targeted radioligand therapy. Using high-throughput imaging and digital AI pathology algorithms, a four-color immunofluorescence assay has been developed to find PSMA protein expression on CTCs on a glass slide. Cell line cells (LNCaP/PC3s/22Rv1) spiked into healthy donor blood were used to study the precision, specificity, sensitivity, limit of detection, and overall accuracy of the assay. Clinical validation and low-pass whole-genome sequencing were performed in PSMA-PET-positive patients with high-risk mCRPC (N = 24) utilizing 3 mL of blood. The PSMA CTC IF assay achieved analytical specificity, sensitivity, and overall accuracy above 99% with high precision. In the clinical validation, 76% (16/21) of the cases were PSMA positive with CTC heterogeneity, and 88% (21/24) of the patients contained at least one conventional CTC per milliliter of blood. Thirty-six low-pass-sequenced CTCs from 11 individuals with mCRPC frequently exhibited copy number increases in AR and MYC and losses in RB1, PTEN, TP53, and BRCA2 locus. The analytical validation utilizing Epic Sciences' liquid biopsy CTC platform demonstrated the potential to detect PSMA protein expression in CTCs from patients with mCRPC. This assay is positioned as an effective research tool to evaluate PSMA expression, heterogeneity, and therapeutic response in many ongoing clinical studies to target tumors that express PSMA.

Development and analytical characteristics of a quantitative real-time PCR assay for detection of spheniscid alphaherpesvirus 1 in penguins.

Herpesviruses are associated with disease in many penguin species. Herpesvirus-associated lesions can cause significant morbidity and mortality in penguins and have been identified in African penguins (Spheniscus demersus), Humboldt penguins (Spheniscus humboldti), and a little blue penguin (Eudyptula minor) infected with spheniscid alphaherpesvirus 1 (SpAHV1). Further investigation is necessary to understand the impact of herpesviruses on penguin health, but there are no rapid, sensitive, and specific methods for detecting and quantifying herpesviral load. We therefore developed a quantitative real-time PCR (qPCR) assay for the detection of SpAHV1 in penguins. TaqMan primer-probes targeting the DNA polymerase gene were designed using a commercial software program. Inter- and intra-assay variability, dynamic range, limit of detection, and analytical specificity were assessed. We used our assay to analyze previously collected field samples from Punta San Juan, Peru, in which conventional consensus PCR had detected one SpAHV1-positive penguin sample. Our qPCR assay was highly specific for SpAHV1. It had a dynamic range of 107-101 target copies per reaction and performed with high efficiency and low intra- and inter-assay variability. Reaction efficiency was not impacted by penguin DNA from SpAHV1-negative tracheal swabs. We detected an additional field sample as positive with our newly developed qPCR assay, and although this likely represents detection of another infected penguin, the true disease status of this population is currently uncharacterized given that no gold-standard test exists for SpAHV1. Our qPCR assay may provide a valuable tool in the surveillance and characterization of SpAHV1 in penguins.

Rapid Isothermal Detection of Pathogenic Clostridioides difficile Using Recombinase Polymerase Amplification.

Nosocomial-associated diarrhea due to Clostridioides difficile infection (CDI) is diagnosed after sample precultivation by the detection of the toxins in enzyme immunoassays or via toxin gene nucleic acid amplification. Rapid and direct diagnosis is important for targeted treatment to prevent severe cases and recurrence. We developed two singleplex and a one-pot duplex fluorescent 15 min isothermal recombinase polymerase amplification (RPA) assays targeting the toxin genes A and B (tcdA and tcdB). Furthermore, we adapted the singleplex RPA to a 3D-printed microreactor device. Analytical sensitivity was determined using a DNA standard and DNA extracts of 20 C. difficile strains with different toxinotypes. Nineteen clostridial and gastrointestinal bacteria strains were used to determine analytical specificity. Adaptation of singleplex assays to duplex assays in a 50 μL volume required optimized primer and probe concentrations. A volume reduction by one-fourth (12.4 μL) was established for the 3D-printed microreactor. Mixing of RPA was confirmed as essential for optimal analytical sensitivity. Detection limits (LOD) ranging from 119 to 1411 DNA molecules detected were similar in the duplex tube format and in the singleplex 3D-printed microreactor format. The duplex RPA allows the simultaneous detection of both toxins important for the timely and reliable diagnosis of CDI. The 3D-printed reaction chamber can be developed into a microfluidic lab-on-a-chip system use at the point of care.

Analytical Validation of a 37-Gene Next-Generation Sequencing Panel for Myeloid Malignancies and Review of Initial Findings Incorporating Updated 2022 Diagnostic and Prognostic Guidelines

Myeloid neoplasms are clonal disorders that arise via acquisition of genetic mutations leading to excessive proliferation and defective differentiation. Mutational profiling is vital as it has implications on diagnosis, prognosis, and therapeutic decision making. Next generation sequencing (NGS) has become a mainstay in the evaluation of myeloid malignancies, as it enables efficient characterisation of multiple genetic changes. Herein the analytical validation of the 37-gene Archer VariantPlex Core Myeloid panel is reported, using 58 DNA specimens with 87 single nucleotide variants (SNV) and 23 insertions/deletions (INDEL). The panel achieved good depth of coverage, 100% analytical sensitivity and specificity for SNV and INDELs ≤21bp, and 100% reproducibility, with a reportable limit of detection determined as 5%. The Archer NGS panel can accurately and reproducibly detect variants of clinical significance in myeloid neoplasms.A retrospective analysis of 535 clinical specimens tested with the Archer NGS panel showed a frequency and pattern of mutations across myeloid malignancies that were similar to other published studies. A review of the diagnostic classification of patients with acute myeloid leukaemia and myelodysplastic syndrome using the World Health Organisation 2017/2022 and International Consensus Classification 2022 guidelines, in addition to European LeukemiaNet 2017/2022 risk stratification of AML patients, was also performed to assess the utility of the molecular information provided by the Archer NGS panel.

Rapid detection of porcine sapelovirus by reverse transcription recombinase polymerase amplification assay.

Porcine Sapelovirus (PSV) infection has been confirmed in pigs worldwide, mostly asymptomatic, but in some cases, it can lead to significant issues in the gastrointestinal, respiratory, neurological, or reproductive systems. PSV is considered an emerging pathogen of porcine species. Recombinase polymerase amplification (RPA) is a simple and fast isothermal technique that uses three enzymes for amplification without the use of any sophisticated equipment. The reverse transcription recombinase polymerase amplification (RT-RPA) assay was developed and optimized for field based detection of PSV. The assay was developed by targeting 5´UTR region of PSV genome and optimized for reaction time, temperature, primer and MgOAc concentration. The analytical sensitivity and specificity of assay was determined. The assay was evaluated on 85 porcine faecal samples collected from field. In addition to conventional format, this assay was also optimized for visual dye-based detection format and lateral flow strips based detection (in combination with probe). The developed assay works at constant temperature of 35°C for 20min with forward primer concentration 20pm, reverse primer concentration 10pm and MgOAc concentration of 14mM. This assay is highly sensitive and detects up to 28 copies of viral nucleic acid both in the conventional as well as in fluorescent dye based detection format. Using the newly developed assay 21 samples out of 85 samples were found positive, showing positivity rate of 24.7%. The positivity rate of RT-RPA assay corroborated with the gold standard RT-PCR test. This study presented the development of an RT-RPA isothermal assay for rapid and accurate detection of PSV. The assay is highly sensitive, specific, works at a low and constant temperature, does not require any high-end instrument and can be a potential diagnostics tool for pen-side testing of PSV in the field conditions. The newly developed RT-RPA assay could successfully detect PSV circulating in swine population of Haryana, India. This is a first report of this kind from the region.

Identification of the ambrosia beetle Xyleborinus saxesenii (Ratzeburg, 1837) (Coleoptera: Curculionidae: Scolytinae) from frass and adult DNA by TaqMan Probe real‐time‐PCR

AbstractA molecular tool has been set up for the unambiguous molecular identification of the ambrosia beetle, Xyleborinus saxesenii (Ratzeburg, 1837) (Coleoptera Curculionidae Scolytinae), the cosmopolitan fruit‐tree pinhole borer, widely distributed in temperate regions of the five continents, where it infests a wide range of hardwoods and softwoods. The test was based on real‐time PCR with TaqMan probe technology and was developed on whole insect bodies (adults) as well as on frass produced by the beetle. The test was shown to meet the criteria established by EPPO for the harmonization of molecular diagnostic methods. In particular, the test gave good results in terms of analytical specificity (inclusivity and exclusivity) and analytical sensitivity, and was fully repeatable and reproducible. Since X. saxesenii is one of the most commonly intercepted ambrosia beetles during phytosanitary controls worldwide, this practical diagnostic tool will be useful for its rapid identification of the beetle in biological material (frass, body fragments). The test can be useful in countries where X. saxesenii is a quarantine species, as well as in the EPPO region.

Development and application of an ultra-sensitive ctDNA mutation profiling assay in monitoring therapy response and drug resistance.

264 Background: Next-generation sequencing (NGS) assays offer efficient high-throughput profiling methods for analyzing circulating tumor DNA (ctDNA) in blood or other liquid biopsy specimens. The ctDNA mutant allele fractions of patients after treatment is often very low and below the detection limit of regular cfDNA assays. Here we report the development and clinical application of a CLIA-certified ultra-sensitive NGS cfDNA assay in detecting the low-frequency ctDNA mutations and monitoring therapy response and drug resistance in patients with metastatic gastroesophageal adenocarcinoma under combined blockade treatments. Methods: PredicineCARE ULTRA cfDNA assay with 100,000X sequencing depth was validated under CLIA settings. Limit of blank (LoB) and limit of detection (LoD) were established by profiling 38 healthy donor plasma samples, 23 contrived human cfDNAs samples from patients with various cancers, and 30 replicates of well-established ctDNA reference standards. In silico down-sampling of FASTQ files was carried out to test the sensitivity of this assay with a lower coverage (50,000X). This assay was then adopted for longitudinal sequencing of 57 serial plasmas from 6 patients with HER2+ gastroesophageal adenocarcinomas (GEC) who underwent combined treatments (capecitabine, oxaliplatin, bevacizumab and trastuzumab) at different time points (baseline, response, and progression). Results: PredicineCARE ULTRA cfDNA assay exhibited exceptional sensitivity in calling single-nucleotide variants and indels, with a 98.0% detection rate at a LoD of 0.075% mutant allele frequency (MAF) for 60 ng cfDNA. This is significantly lower than the LoD (0.25% MAF) of a standard PredicineCARE cfDNA assay. The ultra-sensitive assay also displayed decent analytical specificity (>99.99%) and precision (intra-assay 100%; inter-assay 99.41%). In 6 GEC patients’ longitudinal samples, PredicineCARE ULTRA cfDNA assay detected 36 additional somatic mutations with the MAFs spanning in a range from 0.024% to 0.1% beyond 124 baseline mutations identified using standard PredicineCARE. In two representative cases presented here, all baseline mutations (genes TP53 and PIK3CA etc.) were consistently reported in the follow-up time points with a noticeable MAF reduction (lowest MAFs from 0.046% to 0.024%) during response. Subsequent elevations were observed in more genes, including low-frequency mutations (KRAS and ERBB2) not detected at baseline or only detected in PredicineCARE ULTRA. Conclusions: This study demonstrated the promise and clinical utility of the ultra-sensitive cfDNA molecular profiling at 100,000X sequencing depth in treatment selection, therapy monitoring, and drug resistance studies.

Diagnostic Tool for the Identification of Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) Using Real-Time PCR.

Accurate identification of Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), commonly known as the Oriental fruit fly, is a significant challenge due to the morphological convergence and taxonomic uncertainties of species belonging to the same genus. This highly polyphagous species poses a significant threat to fruit crops. With its potential establishment in Europe becoming a growing concern, there is an urgent need for rapid and efficient diagnostic methods. The study presented here introduces a diagnostic protocol based on real-time PCR using a TaqMan probe for the early and reproducible identification of B. dorsalis. Specimens representing the genetic diversity of the Italian population were collected and analyzed. Specific primers and probe were designed based on the conserved regions and an in silico analysis confirmed their specificity. The assay conditions were optimized, and analytical sensitivity, specificity, repeatability, and reproducibility were evaluated. The protocol showed high sensitivity and specificity, accurately detecting low DNA concentrations of B. dorsalis. This standardized method provides a reliable tool for routine diagnostics, enhancing the accuracy and efficiency of identifying the Oriental fruit fly at all stages of its development, thereby facilitating effective pest management measures. The development of this diagnostic protocol is crucial for monitoring and supporting efforts to prevent the passive spread of B. dorsalis in Europe, particularly in light of the recent active infestations detected in Italy.

Development and accuracy evaluation of a new loop-mediated isothermal amplification assay targeting the HSP70 gene for the diagnosis of cutaneous leishmaniasis.

Cutaneous leishmaniasis (CL) is a global public health problem caused by species on the genus Leishmania and is the most prevalent clinical form of leishmaniasis. The aim of this study was to develop a new LAMP assay for Leishmania sp. based on HSP70 gene and evaluate it clinically for molecular diagnosis of CL. The study was carried out in the following stages: i) design of primers based on HSP70 gene of Leishmania sp.; ii) evaluation of detection limit and analytical specificity; iii) estimation of the accuracy of LAMP-Leish/HSP70 assay for diagnosing CL. A total of 100 skin biopsy samples from patients, comprising 60 CL cases and 40 non-cases, were analyzed in this study. One LAMP assay using HSP70 gene as molecular target were standardized, and the observed detection limit was 100fg of L. braziliensis purified DNA. The LAMP-Leish/HSP70 assay was specific for Leishmania spp. The LAMP-Leish/HSP70 assay showed an accuracy of 92%, and positivity rates were not affected by lesion onset time or parasite load. This novel LAMP assay targeting the HSP70 gene of Leishmania sp. has the potential to be a useful tool to integrate into routine diagnosis for suspected cases of CL.

Avaliação do desempenho analítico de um teste imunocromatográfico rápido para o diagnóstico da brucelose bovina baseado em uma proteína recombinante BP26

ABSTRACT Brucellosis is an important bacterial disease of global distribution with zoonotic potencial. Serological tests used in Brazil for diagnosis of bovine brucellosis, including the Rose Bengal test (RBT), 2-mercaptoethanol (2-ME), fluorescent polarization (FPA), and complement fixation (FC), are based on the smooth lipopolysaccharide antigen (S-LPS) of Brucella abortus. The aim of this study was to evaluate a recombinant BP26 protein used as antigen in a rapid lateral flow immunochromatographic assay (rBP26-LFIA) for serological diagnosis of bovine brucellosis. Analytical performance of rBP26-LFIA was evaluated in positive and negative bovine serum samples previously characterized by RBT and 2-ME. Estimates of analytical sensitivity and specificity were 73.91% and 97.14%, respectively. Bovine sera reactive to Neospora, Trypanosoma vivax or Leptospira were used to assess specificity because these diseases are commonly associated with abortion in cattle. In addition to a possible cross-reaction induced by commercial vaccines against Leptospira in serological tests for bovine brucellosis using S-LPS as an antigen. In conclusion, rBP26-LFIA, with its current standardization, had good analytical performance. However, a future evaluation of diagnostic performance by rBP26-LFIA with samples from regions with known prevalence is necessary for its recommendation for use in the Brazilian program for the control and eradication of bovine brucellosis.

Basics of Method Evaluation in Clinical Laboratory Testing: A Mini-Review

Clinical laboratory testing advances have improved diagnostic accuracy, emphasising the need for effective methodologies within evidence-based medicine. Evaluation of methods is an essential function of the monitoring system that guarantees the continuous excellence of a clinical laboratory. This mini-review addresses the basic principles of method evaluation in clinical laboratories, highlighting key factors that support accurate diagnoses. The systematic process of method evaluation involves validation and verification, while considering scope, parameters and regulatory compliance. Analytical performance characteristics, sensitivity, specificity, accuracy, precision, linearity, method comparison, matrix effect and carryover determine test suitability, requiring reference materials and standardisation for accuracy. This comprehensive process includes assessing test performance when there are alterations in reagents, instruments or methodologies. Furthermore, the success of the evaluation procedure hinges on the careful definition of experimental design and subsequent statistical analysis, emphasising their intimate connection, which must be established before initiation. Current trends highlight automation and the transformative impact of artificial intelligence (AI), reshaping the role of laboratory professionals in predicting disease risk and guiding treatment decisions. While advances are celebrated, emphasis is given to the inherent limits of evaluation and clinical methods. Challenges persist, including variations in test accuracy and inconsistencies between laboratories. To address these, proposed solutions include clear guidance, harmonising terminology, setting minimum standards and standardising study design components.

Определение аналитической чувствительности и специфичности методов ПЦР для диагностики черной бактериальной пятнистости томата

The work is devoted to molecular genetic methods for the diagnosis of pathogens of bacterial spot of tomato – a harmful bacterial disease of tomatoes and peppers, predominantly spread in the open ground in the southern regions. The research was conducted on the basis of the All- Russian Plant Quarantine Center (FGBU “VNIIKR”) in 2022–2023. The objective of the work was to determine the analytical sensitivity and specificity of molecular genetic methods for the detection and identification of three species of different pathological types of bacteria of the genus Xanthomonas – pathogens of bacterial spot of tomato. Due to the necessity of import substitution of expensive reagents, the tests were carried out with domestic reagents produced by OOO “Evrogen” and ZAO “Dialat”. The results of the effectiveness of real-time PCR (qPCR) are presented, the analysis of which showed that all tested primer systems can be recommended for the detection of bacteriosis pathogens. At the same time, qPCR AFLP derived Taqman PCR and XopD Taqman PCR were found to have high analytical sensitivity (102–103 CFU/ml). It has been shown that three out of four primer systems according to to the methodology of Koenraadt et al. (2009) also have a high sensitivity of 102 CFU/ml. The analytical sensitivity of the Bs-XpF/R primers for the detection of X. euvesicatoria pv. perforans was 104 CFU/ml, which is sufficient for samples with a high concentration of the pathogen and for the identification of a pure bacterial culture. All primers are 100% specific for the target strains of pathogens; no cross-reactions with other strains have been observed. The proposed reliable operational method for detecting pathogens of bacterial spot in tomato and pepper seeds will significantly reduce yield losses and increase the economic efficiency of domestic vegetable production.

Unexpected Factors That Influence Viral Detection and Viral Load Using Real-Time PCR

This communication takes note of unexpected factors that can influence the results of RT-PCR in quantitation of copy numbers such as in determination of viral loads and in viral identification. We show that the presence of serum separator gel in authorized collection tubes for hepatitis C (HCV) viral load determinations causes underestimation of viral loads by blocking viral diffusion into plasma and that the presence of more than one targeted virus in a multiplex RT-PCR viral assay, while not affecting analytical specificity, results in raising of the minimal detectable viral titer and therefore a decreased analytical sensitivity. Our results suggest the possibility that HCV samples should be placed in cell lysis buffer for full viral load determination and that multiplex assays should be carefully validated and modified if necessary to minimize loss of sensitivity.

Analytical validation of a novel comprehensive genomic profiling informed circulating tumor DNA monitoring assay for solid tumors.

Emerging technologies focused on the detection and quantification of circulating tumor DNA (ctDNA) in blood show extensive potential for managing patient treatment decisions, informing risk of recurrence, and predicting response to therapy. Currently available tissue-informed approaches are often limited by the need for additional sequencing of normal tissue or peripheral mononuclear cells to identify non-tumor-derived alterations while tissue-naïve approaches are often limited in sensitivity. Here we present the analytical validation for a novel ctDNA monitoring assay, FoundationOne®Tracker. The assay utilizes somatic alterations from comprehensive genomic profiling (CGP) of tumor tissue. A novel algorithm identifies monitorable alterations with a high probability of being somatic and computationally filters non-tumor-derived alterations such as germline or clonal hematopoiesis variants without the need for sequencing of additional samples. Monitorable alterations identified from tissue CGP are then quantified in blood using a multiplex polymerase chain reaction assay based on the validated SignateraTM assay. The analytical specificity of the plasma workflow is shown to be 99.6% at the sample level. Analytical sensitivity is shown to be >97.3% at ≥5 mean tumor molecules per mL of plasma (MTM/mL) when tested with the most conservative configuration using only two monitorable alterations. The assay also demonstrates high analytical accuracy when compared to liquid biopsy-based CGP as well as high qualitative (measured 100% PPA) and quantitative precision (<11.2% coefficient of variation).

Multidimensional mass profiles increase confidence in bacterial identification when using low-resolution mass spectrometers.

Field-forward analytical technologies, such as portable mass spectrometry (MS), enable essential capabilities for real-time monitoring and point-of-care diagnostic applications. Significant and recent investments improving the features of miniaturized mass spectrometers enable various new applications outside of small molecule detection. Most notably, the addition of tandem mass spectrometry scans (MS/MS) allows the instrument to isolate and fragment ions and increase the analytical specificity by measuring unique chemical signatures for ions of interest. Notwithstanding these technological advancements, low-cost, portable systems still struggle to confidently identify clinically significant organisms of interest, such as bacteria, viruses, and proteinaceous toxins, due to the limitations in resolving power. To overcome these limitations, we developed a novel multidimensional mass fingerprinting technique that uses tandem mass spectrometry to increase the chemical specificity for low-resolution mass spectral profiles. We demonstrated the method's capabilities for differentiating four different bacteria, including attentuated strains of Yersinia pestis. This approach allowed for the accurate (>92%) identification of each organism at the strain level using de-resolved matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data to mimic the performance characteristics of miniaturized mass spectrometers. This work demonstrates that low-resolution mass spectrometers, equipped with tandem MS acquisition modes, can accurately identify clinically relevant bacteria. These findings support the future application of these technologies for field-forward and point-of-care applications where high-performance mass spectrometers would be cost-prohibitive or otherwise impractical.

Design and implementation of a TaqMan® real-time PCR method for detection and quantification of bovine leukemia virus.

The bovine leukemia virus (BLV) is an important infectious agent transmitted from cattle to humans. It is considered one of the oncogenic viruses in breast cancer, so an accurate detection of this virus is important. The study aimed to design a specific and sensitive method based on TaqMan® real-time polymerase chain reaction (RT-PCR) for BLV detection. Probes and primers were designed using bioinformatics software for a 108 pairs region of the BLV tax gene. Criteria employed for determining analytical sensitivity were prepared using in-vitro RNA transcriptions. The National Center for Biotechnology Information (NCBI), basic local alignment search tool (BLAST) databases various viral panels and genomic samples from healthy individuals (Qom Province, Iran in 2023) were used to verify analytical specificity and clinical specificity, respectively. This method can measure a minimum of 10 copies of DNA and RNA mL-1. Moreover, the assay is linear in the range of 100 - 109 copies mL-1. By testing negative specimens, the method specificity was 100%. The reproducibility results of the reaction were examined at the intra- and inter-assay comparison. In fact, 10 technical replicates of each concentration of the control sample were analyzed in each working reaction. Due to the locally made kit, exact sensitivity and specificity, rapid analysis, and relatively low cost, as compared to commercial kits of other countries, the method introduced in the present study could be suitable for accurate detection of the BLV. Also, the TaqMan® real-time PCR method could be detected in cattle and human and before malignant changes of breast cancer which could reduce infection and breast cancer.

ADAPTING THE EURASIAN H5 TAQMAN RT-QPCR ASSAY FOR THE DETECTION OF AVIAN INFLUENZA STRAINS CIRCULATING IN INDIA

The development of molecular diagnostic for avian influenza virus (AIV) is a continuous process due to evolution of virus after each passing outbreak. The molecular tests need to be reviewed after each outbreak for obtaining consistent laboratory results. In the present study, the oligos sequences of validated H5 Eurasian taqman RT-qPCR for H5 subtyping have been improved matching to the currently circulating strains for laboratory diagnosis of AIV. All available influenza H5 hemagglutinin gene sequences of Eurasian strains from the public databases were aligned in-silico with the recommended RT-qPCR oligos and modifications were done according to the matching sequences of the recently evolved strains. The modified oligos were validated with clinical samples and reference AI H5N1 isolates belonging to different clades. Multiple sequence alignment suggested the modifications at two, three and one positions respectively in probe, forward and reverse primers. Out of 1295 clinical samples tested, 251 samples were found positive. Assay could identify all the 115 virus strains of AI H5 subtype belonging to clade 2.2, 2.2.2, 2.3.2.1C, 2.3.2.1a and 2.3.4.4b. On comparison to the virus isolation, the positive and negative agreement was found to be 0.925 ± 0.025 and 0.983 ± 0.002 respectively. Analytical specificity of the modified assay was confirmed specifically with AI H5 subtype only whereas analytical sensitivity was found to be 13-130 copies of IVTRNA and 0.1 EID50 of AI H5N1 virus. We propose that the modified RT-qPCR assay can be a choice for routine diagnosis of Eurasian strains of AI H5 subtypes.