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Background: COVID-19 has been associated with cerebral microbleeds (CMB). Previously, an association of ApoE4 with COVID-19 severity and CMBs in autopsy was found. In this study, we investigated if carrying the Apoe4 allele relates to the number of CMBs in magnetic resonance imaging (MRI) in patients recovered from COVID-19. Material(s) and Method(s): Adult patients recovered from COVID-19 and a control group without a history of COVID-19 was recruited. Exclusion criteria were major neurologic disease, developmental disability or pregnancy. The participants underwent brain MRI 6 months after infection, and a blinded neuroradiologist analyzed the findings. ApoE was genotyped using a microarray. Statistical analysis was performed using the statistical software R. A negative binomial model was chosen based on the distribution of CMBs. Result(s): Of the 216 subjects that underwent MRI, 168 consented to genetic testing, additionally 2 patients were excluded due to extensive CMBs and 1 due to diffuse axonal injury. We included 113 COVID-19 patients (49 ICU-treated, 29 ward-treated and 35 home-isolated) and 52 controls. The most prevalent comorbidities were hypertension, asthma and diabetes. CMBs was found in 47 subjects, with the number of CMBs ranging from 0 to 26. The ApoeE4 allele was carried by 37%, equally distributed among the groups. After adjustment, age (aRR = 1.06, p = 0.007) and COVID-19 (aRR = 2.59, p = 0.038) were independently associated with CMBs. The ApoE4 allele (aRR = 2.16, p = 0.07, CI = 0.94-5.10) was not significant. Conclusion(s): Age and previous COVID-19, but not possession of the ApoeE4 allele, were independently associated with the number of CMBs.
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Objective To explore the core targets and important pathways of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) induced atherosclerosis (AS) progression from the perspective of immune inflammation, so as to predict the potential prevention and treatment of traditional Chinese medicine (TCM). Methods Microarray data were obtained from the Gene Expression Omnibus (GEO) database for coronavirus disease 2019 (COVID-19) patients and AS patients, and the "limmar" and "Venn" packages were used to screen out the common differentially expressed genes (DEGs) genes in both diseases. The gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses were performed on the common DEGs to annotate their functions and important pathways. The two gene sets were scored for immune cells and immune function to assess the level of immune cell infiltration. The protein-protein interaction (PPI) network was constructed by STRING database, and the CytoHubba plug-in of Cytoscape was used to identify the hub genes. Two external validation datasets were introduced to validate the hub genes and obtain the core genes. Immuno-infiltration analysis and gene set enrichment analysis (GSEA) were performed on the core genes respectively. Finally the potential TCM regulating the core genes were predicted by Coremine Medical database. Results A total of 7898 genes related to COVID-19, 471 genes related to AS progression;And 51 common DEGs, including 32 highly expressed genes and 19 low expressed genes were obtained. GO and KEGG analysis showed that common DEGs, which were mainly localized in cypermethrin-encapsulated vesicles, platelet alpha particles, phagocytic vesicle membranes and vesicles, were involved in many biological processes such as myeloid differentiation factor 88 (MyD88)-dependent Toll-like receptor signaling pathway transduction, interleukin-8 (IL-8) production and positive regulation, IL-6 production and positive regulation to play a role in regulating nicotinamide adenine dinucleotide phosphate oxidase activity, Toll-like receptor binding and lipopeptide and glycosaminoglycan binding through many biological pathways, including Toll-like receptor signaling pathways, neutrophil extracellular trap formation, complement and coagulation cascade reactions. The results of immune infiltration analysis demonstrated the state of immune microenvironment of COVID-19 and AS. A total of 5 hub genes were obtained after screening, among which Toll-like receptor 2 (TLR2), cluster of differentiation 163 (CD163) and complement C1q subcomponent subunit B (C1QB) genes passed external validation as core genes. The core genes showed strong correlation with immune process and inflammatory response in both immune infiltration analysis and GSEA enrichment analysis. A total of 35 TCMs, including Chuanxiong (Chuanxiong Rhizoma), Taoren (Persicae Semen), Danggui (Angelicae Sinensis Radix), Huangqin (Scutellariae Radix), Pugongying (Taraxaci Herba), Taizishen (Pseudostellariae Radix), Huangjing (Polygonati Rhizoma), could be used as potential therapeutic agents. Conclusion TLR2, CD163 and C1QB were the core molecules of SARS-CoV-2-mediated immune inflammatory response promoting AS progression, and targeting predicted herbs were potential drugs to slow down AS progression in COVID-19 patients.Copyright © 2023 Editorial Office of Chinese Traditional and Herbal Drugs. All rights reserved.
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Breast milk is generally accepted as the perfect source of nutrition for the health and development of infants. It also assists in infant innate and adaptive immunity through many proteins that are decorated with glycans. Examples of these glycoproteins include IgA, IgG, and innate immune lectins. Maternal diet and environmental exposure such as pathogens and pollutants affect human milk composition including its glycoprofile. Despite altered glycosylation can have a consequence on the nursing infant's health and immunity, the current knowledge is still emerging in this area of study. COVID-19 has gained attention in recent years by causing severe morbidity and mortality. Similar to other infectious diseases such as influenza, our lab recently revealed alterations in glycome of plasma and different tissue samples of COVID-19 infected patients. Inspired by these findings, we are interested in disclosing the effect of SARS-CoV-2 on glycosylation of breast milk proteins. Toward this, we performed a large-scale systematic study using our high-throughput lectin microarray analysis technology. We analyzed 132 control samples (breast milk collected pre- COVID) and breast milk from 78 COVID-19 infected mothers. Our data showed there is a 4-fold increase in -2,3 sialic acid on glycoproteins that is associated with SARS-CoV-2 infection in lactating mothers. Lectin pulldown experiments further testified to these findings. Given the significance of -2,3 sialic acid glycan signature in infectious diseases, our finding could provide valuable insight into therapeutic development.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
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Background: It is well established that diabetic patients infected with COVID-19- are at higher risk of developing severe symptoms that may lead to death. Such observation argues for the possibility that SARS-CoV-2 may target and infect pancreatic islets. SARSCoV- 2 is thought to enter the cells through the binding of viral spike S1 protein to ACE2. The cellular entry process includes priming of the S protein by TMPRSS2 and ADAM17, which facilitate the binding and promote ACE2 shedding. To date, no conclusive evidence has emerged to address the expression of TMPRSS2 and ADMA17 or the interaction between SARS-CoV-2 and human pancreatic islets. Method(s): Microarray and RNA-sequencing (RNA-seq) expression data from human islets were used to profile the expression pattern of ACE2, ADAM17, and TMPRSS2 in diabetic and non-diabetic subjects. Result(s): Pancreatic islets express all three receptors regardless of diabetes status. ACE2 expression was significantly elevated in diabetic islets than non-diabetic. Female donors showed to have higher ACE2 expression compared to males, whereas ADAM17 and TMPRSS2 were not affected by gender. No difference in the expression of the three receptors in young (<=40 years old) compared to old (>=60 years old) islets. Obese donors (BMI>30) showed significantly higher expression levels of ADAM17 and TMPRSS2 as compared to non-obese (BMI<25). Expression of TMPRSS2 was associated positively with HbA1c and inversely with age, while ADAM17 and TMPRSS2 were associated positively with BMI. Muscle and subcutaneous adipose tissues showed similar expression of the three receptors in diabetic and nondiabetic donors. Conclusion(s): ACE2 expression is increased in diabetic human islets. More studies are warranted to understand the permissiveness of human pancreatic beta-cells to SARS-Cov-2 and whether variations of ACE2 expression could explain the severity of COVID-19 infection between diabetics and non-diabetic patients.
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Recent advances in biosensing analytical platforms have brought relevant outcomes for novel diagnostic and therapy-oriented applications. In this context, 3D droplet microarrays, where hydrogels are used as matrices to stably entrap biomolecules onto analytical surfaces, potentially provide relevant advantages over conventional 2D assays, such as increased loading capacity, lower nonspecific binding, and enhanced signal-to-noise ratio. Here, we describe a hybrid hydrogel composed of a self-assembling peptide and commercial agarose (AG) as a suitable matrix for 3D microarray bioassays. The hybrid hydrogel is printable and self-adhesive and allows analyte diffusion. As a showcase example, we describe its application in a diagnostic immunoassay for the detection of SARS-CoV-2 infection. © 2023, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
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SESSION TITLE: Disseminated Bacterial Infections SESSION TYPE: Rapid Fire Case Reports PRESENTED ON: 10/18/2022 10:15 am - 11:10 am INTRODUCTION: Tularemia is a rare infectious disease caused by Francisella Tularensis that typically affects the skin, eyes, lymph nodes, and lungs. There are a variety of forms of tularemia with varying rates of contagiousness and mortality. Respiratory tularemia has a high mortality rate if left untreated and presents with non-specific viral like symptoms occurring in conjunction with respiratory symptoms: cough, hemoptysis, and pleuritic chest pain. In this COVID ARDS era, it is important to evaluate a broad differential diagnosis. Therefore, the authors describe a patient presenting with flu-like respiratory symptoms whom was ultimately was diagnosed with acute respiratory distress syndrome (ARDS) due to F. Tulerensis. CASE PRESENTATION: A 44-year-old male presented with a four-day history of night sweats, shortness of breath, a productive cough which progressed to hemoptysis, and oliguria. Prior to admission, his initial symptoms were treated as chronic sinusitis with varied antibiotics. Social history including tobacco abuse and deer hunting 1 month prior to presentation. Vitals were stable except for tachycardia, hypoxia, and tachypnea. Laboratory findings were significant for AKI, lactic acidosis, mild transaminitis, hyperbilirubinemia, and leukocytosis with predominant neutrophilia. Thoracic CTA showed bilateral diffused pulmonary edema without evidence of pulmonary embolism. Due to the patient's worsening respiratory status, he was intubated for support. The patient progressed to Severe ARDS per Berlin Criteria eventually requiring pronation and continuous paralyzing. Bronchoscopy was performed with bronchial lavage. Bacterial, viral, and fungal cultures did not show growth while vasculitic work-up was negative. Empiric antibiotic treatment did not show improvement until the patient was diagnosed with F. Taularensis via serological testing with an IgM of 20 U/mL, and patient was transitioned to gentamycin. Ultimately, the patient was extubated, transitioned to oral doxycycline, and discharged home. DISCUSSION: Approximately 250 cases of tularemia are reported to CDC each year. Respiratory tularemia has a mortality rate up to 30% if not treated. For this reason, F. tularensis is a potential biological weapon and is categorized as a Group A pathogenic agent. Serological testing may be negative early in disease progression;therefore, early inflammatory markers with clinical suspicion are essential to diagnose the disease early in its course. DNA microarray has high specificity and sensitivity for rapid diagnosis of tularemia while being cost effective. After prompt diagnosis, intravenous aminoglycosides;such as gentamycin or streptomycin;must be started. CONCLUSIONS: In the above case, we illustrate the gradual onset and rapid patient deterioration when treatment is delayed;yet, there is rapid recovery once appropriate treatment is used. Reference #1: 1. Ranjbar, Reza, Payam Behzadi, and Caterina Mammina. "Respiratory tularemia: Francisella tularensis and microarray probe designing.” The open microbiology journal 10 (2016): 176. Reference #2: 2. Akhvlediani, N., I. Burjanadze, D. Baliashvili, T. Tushishvili, M. Broladze, A. Navdarashvili, S. Dolbadze et al. "Tularemia transmission to humans: a multifaceted surveillance approach.” Epidemiology & Infection 146, no. 16 (2018): 2139-2145. Reference #3: 3. Tularemia in British Columbia: A case report and review. Issue: BCMJ, vol. 52, No. 6, July August 2010 (Pages 303- 307). Megan Isaac-Renton, BSc, Muhammad Morshed, PhD, SCCM Eleni Galanis, MD, MPH, FRCPC Sunny Mak, MSc Vicente Loyola, MD, FRCPC, Linda M.N. Hoang, MD, MHSc, FRCPC DISCLOSURES: No relevant relationships by Munish Adhikari No relevant relationships by Ashma Ul Husna No relevant relationships by Yan Jiang No relevant relationships by Divya Kharel No relevant relationships by Gregory Polcha
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Recombinant live adenovirus (Ad) vectors represent a readily modular vaccine construct that can be engineered to include any antigen of interest, thereby enabling rapid vaccine development against a myriad of infectious pathogens, including coronaviruses. However, current approaches used for delivery, storage, and distribution of Ad vaccines hinder their full potential for effective global immunization campaigns. Here, we developed simple, effective, practical, and needle-free Ad vaccines based on microarray patches (MAPs) to enable sustainable mass vaccination against SARS-CoV-2. Rational formulation of live Ads with nonreducing sugars and mechanically strong carbohydrates into dissolvable MAPs enabled effective skin-targeted delivery of Ads and efficient cutaneous transduction as determined by in vivo live imaging of mice following skin application of MAPs integrating Ad vectors with a reporter gene. Immunogenicity assessment of dissolving MAP-based Ad vectors encoding SARS-CoV-2 proteins in mice demonstrated that skin immunization via MAP delivery of Ad-vectored COVID-19 vaccines elicited robust antigen-specific antibody responses, and these antibodies led to virus-specific neutralization activities, which were enhanced compared to those obtained with traditional intramuscular immunization. Furthermore, MAP delivery of Ad-vectored vaccines elicited potent cell-mediated immune responses, including polyfunctional virus-specific CD8+ and CD4+ T-cell responses in spleens and lungs of immunized mice, as determined by intracellular cytokine staining and flow cytometry, as well as antigen-specific cytotoxic T-cell responses in spleens of mice, as determined by lytic assay. Collectively, our results suggest that dissolvable MAPs could enable the development of skin-targeted Ad-based vaccines that may increase the effectiveness of global immunization programs for SARS-CoV-2 and other existing or future pathogens.
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Aims: The aim of this study was to extract the signaling mediators or biological pathways that link covid-19 to other diseases such as type 1 diabetes mellitus (T1DM). Methods: Microarray data of covid-19 (GSE164805) was extracted from Gene Expression Omnibus (GEO) and analyses were performed by R package and GEO2R. Functional enrichment analysis was done to extract enriched molecular pathways (MP), biological process (BP) and molecular function (MF). Then commonly up- and down-regulated genes in covid-19 and T1DM were extracted by comparing deferentially expressed genes (DEGs) of GSE164805 and GSE9006. Results: Down-regulated DEGs in the severely progressing covid-19 patients (SPCP) had a link to T1DM. Major histocompatibility system (MHC) class II, gamma interferon (IFNγ), and IL-1B were enriched in extracted pathway that leads to T1DM. In addition, comparing extracted DEGs from GSE164805 and GSE9006 indicated that MTUS1, EGR1 and EGR3 are the genes that are up-regulated in both SPCP and T1DM. Conclusion: The findings of this study indicate that coincidence of SARS-COV-2 infection and T1DM may increase the severity of both diseases. Although covid-19 reduced the T cell mediated immune response, but increased mediators of T-cell signaling pathway such as IL-1 in both diseases. This could potentiate the inflammation response and worsens the severity of covid-19 cytokine storm or increase the resistance to insulin.
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Background: SARS-CoV-2 infection has resulted in over 219 million confirmed cases of COVID-19 with 4.5 million fatalities, highlighting the importance of elucidating mechanisms of severe disease. Here we utilized machine learning (ML) technologies to identify DNA methylation footprints of COVID-19 disease from publicly available data. Methods: Genome-wide DNA methylation of SARS-CoV-2 infected and uninfected patients using Illumina HumanMethylationEPIC microarray platform from whole blood was publicly available through NCBI Gene Expression Omnibus. A training cohort (GSE167202) consisting of 460 individuals (164 COVID-19-infected and 296 non-infected) and an external validation dataset (GSE174818) consisting of 128 individuals (102 COVID-19-infected and 26 non-COVID with pneumonia diagnosis) were obtained. COVID-19 severity score (SS) was classified as follows: 0. uninfected;1. released from department to home;2. admitted to in-patient care;3. progressed to ICU;and 4. death. Participants were then dichotomized by SS=0 or SS≥3. Raw data was processed using ChAMP in R 4.1.1, resulting in over 850,000 methylation sites per sample for analysis. Beta values were logit transformed to M values using CpGTools in Python 3.8.8. JADBio AutoML platform was leveraged to analyze these datasets with the goal of identifying a methylation signature indicative of COVID-19 disease. Results: From our training cohort, JADBio utilized LASSO feature selection (penalty=1.5) to identify 4 unique methylation sites capable of carrying the predictive weight of a classification random forest trained on 100 trees with Deviance splitting criterion (minimum leaf size=3). The average area under the curve of receiver operator characteristic (AUC-ROC) of the model was 0.933 (95% confidence interval [0.885, 0.970]), while the average area under the precision-recall curve (AUC-PRC) of 0.965 [0.932, 0.986]. When COVID-19 mild infections (SS = 1 or 2) were returned to the training dataset as an internal control, the model retained its predictive power (AUC-ROC=0.985, AUC-PRC=0.992). When applied to our external validation, this model produced an AUC-ROC of 0.901 with an AUC-PRC of 0.748. Conclusion: We developed a Random Forest Classification model capable of accurately predicting COVID-19 infection leveraging JADBio AutoML platform. These results enhance our understanding of epigenetic mechanisms used by SARS-CoV-2 in disease pathogenesis and identify potential therapeutic targets.
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Background: After the first case of COVID-19 being announced in China in December 2019, various diagnostic technologies have been developed at unprecedented pace with the aim of providing a basis for accurate clinical intervention. However, some assays including CRISPR-based diagnostics and loop-mediated isothermal amplification (LAMP) have been less explored. As new COVID-19 technologies emerge, there is need for them to be assessed, validated and improved upon. Moreover, there is paucity of data on the essential factors governing the selection of an appropriate diagnostic approach within the correct timeframe. Myths and origin of SARS-CoV-2 remain to be controversial. Consequently, this review aims at exploring the current COVID-19 diagnostic technologies, performance evaluation, principles, suitability, specificity, sensitivity, successes and challenges of the technologies for laboratory and bedside testing. Main Body: To date, there exist more publications on COVID-19 diagnostics as compared to the Zika virus. The SARS-CoV-2 virus genome profiles were readily available by 31st of December 2019. This was attributed to the fast-paced sharing of the epidemiological and diagnostics data of COVID-19. Timely profiling of the virus genome accelerated the development of diagnostic technologies. Furthermore, the rapid publication of studies that evaluated several diagnostic methods available provided baseline information on how the various technologies work and paved way for development of novel technologies. Conclusion: Up to date, RT-PCR is the most preferred as compared to the other assays. This is despite the repeated false negatives reported in many of the study findings. Considering that COVID-19 has caused devastating effects on the economy, healthcare systems, agriculture and culture, timely and accurate detection of the virus is paramount in the provision of targeted therapy hence reducing chances of drug resistance, increased treatment costs and morbidity. However, information on the origin of SARS-CoV-2 still remains elusive. Furthermore, knowledge and perception of the patients toward management of SARS-CoV-2 are also paramount to proper diagnosis and management of the pandemic. Future implications of the misperceptions are that they may lead to increased non-compliance to SARS-CoV-2-related World Health Organization (WHO) policies and guidelines.
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Introduction: Chronic kidney disease (CKD) is a debilitating disorder associated with significant morbidity and mortality. CKD diagnoses can have overlapping, non-specific clinical symptoms and histology findings, and the underlying etiology can remain unknown. Recent studies have shown that 1 in 10 adults with CKD has a genetic component to their disease. However, genetic services are limited in this patient population and disproportionally impact those from medically underserved communities. Therefore, an adult kidney genetics clinic was developed within the Division of Nephrology at a large urban academic medical center to increase access to genetic services and testing in adults with kidney disease. Methods: In June 2019, the Division of Nephrology at Columbia University Irving Medical Center created a Kidney Genetics Clinic staffed by genetic counselors (GC) and nephrologists. Initially, appointments were held in-person but transitioned to telemedicine beginning in May 2020 due to the COVID-19 pandemic. The clinic utilized two appointment types: full genetic consults (staffed by a GC and nephrologist) and genetic counseling visits (staffed by a GC only). Genetic counselors implemented several genetic education initiatives to increase clinic referrals and increase provider interest. These included bi-monthly genetic case seminars, monthly genetic research sign-out rounds, a continuing education course focusing on clinical genetics, and genetic counseling student rotations. Results: Between June 2019 and June 2021, the clinic received 277 referrals, averaging 11 per month. Of those referred, 83% were scheduled, and 212 patients underwent genetic evaluation. The median wait time from referral to appointment was 37 days, and the no-show rate was 8%. The majority (89%) of appointments were via telehealth, either by phone or video, while the rest occurred in person. Genetic counseling visits accounted for 21% of patient appointments, and the remaining ones were full genetic consults. Most patients who attended their genetics appointment were in the NY tri-state area (87%), but 12% resided in nine additional states, three other countries, and one US territory. The primary insurance was Medicare in 10% of patients and Medicaid in 17%. Most patients described themselves as white (n=126), while 47 patients reported Hispanic or Latino ethnicity, 36 identified as Black, 15 Asian, and 4 Native Hawaiian or Pacific Islander. The average age of the patient population was 44 years old (ranging from 18 to 87). Patients seen in the genetics clinic were referred for a variety of indications and included several different kidney diagnoses, including: CAKUT (n=6), tubulointerstitial disease (n=26), suspected or clinical diagnosis of a collagenopathy (n=38), focal segmental glomerulosclerosis (FSGS) (n=28), tubulopathy or electrolyte disorder (n=16), cystic kidney disease (including PKD) (n=24), hematuria and/or proteinuria (n=31), complement dysregulation (n=8), tumor or cancer (n=4), and CKD of unknown etiology (n=23). Six patients had a known genetic diagnosis, and 23 were healthy relatives of individuals with a known genetic diagnosis or potential kidney donors. Of patients seen in the kidney genetics clinic, 42% reported a family history of CKD or a personal or family history of a genetic diagnosis. A total of 186 clinical genetic tests were ordered on 174 patients;nine tests still have results pending, and ten were canceled. Genetic tests that were ordered included: small (>50) and large gene panels (n=146), exome sequencing (n=6), microarrays (n=4), and single gene and targeted variant testing (n=20). In patients that did not undergo genetic testing, reasons included: not clinically indicated, testing already ordered, and financial concerns. A diagnostic or candidate diagnostic positive result was reported in 29% of patients, involving 18 different genes. Pathogenic or likely pathogenic variants were most common in COL4A4 (n=11), followed by PKD1 (n=8). Similarly, the highest diagnostic yield was in patients with a referral ndication of a suspected collagenopathy (diagnosis in 50%) or cystic disease (diagnosis in 50%). A non-diagnostic positive finding was identified in 9% of patients and included results such as secondary findings (n=1), carrier status (n=5), and risk factors, such as an APOL1 high-risk genotype (n=9). The identification of a genetic diagnosis in patients impacted several areas of clinical care, including referrals to specialists, kidney donor selection, clinical trial eligibility (for example, in patients with a genetic Alport diagnosis), and increased access to medications (such as tolvaptan in patients with PKD1 variants). In addition, those with non-diagnostic findings were referred to ongoing research studies at the medical center to elucidate the genetics of kidney disease. Conclusion: Here, we describe the successful creation and implementation of an adult kidney genetics clinic at a large medical center. By utilizing a combination of in-person appointments and telemedicine, the clinic was able to provide access to genomic services across a broad geographic region and to a diverse patient population of adults with kidney disease. Genetic education efforts were an integral component of the clinic's success, as it increased visibility and helped providers identify patients who would benefit from genetic services, as evidenced by the high percentage of referred patients scheduling appointments and high diagnostic yield in patients undergoing testing. Identifying genetic diagnoses in this patient population has several clinical implications, including changes in management, eligibility for genetically stratified clinical trials, and treatment decisions. Continued and ongoing access to genomic services is a fundamental component of patient care in adults with kidney disease.
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Background. Nucleic acid amplification testing (NAAT) is an essential tool both for biomedical research and for clinical molecular diagnostics. Currently, there are multiple NAAT platforms available, each offering certain performance and utility advantages and disadvantages as compared to each other. Next generation NAAT platforms aim to deliver increased target detection sensitivity and specificity, low limits of target detection, quantitative high multiplex target capacity, rapid time to results, and simple sample-to-answer workflow. Methods. Here we describe the Torus Synestia System, a NAAT platform capable of rapid, highly multiplexed amplification and detection of both DNA and RNA targets. The platform comprises a small, portable (~ 2kg) amplification and detection device and a disposable single-use cartridge housing a PCR amplification chamber with an integrated label-free microarray for real-time data acquisition and interpretation. The platform offers a 30-min turnaround time with a detection limit of 10 DNA/RNA molecules per assay and single nucleotide discrimination. Results. We demonstrate the Synestia System performance and utility with three distinct molecular applications: 1) detection of 20 genetic loci and 30 single nucleotide polymorphisms in human genomic DNA;2) detection and genotyping of 43 unique bacterial species associated with human urinary tract infections;and 3) detection and profiling human respiratory viral pathogens including SARS-CoV-1/2, seasonal coronaviruses, Influenza A/B, and human respiratory syncytial viruses. In addition, the single-nucleotide specificity of our label-free microarray probes allowed for robust identification and discrimination of newly emerging SARS-CoV-2 lineages, such as B.1.1.7 (a.k.a. UK), B.1.351 (a.k.a. South African), P.1 (a.k.a. Brazilian), and B.1.617 (a.k.a. Indian). Conclusion. The Torus Synestia System has broad applicability in both clinical and research environments. We are confident that the Torus Synestia System will revolutionize syndromic diagnostics at the point of care (PoC) and lead to improved response times during future epidemic and pandemic pathogen outbreaks.
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Goals: The COVID-19 pandemic continues to strain healthcare systems globally. The ESMO COVID-19 adapted recommendations1 advocate for the use of pre-operative/neoadjuvant endocrine therapy as a strategy to defer surgery by 6–12 months in clinical stage I-II breast cancers to prioritize resources for patients that require urgent care. Accurate risk assessment is an integral component of this prioritization process. Adjuvant studies such as MINDACT showed that up to 46% of clinically high risk tumors were classified as genomic Low Risk with MammaPrint, and still have excellent outcomes at 8-yrs with endocrine therapy alone, highlighting the potential for overtreatment if using clinical-risk alone. Here, gene expression results with MammaPrint (MP) and BluePrint (BP) were compared between pre-operative core needle biopsy (CNB) and postoperative surgical resection (SR) specimens to evaluate test performance across specimen type. Methods: 10,574 routine diagnostic samples from outside the US submitted to Agendia between Jan 2017 and Oct 2020 were included in this study.MP and BP testingwere processed according to standard FFPE microarray procedures. MP was used to stratify samples into Ultra LowRisk (UL), LowRisk (LR), and High Risk (HR). BPwas used to classify samples into Basal, Luminal or HER2-type. MP Index (MPI) distribution on BP defined Luminal-type tumors were compared between CNB and SR samples. Comparative “logistics metrics” (avg. turnaround time [TAT] and success rate) were also assessed between these specimen types. Results: 10% of samples were CNB and 90% were SR (Table 1). BP Basal, Luminal and HER2-type distributions were 2%, 97%, and 1% respectively for CNB samples and 1%, 98.6%, and 0.4% respectively for SR samples. Within Luminal-type tumors (majority of the samples), the frequency of UL, LR, and HR results were 14%, 61%, and 39% for CNB, and 13%, 58%, and 42% for SR, respectively. Overall, MP Index distributions were similar between samples tested from CNB vs. SR. Average TAT and success rate % between CNB and SR were similar (Table 2).(Table Presented)Definitions: Turnaround Time (TAT) is calculated from the time a specimen is received at the laboratory to the time a result is available. Success % excludes test failures due to insufficient RNA yield % and sub-optimal RNA quality, and evaluates the total number of specimens that have met the pre-requisite 30% minimum invasive tumor requirement that have a valid result. Conclusion(s): The frequency of each MP risk group as well as the distribution pattern of MP Index were essentially identical between CNB and SR samples, indicating comparable performance regardless of specimen type. With timely TAT and no meaningful difference in MPI distribution between CNB and SR specimens, pre-operative use of MP+BP genomic testing on CNB can be incorporated into the preoperative treatment decision making process. Conflict of Interest: Employee of Agendia, equity/stock ownership interest.