Positive Percentage Research Articles

Discovery and characterization of novel jeilongviruses in wild rodents from Hubei, China

The genus Jeilongvirus comprises non-segmented negative-stranded RNA viruses that are classified within the Paramyxoviridae family by phylogeny. Jeilongviruses are found in various reservoirs, including rodents and bats. Rodents are typical viral reservoirs with diverse spectra and zoonotic potential. Little is currently known about jeilongviruses in rodents from central China. The study utilized high-throughput and Sanger sequencing to obtain jeilongvirus genomes, including those of two novel strains (HBJZ120/CHN/2021 (17,468 nt) and HBJZ157/CHN/2021 (19,143 nt)) and three known viruses (HBXN18/CHN/2021 (19,212 nt), HBJZ10/CHN/2021 (19,700 nt), HBJM106/CHN/2021 (18,871 nt)), which were characterized by genome structure, identity matrix, and phylogenetic analysis. Jeilongviruses were classified into three subclades based on their topology, phylogeny, and hosts. Based on the amino acid sequence identities and phylogenetic analysis of the L protein, HBJZ120/CHN/2021 and HBJZ157/CHN/2021 were found to be strains rather than novel species. Additionally, according to specific polymerase chain reaction screening, the positive percentage of Beilong virus in Hubei was 6.38%, suggesting that Beilong virus, belonging to the Jeilongvirus genus, is likely to be widespread in wild rodents. The identification of novel strains further elucidated the genomic diversity of jeilongviruses. Additionally, the prevalence of jeilongviruses in Hubei, China, was profiled, establishing a foundation for the surveillance and early warning of emerging paramyxoviruses.

Evaluating the diagnostic accuracy of QIAreach QuantiFERON-TB compared to QuantiFERON-TB Gold Plus for tuberculosis: a systematic review and meta-analysis

Accurate tuberculosis (TB) diagnosis remains challenging, especially in resource-limited settings. This study aims to assess the diagnostic performance of the QIAreach QuantiFERON-TB (QFT) assay, with a specific focus on comparing its diagnostic performance with the QuantiFERON-TB Gold Plus (QFT-Plus). We systematically reviewed relevant individual studies on PubMed, Scopus, and Web of Science up to January 20, 2024. The focus was on evaluating the diagnostic parameters of the QIAreach QFT assay for TB infection, which included sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), positive likelihood ratio (PLR), negative likelihood ratio (NLR), and concordance with the QFT-Plus assay. QIAreach QFT demonstrated strong diagnostic performance with a pooled sensitivity of 99% (95% CI 95–100%) and specificity of 94% (95% CI 85–97%). Additionally, it showed a PLR of 15.6 (95% CI 6.5–37.5) and NLR of 0.01 (95% CI 0–0.03). The pooled PPV and NPV were 88% (95% CI 70–98%) and 100% (95% CI 99–100%), respectively. Concordance analysis with QFT-Plus revealed a pooled positive percent agreement of 98% (95% CI 88–100%) and pooled negative percent agreement of 91% (95% CI 81–97%), with a pooled overall percent agreement of 92% (95% CI 83–98). In conclusion, QIAreach QFT has shown promising diagnostic performance, with a strong concordance with QFT-Plus. However, further studies are needed to comprehensively evaluate its diagnostic performance in the context of TB infection.

Evolution of influenza and acute respiratory infections in the Republic of Moldova during the 2014/15-2022/23 seasons

Introduction. Influenza-like illness (ILI), Acute Respiratory Infections (ARI) and Severe Acute Respiratory Infections (SARI) are the most common infectious diseases globally, accounting for up to 95% of infectious diseases in some countries. They cause severe forms every year especially in at-risk groups. Material and methods. The descriptive-retrospective epidemiological study analyzed morbidity by ILI, ARI and SARI and laboratory results in the presence of influenza viruses during the 2014/2015-2022/2023 seasons. Results. ILI has been of low to medium intensity except for 2 seasons and ARI has been of very high intensity in one season. ILI, ARI and SARI primarily affected children aged 0-14 years. During the 9 seasons (exception 2020/2021) influenza virus types A(H1N1)pdm09, A(H3N2) and B have been identified, with the percentage of positives decreasing considerably in the last 2 seasons. During the period under review, each influenza virus dominated, and in 3 seasons 2-3 virus types co-dominated. Genetic characterization of the identified strains demonstrated that influenza viruses fully fit the phylogenetic tree constructed in the nominated period, do not differ antigenically from strains identified in other regions of the northern hemisphere and are susceptible to antivirals. Conclusions. The national surveillance system of ILI, ARI and SARI makes it possible to monitor the evolution of the epidemic process in real time and geographic space and facilitates prompt intervention with control and response measures. Keywords: influenza, ILI, ARI, SARI

C4d expression in focal segmental glomerulosclerosis

BackgroundThere is a little information about of expression of C4d (complement fragment) in Focal segmental glomerulosclerosis (FSGS) subtypes. Our aim was to determine the expression of C4d in FSGS subtypes in percutaneous native renal biopsies in a second-level hospital and its correlation with clinical, biochemical and histological variables. Material and methodsA retrospective study in paraffin blocks of patients with biopsy with FSGS aged 16–65 years, indistinct sex, not diabetic or obese. Immunohistochemistry was performed for C4d and their expression was analyzing in non-sclerosed glomerular capillaries (GC) and sclerosis areas (SA). Clinical and biochemical variables were recorded. The cases were divided into C4d positive and C4d negative groups and compared. The correlation between C4d staining scores in CG and SA with clinical and biochemical variables were analyzed. ResultsTwenty samples were analyzed, 4 for each subtype. At the time of biopsy average age 38.8 ± 18.6 years, 65% male, 8.7% were hypertension. The percentage of positivity for C4d was 40% in GC, 30% SA and 35% in mesangium. The highest expression was for cellular and collapsing subtypes. C4d positivity cases had increased proteinuria (p = 0.035). A significant correlation was found between percentage of C4d expression in CG with SA (p = 0.012) and SA with tubular atrophy and interstitial fibrosis (p < 0.05). ConclusionsC4d expression in FSGS predominated in the cellular and collapsing subtypes, which translates complement activation. C4d is a possible surrogate marker in GSFS.

In-house homologous recombination deficiency testing in ovarian cancer: a multi-institutional Italian pilot study

AimsPoly (ADP-ribose) polymerase (PARP) inhibitors (PARPIs) represent a standard of care for the clinical management of high-grade serous ovarian cancer (HGSOC). The recognition of homologous recombination deficiency (HRD) has emerged...

Is the percentage of hormone receptor positivity in HR+ HER2-metastatic breast cancer patients receiving CDK 4/6 inhibitor with endocrine therapy predictive and prognostic?

There is no clear information in the literature about the relationship between the efficacy of CDK 4/6i combined with ET and HR positivity. However, we know that the longest overall survival was in the ER-strong positive/PR intermediate or strong positive groups. Therefore, we aimed to investigate CDK4/6i treatments that create positivity in HR. Patients with the diagnosis of HR+/HER2- MBC who were treated with CDK 4/6i and HR >10% were retrospectively evaluated. To analyze the role of HR positivity, ER was moderately positive (10-49%) and ER was strongly positive (50-100%); PR was grouped as moderately positive (10-49%) and PR strongly positive (50-100%). Median follow-up of 150 patients included in the study was 15.2 months (95% CI, 2.1-40.9 months). The highest response in the whole group was obtained in the ER-strong positive/PR moderate or strong positive group, and the ER moderate positive/PR moderate or strong group. This was followed by the ER strong positive/PR negative group, and then the ER moderate positive/PR negative group. Although these advantages were not statistically significant, they were numerically higher (ORR: 83.8% vs. 83.3% vs. 77.4% vs. 62.5%, p=0.488, respectively). The highest survival in the whole group was achieved in the ER strong positive/PR moderate or strongly positive group, followed by the ER moderately positive/PR moderate or strongly positive group, the ER strongly positive/PR negative group followed by the ER moderate positive/PR negative group, respectively(p=0.410). However, these advantages were not statistically significant. As a result, HR+/HER2- MBC patients receiving CDK 4/6i combined with ET suggest that the percentage of HR positivity may have a predictive and prognostic role.

Comparison of the diagnostic accuracy of the Pluslife Mini Dock RHAM technology with Abbott ID Now and Cepheid GenXpert: A retrospective evaluation study

Rapid and sensitive detection of pathogens is critical in interrupting the transmission chain of infectious diseases. Currently, real-time (RT-)PCR represents the gold standard for the detection of SARS-CoV-2. RNase HII-assisted amplification (RHAM) is a promising technology, enabling reliable point-of-care (PoC) testing; however, its diagnostic accuracy has not yet been investigated. The present study compared the Pluslife Mini Dock (RHAM technology), with Abbott ID Now and Cepheid GeneXpert IV. The positive percent agreement (PPA) and negative percent agreement (NPA) were determined in 100 SARS-CoV-2 positive and 210 SARS-CoV-2 negative samples. Further, the reliability of the Pluslife Mini Dock was investigated in different SARS-CoV-2 variants (Delta and Omicron subvariants). The PPA was 99.00% for Pluslife, 100.00% for Abbott ID Now, and 99.00% for Cepheid GeneXpert, with an NPA of 100.00%, 98.90%, and 93.72%, respectively. Abbott ID Now demonstrated the highest rate of invalid results. All SARS-CoV-2 analysed variants were detected by the Pluslife device. Altogether, the Pluslife Mini Dock demonstrated a PPA of 99.16% (235/237) for CT < 36 and an NPA of 100.00% (313/313), respectively. In conclusion, the Pluslife Mini Dock demonstrated better analytical performance than Abbott ID Now and Cepheid GeneXpert IV, representing a highly accurate and rapid PoC alternative to RT-PCR.

Clinical application of targeted tumour sequencing tests for detecting ERBB2 amplification and optimizing anti-HER2 therapy in gastric cancer

BackgroundEvaluation of human epidermal growth factor receptor 2 (HER2) overexpression caused by erb-b2 receptor tyrosine kinase 2 (ERBB2) amplification (AMP) by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) is essential for treating unresectable metastatic gastric cancer (GC). A targeted tumour sequencing test enables comprehensive assessment of alterations in cancer-related genes, including ERBB2. This study aimed to evaluate the concordance between the targeted tumour sequencing test and IHC/FISH for detecting HER2-positive GC and to clarify the significance of ERBB2 AMP and concomitant genetic alterations in HER2 downstream pathways (DPs) in anti-HER2 therapy for unresectable metastatic GC patients.MethodsERBB2 copy number alteration (CNA) was examined via a targeted tumour sequencing test in 152 formalin-fixed paraffin-embedded (FFPE) GC tissues. ERBB2 CNA was compared to HER2 status evaluated by IHC/FISH in FFPE block sections, which were identical to those subjected to the targeted tumour sequencing test. Treatment outcomes of anti-HER2 therapy in 11 patients with unresectable metastatic GC was evaluated.ResultsERBB2 AMP (≥ 2.5-fold change) was detected by the targeted tumour sequencing test in 15 patients (9.9%), and HER2 positivity (IHC 3 + or IHC 2+/FISH positive) was detected in 21 patients (13.8%). The overall percent agreement, positive percent agreement, negative percent agreement and Cohen’s kappa between ERBB2 CNA and HER2 status were 94.7%, 66.7%, 99.2% and 0.75, respectively. Progression-free survival for trastuzumab therapy in patients with ERBB2 AMP was significantly longer than that in patients with no ERBB2 AMP detected by the targeted tumour sequencing test (median 14 months vs. 4 months, P = 0.007). Treatment response to trastuzumab therapy was reduced in patients with ERBB2 AMP and concomitant CNAs of genes in HER2 DPs. One patient with ERBB2 AMP and concomitant CNAs of genes in HER2 DPs achieved a durable response to trastuzumab deruxtecan as fourth-line therapy.ConclusionsA targeted tumour sequencing test is a reliable modality for identifying HER2-positive GC. ERBB2 AMP and concomitant genetic alterations detected through the targeted tumour sequencing test are potential indicators of treatment response to trastuzumab therapy. The targeted tumour sequencing test has emerged as a plausible candidate for companion diagnostics to determine indications for anti-HER2 therapy in the era of precision medicine for GC.

A Prospective Questionnaire-Based Study Evaluating Genetic Literacy and Impact of Brief Educational Intervention Among Breast Cancer Patients in a Low- to Middle-Income Country.

A significant proportion of breast cancer cases are hereditary and are potentially preventable. However, adoption of the preventive measures remains a significant challenge, particularly because of to lack of knowledge and awareness in low- to middle-income countries. This prospective study conducted at a high-volume tertiary care cancer center in North India to assess the knowledge, awareness, and attitudes of female breast cancer patients and impact of a brief educational intervention. The study involved three phases: pre-interventional assessment, educational intervention, and post-interventional assessment utilizing a structured questionnaire. The study involved 300 newly diagnosed breast cancer patients; 16.7% were familial. At the outset, 87.0% patients had low knowledge of risk factors, 90.3% about screening, and 32.7% about treatment. Awareness levels were low: 13.7% aware of familial risk and 2.7% of breast cancer genes. Affordability of genetic testing was low (15.2%), and interest in testing for self and family members was limited (32.0% and 26.3%). Following educational intervention, a significant positive percentage change was noticed in knowledge (risk factors: 12.8%, screening: 36.2%, treatment: 82%), awareness (familial risk: 66.7%, BRCA gene: 12.3%), and attitude (testing for self: 17.8%, family: 19.5%). This study highlights the significant knowledge gaps among breast cancer patients regarding genetics. The educational intervention led to notable improvements in knowledge, awareness, and attitudes, underscoring the importance of tailored patient education in breast cancer care.

Enlarged perivascular spaces are associated with brain microangiopathy and aging in multiple sclerosis

Background: Growing evidence links brain-MRI enlarged perivascular spaces (EPVS) and multiple sclerosis (MS), but their role remains unclear. Objective: This study aimed to investigate the cross-sectional associations of EPVS with several neuroinflammatory and neurodegenerative features in a large multicentric-MS cohort. Methods: In total, 207 patients underwent 3T axial-T2-weighted brain-MRI for EPVS assessment (EPVS dichotomized into high/low according to ⩾ 2/< 2 rating categories). MRI biomarkers included brain-predicted age and brain-predicted age difference (brain-PAD), central vein sign (CVS)-positive lesion percentage (CVS%), paramagnetic rim and cortical lesions, T2-lesion load, and brain volumetry. The variable relative importance for EPVS-category prediction was explored using a classification random forest approach. Results: High EPVS patients were older (49 vs 44 years, p = 0.003), had ⩾ 1 vascular risk factors (VRFs; p = 0.005), lower CVS% (67% vs 78%, p < 0.001), reduced brain volumes (whole brain: 0.63 vs 0.73, p = 0.01; gray matter: 0.36 vs 0.40; p = 0.002), and older brain-predicted age (58 vs 50 years, p < 0.001). No differences were found for neuroinflammatory markers. After adjusting for age and VFRs (multivariate analyses), the high EPVS category correlated with lower CVS% (odds ratio (OR) = 0.98, 95% confidence interval (CI) = 0.96–0.99; p = 0.02), lower whole brain (OR = 0.01, 95% CI = 0.0003–0.5; p = 0.02), gray matter (OR = 0.0004, 95% CI = 0.0000004–0.4; p = 0.03) volumes, and higher brain-PAD (OR = 1.05, 95% CI = 1.01–1.09; p = 0.02). Random forest identified brain-PAD as the most important predictor of high EPVS. Conclusion: EPVS in MS likely reflect microangiopathic disease rather than neuroinflammation, potentially contributing to accelerated neurodegeneration.

Upregulation of granzyme B and C-X3-C motif receptor 1 in circulating plasmablasts was negatively regulated by Notch signal in patients with systemic lupus erythematosus.

As one molecule related to cytotoxicity, surface expression of C-X3-C motif receptor 1 (CX3CR1) was highly correlated with intracellular granzyme B (GZMB) in NK and cytolytic T cells. However, the expression of CX3CR1 and GZMB in B cells has not been clarified, and their clinical significance in systemic lupus erythematosus (SLE) remains unclear. This study aimed to clarify the changes and clinical significance of peripheral blood B cells expressing GZMB and/or CX3CR1 in SLE. Peripheral blood was collected from 39 SLE patients and 48 healthy controls. We found that GZMB and CX3CR1 expression varied in different B-cell subsets, with plasmablasts possessing the highest positive percentages, consistent with bioinformatics prediction. GZMB+ and CX3CR1+ percentages in circulating B cells and plasmablasts were increased in SLE patients. CX3CR1 was upregulated on B cells after in vitro stimulation. Notch intracellular domain (NICD) expression was significantly decreased in plasmablasts of SLE patients and CX3CR1 in plasmablasts was downregulated with the addition of JAG1. In conclusion, GZMB and CX3CR1 were increased in B cells and in plasmablasts of SLE patients and CX3CR1 was negatively regulated by Notch signal in plasmablasts, which may be involved in SLE pathogenesis.

Diagnostic performance of mpox virus (MPXV) real-time PCR assays: multicenter assessment and extended sensitivity analysis.

To comprehensively investigate the diagnostic performance of routinely used assays in MPXV testing, the National Center of Clinical Laboratories in China conducted a nationwide external quality assessment (EQA) scheme and an evaluated nine assays used by ≥ 5 laboratories in the EQA. MPXV virus-like particles with 2700, 900 and 300 copies/mL were distributed to 195 EQA laboratories. For extended analysis, triple-diluted samples from 9000 to 4.12 copies/mL were repeated 20 times using the assays employed by ≥ 5 laboratories. The diagnostic performance was assessed by analyzing EQA data and calculating the limits of detection (LODs). The performance was competent in 87.69% (171/195) of the participants and 87.94% (175/199) of the datasets. The positive percentage agreements (PPAs) were greater than 99% for samples at 2700 and 900 copies/mL, and 95.60% (761/796) for samples at 300 copies/mL. The calculated LODs for the two clades ranged from 228.44 to 924.31 copies/mL and were greater than the LODs specified by the respective kits. EasyDiagnosis had the lowest calculated LODs and showed superior performance in EQA, whereas BioGerm and Sansure, with higher calculated LODs, did not perform well in EQA. This study provides valuable information from the EQA data and evaluation of the diagnostic performance of MPXV detection assays. It also provided insights into reagent optimization and enabled prompt public health interventions for the outbreak.

Dynamic changes of SCGN expression imply different phases of clear cell renal cell carcinoma progression

The secretagogin (SCGN) was originally identified as a secreted calcium-binding protein present in the cytoplasm. Recent studies have found that SCGN has a close relationship with cancer. However, its role in the occurrence, progression, and prognosis of clear cell renal cell carcinoma (ccRCC) remains unclear. In this study, we utilized a mutual authentication method based on public databases and clinical samples to determine the role of SCGN in the progression and prognosis of ccRCC. Firstly, we comprehensively analyzed the expression characteristics of SCGN in ccRCC in several public databases. Subsequently, we systematically evaluated SCGN expression on 252 microarrays of ccRCC tissues from different grades. It was found that SCGN was absent in all the normal kidney tissues and significantly overexpressed in ccRCC tumor tissues. In addition, the expression level of SCGN gradually decreased with an increase in tumor grade, and the percentage of SCGN staining positivity over 50% was 86.7% (13/15) and 73.4% (58/79) in Grade1 and Grade2, respectively, while it was only 8.3% (12/144) in Grade3, and the expression of SCGN was completely absent in Grade4 (0/14) and distant metastasis group (0/4). Additionally, the expression of SCGN was strongly correlated with the patient's prognosis, with the higher the expression levels of SCGN being associated with longer overall survival and disease-free survival of patients. In conclusion, our results suggest that reduced expression of SCGN in cancer cells is correlated with the progression and prognosis of ccRCC.

Determination of Serum Vitamin D Levels in Patients with COVID-19

Background: In 2019, the first cases of an acute respiratory infectious disease were announced in the city of Wuhan, China. In places where the speed of transmission and the resulting high prevalence and death from this virus is high, it is important to find things that help prevent and reduce the symptoms and complications of the disease, one of these things. Things are serum levels of vitamin D. As a result of this study, serum levels of vitamin D were measured in patients with Covid-19. Methods: From December to March of 1400, 100 samples of people hospitalized in Khurshid laboratory were examined to identify the RNA of the Covid-19 virus by Real Time PCR method and at the same time to check the serum levels of vitamin D. The data was statistically analyzed using SPSS software. Results: The average age of the patients was between 12.45 and 40.8 years. Comparison the two Covid-19 positive and negative groups in terms of symptoms, it was found that the patients with RH positive had more positive PCR percentage and a significant difference was reported between RH positive and Covid-19 (p=0.006). In comparing the relationship between disease symptoms and the rate of PCR positive reports of gastrointestinal symptoms, history of significant disease, cough, fever, a significant difference was reported (p&lt;0.001). Also, 50% of the samples were PCR positive. Based on the t-test, a significant difference was reported between the serum levels of vitamin D and Covid-19 (p&lt;0.001). Conclusion: The results showed that the vitamin D is an acceptable protective factor against Covid19 infection and its deficiency increases the probability of infection.

Performance of and Severe Acute Respiratory Syndrome Coronavirus 2 Diagnostics Based on Symptom Onset and Close Contact Exposure: An Analysis From the Test Us at Home Prospective Cohort Study.

Understanding changes in diagnostic performance after symptom onset and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure within different populations is crucial to guide the use of diagnostics for SARS-CoV-2. The Test Us at Home study was a longitudinal cohort study that enrolled individuals across the United States between October 2021 and February 2022. Participants performed paired antigen-detection rapid diagnostic tests (Ag-RDTs) and reverse-transcriptase polymerase chain reaction (RT-PCR) tests at home every 48 hours for 15 days and self-reported symptoms and known coronavirus disease 2019 exposures immediately before testing. The percent positivity for Ag-RDTs and RT-PCR tests was calculated each day after symptom onset and exposure and stratified by vaccination status, variant, age category, and sex. The highest percent positivity occurred 2 days after symptom onset (RT-PCR, 91.2%; Ag-RDT, 71.1%) and 6 days after exposure (RT-PCR, 91.8%; Ag-RDT, 86.2%). RT-PCR and Ag-RDT performance did not differ by vaccination status, variant, age category, or sex. The percent positivity for Ag-RDTs was lower among exposed, asymptomatic than among symptomatic individuals (37.5% (95% confidence interval [CI], 13.7%-69.4%) vs 90.3% (75.1%-96.7%). Cumulatively, Ag-RDTs detected 84.9% (95% CI, 78.2%-89.8%) of infections within 4 days of symptom onset. For exposed participants, Ag-RDTs detected 94.0% (95% CI, 86.7%-97.4%) of RT-PCR-confirmed infections within 6 days of exposure. The percent positivity for Ag-RDTs and RT-PCR tests was highest 2 days after symptom onset and 6 days after exposure, and performance increased with serial testing. The percent positivity of Ag-RDTs was lowest among asymptomatic individuals but did not differ by sex, variant, vaccination status, or age category.

Diagnosing OSA and Insomnia at Home Based Only on an Actigraphy Total Sleep Time and RIP Belts an Algorithm "Nox Body Sleep™".

The COVID-19 pandemic has influenced clinical sleep protocols with stricter hospital disinfection requirements. Facing these new rules, we tested if a new artificial intelligence (AI) algorithm: The Nox BodySleep™ (NBS) developed without airflow signals for the analysis of sleep might assess pertinently sleep in patients with Obstructive Sleep Apnea (OSA) and chronic insomnia (CI) as a control group, compared to polysomnography (PSG) manual scoring. NBS is a recurrent neural network model that estimates Wake, NREM, and REM states, given features extracted from activity and respiratory inductance plethysmography (RIP) belt signals (Nox A1 PSG). Sleep states from 139 PSG studies (CI N = 72; OSA N = 67) were analyzed by NBS and compared to manually scored PSG using positive percentage agreement, negative percentage agreement, and overall agreement metrics. Similarly, we compared common sleep parameters and OSA severity using sleep states estimated by NBS for each recording and compared to manual scoring using Bland-Altman analysis and intra-class correlation coefficient. For 127,170 sleep epochs, an overall agreement of 83% was reached for Wake, NREM and REM states (92% for REM states in CI patients) between NBS and manually scored PSG. Overall agreement for estimating OSA severity was 100% for moderate-severe OSA and 91% for minimal OSA. The absolute errors of the apnea-hypopnea index (AHI) and total sleep time (TST) were significantly lower for the NBS compared to no scoring of sleep. The intra-class correlation was higher for AHI and significantly higher for TST using the NBS compared to no scoring of sleep. NBS gives sleep states, parameters and AHI with a good positive and negative percentage agreement, compared with manually scored PSG.

Unexpected positive cultures of humeral head detected with dithiothreitol in primary shoulder arthroplasty

BackgroundUnexpected positive cultures (UPCs) are frequently observed in primary shoulder arthroplasty and its clinical significance has not yet been well defined. The aim is to evaluate the UPCs in humeral head in primary shoulder replacement and to understand if UPCs increase in patients with risk factors for contamination (previous surgery or infiltrations). MethodsPatients undergoing total shoulder replacement were enrolled in this prospective observational study. To reduce the risk of humeral head contamination, all known procedures to reduce C. acnes burden of the skin were implemented. Patients were divided into 2 groups, namely patients who had undergone previous rotator cuff repair or infiltration and patients with no risk factors for contamination. All the humeral heads harvested were treated with Dithiothreitol, in a specific device (MicroDTTect), to increase the sensitivity of the cultures for bacterial identification. The cultures were analyzed for aerobic and anaerobic bacteria for up to 14 days. ResultsThe UPCs positivity rate of the 80 patients in the study was 19 % (15 patients). The positivity rates for UPCs in the group with and without risk factors were 30 % (12 patients) and 7.5% (3 patients), respectively. The rate of positive culture was higher in men (87%) than in women (13%).The observed positivity was due to Cutibacterium acnes and peptoniphilus asaccarolyticus, both slow-growing anaerobes. ConclusionsPatients with previous surgery or infiltrations had a 4-fold higher rate of positivity for UPCs compared with patients without previous risk factors. The higher percentage of positivity in patients with risk factors could be related to changes in the joint microenvironment after shoulder procedures. We do not know whether the presence of UPCs could be associated with the development of periprosthetic infections at longer follow-up.

Detection of comprehensive oncogenic driver alteration of non-small cell lung cancer from cytology specimens by multi-gene PCR panel.

8579 Background: The analysis of the next-generation sequencing (NGS) panel test requires a sufficient amount of tissue specimens (TS), but the collection of tissue specimens can be sometimes challenging in clinical practice. Despite being easier and safer to collect than TS, cytology specimens (CS) are considered unsuitable for NGS due to the small number of tumor cells. The AmoyDx Pan Lung Cancer PCR Panel (AmoyDx), a multi-gene PCR panel that amplified mutation or fusion variants of 11 genes (EGFR, ALK, ROS1, RET, MET HER2, BRAF, KRAS, and NTRK1-3) by real-time PCR, can be performed with smaller amounts of nucleic acid than NGS, and CS may be suitable for multi-gene analysis using this panel. In this study, we evaluated the feasibility of multi-gene analysis using CS, and the concordance rate of gene alteration between CS and TS in non–small cell lung cancer (NSCLC). Methods: We enrolled consecutive NSCLC patients obtaining CS through bronchoscopy, including transbronchial brushing (TBB) and transbronchial needle aspiration (TBNA) from September 2020 to March 2023. These CS were preserved as frozen pellets. The difference in the amount of nucleic acid, the success rate and the concordance rate of gene alteration with AmoyDx were evaluated between CS and pared TS collected simultaneously with CS. Results: A total of 131 (Ad/Sq/NSCLC-NOS: 113/2/16) cases were enrolled in this study. Fifty-nine specimens were obtained through TBB and another 72 were obtained through TBNB. The median nucleic acid concentration (NanoDrop [ng/μL]) isolated from CS was comparable to that isolated from TS (DNA 114/99, p=0.96; RNA 36/27, p=0.63). However, the median DNA concentration in CS was significantly lower (80/102, p=0.01) in TBB samples, while in TBNA samples, it was higher (134/90, p=0.03). Almost all CS (99.2%,130/131) and TS (99.2%,130/131) were analyzed successfully with AmoyDx, with only one RNA analysis failure in each group. Among CS, 78 (60%) samples exhibit gene alteration, including EGFR/KRAS/BRAF/HER2/ALK/ROS1/MET/RET: 44/9/2/5/8/1/8/1, while 77 (59%); 44/9/2/6/6/1/8/1 in TS. The positive percent agreement, negative percent agreement, and overall percent agreement of CS using analysis compared with the results of TS using analysis were 99% (76/77), 96% (52/54), and 98% (128/131), respectively. Conclusions: CS exhibit an extremely high success rate for multi-gene analysis, with nucleic acid yield comparable to TS. Moreover, the concordance rate of gene alteration between CS and TS is also remarkably high. CS emerge as a viable alternative to TS for analyzing driver gene alteration in multi-gene PCR analysis.

Analytical validation of the Labcorp Plasma Complete test to enable precision oncology through solid tumor liquid biopsy comprehensive genomic profiling.

3063 Background: To help guide treatment decisions and enable clinical trial matching for cancer patients, tumor genomic profiling is an essential precision oncology tool. Liquid biopsy may be used as a complementary approach to assess tumor-specific DNA alterations circulating in the blood. The Labcorp Plasma Complete test is a next-generation-sequencing (NGS), cell-free DNA (cfDNA) comprehensive genomic profiling test that identifies actionable and clinically relevant variants in advanced and metastatic solid cancers across 521 genes. Methods: The Labcorp Plasma Complete test is a hybrid capture based, targeted NGS test, optimized for 25 ng of cfDNA input and is intended for variant detection in all solid cancer indications. The test interrogates all coding exons of 521 genes to comprehensively detect single nucleotide variants (SNVs) and insertion and deletions (indels). The test also reports copy number amplifications (CNAs) and gene translocations in 12 genes, and microsatellite instability (MSI). In total, 631 cancer patient plasma samples were evaluated by the test including lung, breast, colorectal, head and neck, pancreatic, gynecologic, and prostate cancers among other indications. Well-characterized reference samples (Genome in a Bottle) were utilized to assess analytical specificity. Contrived cell lines and clinical samples were utilized to establish analytical sensitivity, accuracy, as well as precision, reproducibility, and repeatability (PRR). Results: The test yielded results for 98.3% (620/631) of cases and identified variants in 94.7% (587/620) with a median of 6 variants per case. Clinically actionable variants were detected in 42.1% of clinical samples. Analytical specificity was ≥99.9999% for SNVs and 100% for indels, CNAs, translocations, and MSI. Analytical sensitivity (limit of detection, 95%) was verified for each variant type, with a median variant allele frequency (VAF) of 1.42% for SNVs and 1.43% for indels, 1.7-fold for amplifications, 0.35% fusion read fraction for translocations, and 0.82% VAF for MSI. The intra-laboratory PRR study resulted in 94.9% average percent agreement (APA) and 99.9% average negative agreement (ANA) for sequence variants (SNVs and indels) and 100% APA and ANA for CNAs, translocations, and MSI. Orthogonal assays including other NGS tests and digital PCR were utilized to assess Labcorp Plasma Complete accuracy which demonstrated an aggregate analytical concordance of 96.28% positive percent agreement and &gt;99.9999% negative percent agreement for all variants. Conclusions: The analytical validation of the Labcorp Plasma Complete test demonstrates that the liquid biopsy approach is highly sensitive, specific, accurate, reproducible, and robust for comprehensive genomic profiling to complement tissue-based testing and inform clinical decision making.

MSK-ACCESS powered with SOPHiA DDM: Performance analysis of a decentralized MSK-ACCESS solution.

e15063 Background: Blood plasma cell-free DNA (cfDNA) testing of cancer patients allows for genomic profiling when tissue sampling is too invasive or of insufficient quality. This approach has demonstrated clinical utility to identify treatment targets, screen for resistance and monitor disease burden. MSK-ACCESS (Memorial Sloan Kettering – Analysis of Circulating cfDNA to Evaluate Somatic Status) is a validated, high sensitivity cfDNA assay employed at MSK to identify biologically actionable tumor alterations in clinical care. SOPHiA GENETICS is developing a decentralized solution of this assay that incorporates major features of MSK-ACCESS such as molecular barcoding, duplex-based variant calling, the inclusion of tumor-informed prior knowledge and identification of somatic alterations through the removal of both germline and clonal hematopoiesis (CH) variants. Here, we present the results of a performance study obtained during product development. Methods: A cohort of 24 plasma cfDNA and matched white blood cell (WBC) DNA samples were collected from patients with solid tumors and processed at MSK according to the validated standard operating procedures and bioinformatic analyses. In parallel, for the same set of materials libraries were constructed at SOPHiA GENETICS using the proprietary CUMIN molecular identifiers, captured with probes targeting the updated MSK-ACCESS v2 set of 146 genes and sequenced on an Illumina NovaSeq 6000. Variants were called using a duplex-aware approach by SOPHiA GENETICS and germline and CH variants were identified and filtered by paired cfDNA – WBC DNA analysis. Accuracy of the decentralized “MSK-ACCESS powered with SOPHiA DDM” solution was assessed through concordance to the orthogonal results obtained by MSK. Results: A total of 104 somatic SNV/Indels were detected with variant allele fractions (VAF) ranging from 0.1% to 97.0% with a median of 5 variants per sample. The positive percent agreement (PPA) for all variants above the limit of detection of the original MSK-ACCESS assay was 98.9% with 99.98% specificity. For the subset of prior-knowledge variants PPA was 95.6% down to 0.1% VAF. A total of additional 59 variants with ≤ 15% VAF were found both in cfDNA and WBC and assigned as CH-derived. Importantly, these occurred not only in CH-associated genes but also in common oncogenes such as BRCA1/2 and ERBB2, highlighting the utility of matched WBC analysis to correctly identify somatic variants. Conclusions: The results demonstrate that the decentralized “MSK-ACCESS powered with SOPHiA DDM” solution exhibits a high degree of agreement to the results achieved by MSK. Further studies will be conducted to expand the analytical performance evaluation.