scholarly journals Clinical Evaluation of a Metagenomics-Based Assay for Pneumonia Management

2021 ◽  
Vol 12 ◽  
Author(s):  
Yangqing Zhan ◽  
Teng Xu ◽  
Fusheng He ◽  
Wei-jie Guan ◽  
Zhengtu Li ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Treatment Initiation ◽  
Antimicrobial Treatment ◽  
Clinical Impact ◽  
Pathogenic Microorganisms ◽  
Clinical Value ◽  
Clinical Diagnoses ◽  
A Prospective Study ◽  
Generation Sequencing ◽  
Missed Diagnoses

Clinical value of metagenomic next-generation sequencing (mNGS) in pneumonia management is still controversial. A prospective study was conducted to evaluate the clinical impact of PneumoSeq in 57 immunocompetent (ICO) and 75 immunocompromised (ICH) pneumonia patients. The value of PneumoSeq for both etiological and clinical impact investigation in pneumonia was assessed. Among the 276 potential pathogens detected with PneumoSeq in our cohort, 251 (90.9%) were cross-validated. Clinical diagnoses of the causative pathogens were obtained for 97 patients, 90.7% of which were supported by PneumoSeq. Compared to conventional testing, PneumoSeq suggested potentially missed diagnoses in 16.7% of cases (22/132), involving 48 additional pathogenic microorganisms. In 58 (43.9%) cases, PneumoSeq data led to antimicrobial treatment de-escalation (n = 12 in ICO, n = 18 in ICH) and targeted treatment initiation (n = 7 in ICO, n = 21 in ICH). The PneumoSeq assay benefited the diagnosis and clinical management of both ICH and ICO pneumonia patients in real-world settings.

scholarly journals Clinical Application of Next-Generation Sequencing of Plasma Cell-Free DNA for Genotyping Untreated Advanced Non-Small Cell Lung Cancer

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2707
Author(s):  
Maria Gabriela O. Fernandes ◽  
Natália Cruz-Martins ◽  
Conceição Souto Moura ◽  
Susana Guimarães ◽  
Joana Pereira Reis ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Clinical Outcomes ◽  
Test Performance ◽  
Molecular Diagnostic ◽  
Test Accuracy ◽  
Newly Diagnosed ◽  
Next Generation ◽  
Clinical Value ◽  
Generation Sequencing

Background: Analysis of circulating tumor DNA (ctDNA) has remarkable potential as a non-invasive lung cancer molecular diagnostic method. This prospective study addressed the clinical value of a targeted-gene amplicon-based plasma next-generation sequencing (NGS) assay to detect actionable mutations in ctDNA in patients with newly diagnosed advanced lung adenocarcinoma. Methods: ctDNA test performance and concordance with tissue NGS were determined, and the correlation between ctDNA findings, clinical features, and clinical outcomes was evaluated in 115 patients with paired plasma and tissue samples. Results: Targeted-gene NGS-based ctDNA and NGS-based tissue analysis detected 54 and 63 genomic alterations, respectively; 11 patients presented co-mutations, totalizing 66 hotspot mutations detected, 51 on both tissue and plasma, 12 exclusively on tissue, and 3 exclusively on plasma. NGS-based ctDNA revealed a diagnostic performance with 81.0% sensitivity, 95.3% specificity, 94.4% PPV, 83.6% NPV, test accuracy of 88.2%, and Cohen’s Kappa 0.764. PFS and OS assessed by both assays did not significantly differ. Detection of ctDNA alterations was statistically associated with metastatic disease (p = 0.013), extra-thoracic metastasis (p = 0.004) and the number of organs involved (p = 0.010). Conclusions: This study highlights the potential use of ctDNA for mutation detection in newly diagnosed NSCLC patients due to its high accuracy and correlation with clinical outcomes.

scholarly journals Clinical Application of Metagenomic Next-Generation Sequencing in Patients with Hematologic Malignancies Suffering from Sepsis

2021 ◽  
Vol 9 (11) ◽  
pp. 2309
Author(s):  
Wang-Da Liu ◽  
Ting-Yu Yen ◽  
Po-Yo Liu ◽  
Un-In Wu ◽  
Prerana Bhan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hematologic Malignancies ◽  
Blood Cultures ◽  
Diagnostic Methods ◽  
Next Generation ◽  
Viral Loads ◽  
A Prospective Study ◽  
Positive Results ◽  
Serology Testing ◽  
Generation Sequencing

Background: Sepsis remains a common but fatal complication among patients with immune suppression. We aimed to investigate the performance of metagenomic next-generation sequencing (mNGS) compared with standard microbiological diagnostics in patients with hematologic malignancies. Methods: We performed a prospective study from June 2019 to December 2019. Adult patients with hematologic malignancies and a clinical diagnosis of sepsis were enrolled. Conventional diagnostic methods included blood cultures, serum galactomannan for Aspergillus, cryptococcal antigen and cytomegalovirus (CMV) viral loads. Blood samples for mNGS were collected within 24 h after hypotension developed. Results: Of 24 patients enrolled, mNGS and conventional diagnostic methods (blood cultures, serology testing and virus RT-PCR) reached comparable positive results in 9 cases. Of ten patients, mNGS was able to identify additional pathogens compared with conventional methods; most of the pathogens were virus. Conclusion: Our results show that mNGS may serve as adjunctive diagnostic tool for the identification of pathogens of hematologic patients with clinically sepsis.

scholarly journals P2.14-29 Clinical Impact of Next-Generation Sequencing (NGS) in Blood Liquid Biopsies for Treatment Decisions in Advanced NSCLC

2019 ◽  
Vol 14 (10) ◽  
pp. S840-S841
Author(s):  
M. Garcia Pardo ◽  
I. Martinez Delfrade ◽  
I. Aparicio Salcedo ◽  
M. Arregui Valles ◽  
M. Alva Bianchi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Advanced Nsclc ◽  
Treatment Decisions ◽  
Clinical Impact ◽  
Next Generation ◽  
Liquid Biopsies ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

scholarly journals Simultaneous Detection of Pathogens and Tumors in Patients With Suspected Infections by Next-Generation Sequencing

2021 ◽  
Author(s):  
Jiachun Su ◽  
Xu Han ◽  
Xiaogang Xu ◽  
Wenchao Ding ◽  
Ming Li ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Chromosomal Abnormalities ◽  
Malignant Tumors ◽  
Simultaneous Detection ◽  
Prior History ◽  
Next Generation ◽  
Clinical Value ◽  
Microbiological Testing ◽  
Number Variation ◽  
Generation Sequencing

Abstract Background: Differential diagnosis of patients with suspected infections is particularly difficult, but necessary for prompt diagnosis and rational use of antibiotics. A substantial proportion of these patients have non-infectious diseases that include malignant tumors. Metagenomic next-generation sequencing (mNGS) technologies are used with increasing frequency to aid clinical diagnosis of patients with suspected infections. Methods: Based upon mNGS technologies and chromosomal copy number variation (CNV) analysis on abundant human genome, a new workflow named Onco-mNGS was established to simultaneously detect pathogens and malignant tumors in patients with suspected infections. Results: Of 140 patients screened by Onco-mNGS testing at four hospitals in Shanghai, 115 patients were diagnosed with infections; 17 had obvious abnormal CNV signals indicating malignant tumors that were confirmed clinically. The sensitivity and specificity of mNGS testing for diagnosis of a clinically relevant infection was 53.0% (61/115) and 60% (15/25), respectively, vs 20.9% (24/115) and 96.0% (24/25), respectively, for conventional microbiological testing (both P<0.01). Klebsiella pneumoniae was the most common pathogen detected by mNGS, followed by E. coli and viruses. The chromosomal abnormalities of the 17 cases included genome-wide variations and local variations of a certain chromosome. Five of 17 patients had a final confirmed with malignant tumors, including three lung adenocarcinomas and two hematological tumors; one patient was highly suspected to have lymphoma; and 11 patients had a prior history of malignant tumor.Conclusions: This preliminary study demonstrates the feasibility and clinical value of using Onco-mNGS to simultaneously search for potential pathogens and malignant tumors in patients with suspected infections.

scholarly journals Clinical Impact of Plasma Metagenomic Next-generation Sequencing in a Large Pediatric Cohort

2021 ◽  
Vol Publish Ahead of Print ◽  
Author(s):  
Denver T. Niles ◽  
Paula A. Revell ◽  
Daniel Ruderfer ◽  
Lucila Marquez ◽  
J. Chase McNeil ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Impact ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Assessment of the Application and Clinical Value of Next-Generation Sequencing for the Diagnosis of Inherited Thrombocytopenia

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 4993-4993
Author(s):  
Miao Jiang ◽  
Qi Wang ◽  
Yiming Zhao ◽  
Ziqiang Yu ◽  
Suning Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Conflicts Of Interest ◽  
Gene Sequencing ◽  
Hereditary Diseases ◽  
Next Generation ◽  
Clinical Value ◽  
Sequencing Platform ◽  
Pathogenic Variants ◽  
Inherited Thrombocytopenia ◽  
Generation Sequencing

Abstract Inherited thrombocytopenia is a group of hereditary diseases with a reduction in platelet count as the main clinical manifestation. Clinically, there is an urgent need for a convenient and rapid diagnosis method. We introduced a high-throughput next-generation sequencing (NGS) platform into the routine diagnosis of patients with unexplained thrombocytopenia and analyzed the gene sequencing results to evaluate the value of NGS technology in the screening and diagnosis of inherited thrombocytopenia. From a cohort of 182 patients with thrombocytopenia, we screened 78 patients with hereditary features. For the blood samples of these 78 patients, a gene sequencing platform for hemorrhagic and thrombotic diseases comprising 89 genes was used to perform gene detection using NGS technology. When we combined the screening results with clinical features and other findings, 23 of 78 patients (29.5%) were diagnosed with inherited thrombocytopenia. In addition, 29 pathogenic variants, including 11 previously unreported variants, were identified in these patients. In summary, NGS could play more important role in the molecular pathology diagnosis of inherited thrombocytopenia. Through the use of this detection platform, we expect to establish a more effective diagnostic approach to such disorders. Disclosures No relevant conflicts of interest to declare.

scholarly journals Asymmetric pathogen spillover favors exotic plants over natives

2021 ◽  
Author(s):  
Lauren Waller ◽  
Warwick Allen ◽  
Amanda Black ◽  
Jonathan Tonkin ◽  
Jason Tylianakis ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Native Plants ◽  
Exotic Plants ◽  
Apparent Competition ◽  
Pathogenic Microorganisms ◽  
Indirect Benefit ◽  
Plant Soil ◽  
Soil Feedback ◽  
Competitive Hierarchies ◽  
Generation Sequencing

Exotic plants can escape from specialist pathogenic microorganisms in their new range, but may simultaneously accumulate generalist pathogens. This creates the potential for pathogen spillover, which could alter plant-competitive hierarchies via apparent competition. To assess the potential for and consequences of pathogen spillover in invaded communities, we conducted a community-level plant-soil feedback experiment in experimental communities that ranged in the extent of exotic dominance, using next-generation sequencing to characterize sharing of putatively-pathogenic, root-associated fungi (hereafter, ‘pathogens’). Exotic plants outperformed natives in communities, despite being subject to stronger negative plant-soil feedbacks in monoculture and harboring higher relative abundance of pathogens. Exotic plants made more general associations with pathogens, making them more prone to sharing pathogens with natives and exerting apparent competition. These data suggest that exotic plants accumulate generalist pathogens that are shared with native plants, conferring an indirect benefit to exotic, over native plants.

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