LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 4 of total 4

Search options

  1. Article ; Online: Next-Generation Sequencing (NGS) in COVID-19

    Goldin John / Nikhil Shri Sahajpal / Ashis K. Mondal / Sudha Ananth / Colin Williams / Alka Chaubey / Amyn M. Rojiani / Ravindra Kolhe

    Current Issues in Molecular Biology, Vol 43, Iss 61, Pp 845-

    A Tool for SARS-CoV-2 Diagnosis, Monitoring New Strains and Phylodynamic Modeling in Molecular Epidemiology

    2021  Volume 867

    Abstract: This review discusses the current testing methodologies for COVID-19 diagnosis and explores next-generation sequencing (NGS) technology for the detection of SARS-CoV-2 and monitoring phylogenetic evolution in the current COVID-19 pandemic. The review ... ...

    Abstract This review discusses the current testing methodologies for COVID-19 diagnosis and explores next-generation sequencing (NGS) technology for the detection of SARS-CoV-2 and monitoring phylogenetic evolution in the current COVID-19 pandemic. The review addresses the development, fundamentals, assay quality control and bioinformatics processing of the NGS data. This article provides a comprehensive review of the obstacles and opportunities facing the application of NGS technologies for the diagnosis, surveillance, and study of SARS-CoV-2 and other infectious diseases. Further, we have contemplated the opportunities and challenges inherent in the adoption of NGS technology as a diagnostic test with real-world examples of its utility in the fight against COVID-19.
    Keywords next-generation sequencing ; COVID-19 ; challenges ; diagnostic assay ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: Alteration in Nasopharyngeal Microbiota Profile in Aged Patients with COVID-19

    Ravindra Kolhe / Nikhil Shri Sahajpal / Sagar Vyavahare / Akhilesh S. Dhanani / Satish Adusumilli / Sudha Ananth / Ashis K. Mondal / G. Taylor Patterson / Sandeep Kumar / Amyn M. Rojiani / Carlos M. Isales / Sadanand Fulzele

    Diagnostics, Vol 11, Iss 1622, p

    2021  Volume 1622

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) is an infectious virus that causes coronavirus disease 2019 (COVID-19) transmitted mainly through droplets and aerosol affecting the respiratory tract and lungs. Little is known regarding why ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) is an infectious virus that causes coronavirus disease 2019 (COVID-19) transmitted mainly through droplets and aerosol affecting the respiratory tract and lungs. Little is known regarding why some individuals are more susceptible than others and develop severe symptoms. In this study, we analyzed the nasopharyngeal microbiota profile of aged patients with COVID-19 (asymptomatic vs. symptomatic) vs. healthy individuals. We examined the nasopharynx swab of 84 aged-matched patients, out of which 27 were negative asymptomatic (NegA), 30 were positive asymptomatic (PA), and 27 patients were positive symptomatic (PSY). Our analysis revealed the presence of abundant Cyanobacterial taxa at phylum level in PA ( p -value = 0.0016) and PSY ( p -value = 0.00038) patients along with an upward trend in the population of Litoricola, Amylibacter, Balneola, and Aeromonas at the genus level. Furthermore, to know the relationship between the nasal microbiota composition and severity of COVID-19, we compared PA and PSY groups. Our data show that the nasal microbiota of PSY patients was significantly enriched with the signatures of two bacterial taxa: Cutibacterium ( p -value = 0.045) and Lentimonas ( p -value = 0.007 ) . Furthermore, we also found a significantly lower abundance of five bacterial taxa, namely: Prevotellaceae ( p -value = 7 × 10 −6 ), Luminiphilus ( p -value = 0.027), Flectobacillus ( p -value = 0.027), Comamonas ( p -value = 0.048), and Jannaschia ( p -value = 0.012) in PSY patients. The dysbiosis of the nasal microbiota in COVID-19 positive patients might have a role in contributing to the severity of COVID-19. The findings of our study show that there is a strong correlation between the composition of the nasal microbiota and COVID-19 severity. Further studies are needed to validate our finding in large-scale samples and to correlate immune response (cytokine Strome) and nasal microbiota to identify underlying mechanisms and develop therapeutic ...
    Keywords microbiota ; nasopharyngeal profile in aged patients with COVID-19 infection and severity ; Medicine (General) ; R5-920
    Subject code 610
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: Clinical performance and utility of a comprehensive next-generation sequencing DNA panel for the simultaneous analysis of variants, TMB and MSI for myeloid neoplasms.

    Nikhil Shri Sahajpal / Ashis K Mondal / Sudha Ananth / Allan Njau / Pankaj Ahluwalia / Kimya Jones / Meenakshi Ahluwalia / Nwogbo Okechukwu / Natasha M Savage / Vamsi Kota / Amyn M Rojiani / Ravindra Kolhe

    PLoS ONE, Vol 15, Iss 10, p e

    2020  Volume 0240976

    Abstract: The extensively employed limited-gene coverage NGS panels lead to clinically inadequate molecular profiling of myeloid neoplasms. The aim of the present investigation was to assess performance and clinical utility of a comprehensive DNA panel for myeloid ...

    Abstract The extensively employed limited-gene coverage NGS panels lead to clinically inadequate molecular profiling of myeloid neoplasms. The aim of the present investigation was to assess performance and clinical utility of a comprehensive DNA panel for myeloid neoplasms. Sixty-one previously well characterized samples were sequenced using TSO500 library preparation kit on NextSeq550 platform. Variants with a VAF ≥ 5% and a total read depth of >50X were filtered for analysis. The following results were recorded-for clinical samples: clinical sensitivity (97%), specificity (100%), precision (100%) and accuracy (99%) whereas reference control results were 100% for analytical sensitivity, specificity, precision and accuracy, with high intra- and inter-run reproducibility. The panel identified 880 variants across 292 genes, of which, 749 variants were in genes not covered in the 54 gene panel. The investigation revealed 14 variants in ten genes, and at least one was present in 96.2% patient samples that were pathogenic/ likely pathogenic in myeloid neoplasms. Also, 15 variants in five genes were found to be pathogenic/ likely pathogenic in other tumor types. Further, the TMB and MSI scores ranged from 0-7 and 0-9, respectively. The high analytical performance and clinical utility of this comprehensive NGS panel makes it practical and clinically relevant for adoption in clinical laboratories for routine molecular profiling of myeloid neoplasms.
    Keywords Medicine ; R ; Science ; Q
    Subject code 610
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19

    Nikhil Shri Sahajpal / Chi-Yu Jill Lai / Alex Hastie / Ashis K. Mondal / Siavash Raeisi Dehkordi / Caspar I. van der Made / Olivier Fedrigo / Farooq Al-Ajli / Sawan Jalnapurkar / Marta Byrska-Bishop / Rashmi Kanagal-Shamanna / Brynn Levy / Maximilian Schieck / Thomas Illig / Silviu-Alin Bacanu / Janet S. Chou / Adrienne G. Randolph / Amyn M. Rojiani / Michael C. Zody /
    Catherine A. Brownstein / Alan H. Beggs / Vineet Bafna / Erich D. Jarvis / Alexander Hoischen / Alka Chaubey / Ravindra Kolhe

    iScience, Vol 25, Iss 2, Pp 103760- (2022)

    2022  

    Abstract: Summary: Impressive global efforts have identified both rare and common gene variants associated with severe COVID-19 using sequencing technologies. However, these studies lack the sensitivity to accurately detect several classes of variants, especially ... ...

    Abstract Summary: Impressive global efforts have identified both rare and common gene variants associated with severe COVID-19 using sequencing technologies. However, these studies lack the sensitivity to accurately detect several classes of variants, especially large structural variants (SVs), which account for a substantial proportion of genetic diversity including clinically relevant variation. We performed optical genome mapping on 52 severely ill COVID-19 patients to identify rare/unique SVs as decisive predisposition factors associated with COVID-19. We identified 7 SVs involving genes implicated in two key host-viral interaction pathways: innate immunity and inflammatory response, and viral replication and spread in nine patients, of which SVs in STK26 and DPP4 genes are the most intriguing candidates. This study is the first to systematically assess the potential role of SVs in the pathogenesis of COVID-19 severity and highlights the need to evaluate SVs along with sequencing variants to comprehensively associate genomic information with interindividual variability in COVID-19 phenotypes.
    Keywords Genetic sample ; Genomics ; Virology ; Science ; Q
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top