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  1. Article ; Online: Fusobacterium nucleatum

    Desai, Sanket / Dharavath, Bhasker / Manavalan, Sujith / Rane, Aishwarya / Redhu, Archana Kumari / Sunder, Roma / Butle, Ashwin / Mishra, Rohit / Joshi, Asim / Togar, Trupti / Apte, Shruti / Bala, Pratyusha / Chandrani, Pratik / Chopra, Supriya / Bashyam, Murali Dharan / Banerjee, Anirban / Prabhash, Kumar / Nair, Sudhir / Dutt, Amit

    NAR cancer

    2022  Volume 4, Issue 1, Page(s) zcac006

    Abstract: Persistent pathogen infection is a known cause of malignancy, although with sparse systematic evaluation across tumor types. We present a comprehensive landscape of 1060 infectious pathogens across 239 whole exomes and 1168 transcriptomes of breast, lung, ...

    Abstract Persistent pathogen infection is a known cause of malignancy, although with sparse systematic evaluation across tumor types. We present a comprehensive landscape of 1060 infectious pathogens across 239 whole exomes and 1168 transcriptomes of breast, lung, gallbladder, cervical, colorectal, and head and neck tumors. We identify known cancer-associated pathogens consistent with the literature. In addition, we identify a significant prevalence of
    Language English
    Publishing date 2022-03-04
    Publishing country England
    Document type Journal Article
    ISSN 2632-8674
    ISSN (online) 2632-8674
    DOI 10.1093/narcan/zcac006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2

    Dharavath, Bhasker / Yadav, Neelima / Desai, Sanket / Sunder, Roma / Mishra, Rohit / Ketkar, Madhura / Bhanshe, Prasanna / Gupta, Anurodh / Redhu, Archana Kumari / Patkar, Nikhil / Dutt, Shilpee / Gupta, Sudeep / Dutt, Amit

    Heliyon. 2020 July, v. 6, no. 7

    2020  

    Abstract: Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically ...

    Abstract Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically analyse the data. Our assay could detect to a limit of 15 copies of SARS-CoV-2 transcripts—based on experiments performed by spiking total human RNA with in vitro synthesized viral transcripts. The assay was evaluated by performing 184 validations for the SARS-CoV-2 Nucleocapsid gene and human RNase P as an internal control reference gene with dilutions ranging from 1-100 ng for human RNA on a cohort of 26 clinical samples. 5 of 26 patients were confirmed to be infected with SARS-CoV-2, while 21 tested negative, consistent with the standards. The accuracy of the assay was found to be 100% sensitive and 100% specific based on the 26 clinical samples that need to be further verified using a large number of clinical samples. In summary, we present a rapid, easy to implement real-time PCR based assay with automated analysis using a novel COVID qPCR Analyzer tool with graphical user interface (GUI) to analyze the raw qRT-PCR data in an unbiased manner at a cost of under $3 per reaction and turnaround time of less than 2h, to enable in-house SARS-CoV-2 testing across laboratories.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; automation ; early diagnosis ; genes ; humans ; nucleocapsid ; quantitative polymerase chain reaction ; ribonucleases ; user interface
    Language English
    Dates of publication 2020-07
    Publishing place Elsevier Ltd
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2020.e04405
    Database NAL-Catalogue (AGRICOLA)

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  3. Article: A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2.

    Dharavath, Bhasker / Yadav, Neelima / Desai, Sanket / Sunder, Roma / Mishra, Rohit / Ketkar, Madhura / Bhanshe, Prasanna / Gupta, Anurodh / Redhu, Archana Kumari / Patkar, Nikhil / Dutt, Shilpee / Gupta, Sudeep / Dutt, Amit

    Heliyon

    2020  Volume 6, Issue 7, Page(s) e04405

    Abstract: Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically ...

    Abstract Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically analyse the data. Our assay could detect to a limit of 15 copies of SARS-CoV-2 transcripts-based on experiments performed by spiking total human RNA with
    Keywords covid19
    Language English
    Publishing date 2020-07-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2020.e04405
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Molecular characterization of lung squamous cell carcinoma tumors reveals therapeutically relevant alterations.

    Joshi, Asim / Mishra, Rohit / Desai, Sanket / Chandrani, Pratik / Kore, Hitesh / Sunder, Roma / Hait, Supriya / Iyer, Prajish / Trivedi, Vaishakhi / Choughule, Anuradha / Noronha, Vanita / Joshi, Amit / Patil, Vijay / Menon, Nandini / Kumar, Rajiv / Prabhash, Kumar / Dutt, Amit

    Oncotarget

    2021  Volume 12, Issue 6, Page(s) 578–588

    Abstract: Introduction: Unlike lung adenocarcinoma patients, there is no FDA-approved targeted-therapy likely to benefit lung squamous cell carcinoma patients.: Materials and methods: We performed survival analyses of lung squamous cell carcinoma patients ... ...

    Abstract Introduction: Unlike lung adenocarcinoma patients, there is no FDA-approved targeted-therapy likely to benefit lung squamous cell carcinoma patients.
    Materials and methods: We performed survival analyses of lung squamous cell carcinoma patients harboring therapeutically relevant alterations identified by whole exome sequencing and mass spectrometry-based validation across 430 lung squamous tumors.
    Results: We report a mean of 11.6 mutations/Mb with a characteristic smoking signature along with mutations in
    Conclusions: We present the first comprehensive landscape of genetic alterations underlying Indian lung squamous cell carcinoma patients and identify
    Language English
    Publishing date 2021-03-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2560162-3
    ISSN 1949-2553 ; 1949-2553
    ISSN (online) 1949-2553
    ISSN 1949-2553
    DOI 10.18632/oncotarget.27905
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2

    Dharavath, Bhasker / Yadav, Neelima / Desai, Sanket / Sunder, Roma / Mishra, Rohit / Ketkar, Madhura / Bhanshe, Prasanna / Gupta, Anurodh / Redhu, Archana Kumari / Patkar, Nikhil / Dutt, Shilpee / Gupta, Sudeep / Dutt, Amit

    Heliyon

    Abstract: Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically ...

    Abstract Early diagnosis of SARS-CoV-2 infected patients is essential to control the dynamics of the COVID-19 pandemic. We develop a rapid and accurate one-step multiplex TaqMan probe-based real-time RT-PCR assay, along with a computational tool to systematically analyse the data. Our assay could detect to a limit of 15 copies of SARS-CoV-2 transcripts—based on experiments performed by spiking total human RNA with in vitro synthesized viral transcripts. The assay was evaluated by performing 184 validations for the SARS-CoV-2 Nucleocapsid gene and human RNase P as an internal control reference gene with dilutions ranging from 1-100 ng for human RNA on a cohort of 26 clinical samples. 5 of 26 patients were confirmed to be infected with SARS-CoV-2, while 21 tested negative, consistent with the standards. The accuracy of the assay was found to be 100% sensitive and 100% specific based on the 26 clinical samples that need to be further verified using a large number of clinical samples. In summary, we present a rapid, easy to implement real-time PCR based assay with automated analysis using a novel COVID qPCR Analyzer tool with graphical user interface (GUI) to analyze the raw qRT-PCR data in an unbiased manner at a cost of under $3 per reaction and turnaround time of less than 2h, to enable in-house SARS-CoV-2 testing across laboratories.Infectious disease; Microbial genomics; Genomics; Molecular biology; Virology; Diagnostics; SARS-CoV-2; Real-time RT- PCR; COVID-19 detection assay; COVID qPCR analyzer; Graphical user interface (GUI)
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #634144
    Database COVID19

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  6. Article ; Online: A one-step, one-tube real-time RT-PCR based assay with an automated analysis for detection of SARS-CoV-2

    Dharavath, Bhasker / Yadav, Neelima / Desai, Sanket / Sunder, Roma / Mishra, Rohit / Ketkar, Madhura / Bhanshe, Prasanna / Gupta, Anurodh / Redhu, Archana Kumari / Patkar, Nikhil / Dutt, Shilpee / Gupta, Sudeep / Dutt, Amit

    Heliyon

    2020  Volume 6, Issue 7, Page(s) e04405

    Keywords covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2020.e04405
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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