0 Ratings

ID

45801

Description

Principal Investigator: Joseph DeRisi, PhD, Howard Hughes Medical Institute, University of California, San Francisco, USA MeSH: Encephalitis,Meningitis,Myelitis https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001067 This is a prospective observational study seeking to identify pathogens in cases of unexplained neurological disease, particularly those in which there is a presumed infectious cause. This next generation analytical approach will hopefully allow for rapid identification of foreign genomic material, and through a sophisticated bioinformatics pipeline developed in the DeRisi lab, these foreign genomic sequences can be aligned to all known sequences in publicly available databases (i.e. GenBank) which may allow for identification of novel pathogens or known pathogens that are not frequently tested for as part of standard diagnostic work-ups.

Link

dbGaP-study=phs001067

Keywords

  1. 6/23/23 6/23/23 - Chiara Middel
Copyright Holder

Joseph DeRisi, PhD, Howard Hughes Medical Institute, University of California, San Francisco, USA

Uploaded on

June 23, 2023

DOI

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License

Creative Commons BY 4.0

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    dbGaP phs001067 Metagenomic Deep Sequencing in Meningitis and Encephalitis

    This sample attributes data table includes body site where sample was collected, analyte type, tumor status, and histological type.

    pht005287
    Description

    pht005287

    Alias
    UMLS CUI [1,1]
    C3846158
    De-identified Sample ID
    Description

    SAMPLE_ID

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C4684638
    UMLS CUI [1,2]
    C1299222
    Body site where sample was collected
    Description

    BODY_SITE

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C0449705
    Analyte Type
    Description

    ANALYTE_TYPE

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C4744818
    Tumor status
    Description

    IS_TUMOR

    Data type

    text

    Alias
    UMLS CUI [1,1]
    C0475752
    Cell or tissue type or subtype of sample
    Description

    HISTOLOGICAL_TYPE

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C2347026
    UMLS CUI [1,2]
    C0007634
    UMLS CUI [1,3]
    C0332307
    UMLS CUI [2,1]
    C2347026
    UMLS CUI [2,2]
    C0007634
    UMLS CUI [2,3]
    C0449560
    UMLS CUI [3,1]
    C1292533
    UMLS CUI [3,2]
    C0332307
    UMLS CUI [4,1]
    C1292533
    UMLS CUI [4,2]
    C0449560

    Similar models

    This sample attributes data table includes body site where sample was collected, analyte type, tumor status, and histological type.

    Name
    Type
    Description | Question | Decode (Coded Value)
    Data type
    Alias
    Item Group
    pht005287
    C3846158 (UMLS CUI [1,1])
    SAMPLE_ID
    Item
    De-identified Sample ID
    string
    C4684638 (UMLS CUI [1,1])
    C1299222 (UMLS CUI [1,2])
    BODY_SITE
    Item
    Body site where sample was collected
    string
    C0449705 (UMLS CUI [1,1])
    ANALYTE_TYPE
    Item
    Analyte Type
    string
    C4744818 (UMLS CUI [1,1])
    Item
    Tumor status
    text
    C0475752 (UMLS CUI [1,1])
    Code List
    Tumor status
    CL Item
    Is not a tumor (N)
    C0027651 (UMLS CUI [1,1])
    C1518422 (UMLS CUI [1,2])
    CL Item
    Is Tumor (Y)
    C0027651 (UMLS CUI [1,1])
    HISTOLOGICAL_TYPE
    Item
    Cell or tissue type or subtype of sample
    string
    C2347026 (UMLS CUI [1,1])
    C0007634 (UMLS CUI [1,2])
    C0332307 (UMLS CUI [1,3])
    C2347026 (UMLS CUI [2,1])
    C0007634 (UMLS CUI [2,2])
    C0449560 (UMLS CUI [2,3])
    C1292533 (UMLS CUI [3,1])
    C0332307 (UMLS CUI [3,2])
    C1292533 (UMLS CUI [4,1])
    C0449560 (UMLS CUI [4,2])

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