0 Bedömningar
ID

45519

Beskrivning

Principal Investigator: Eric O. Johnson, PhD, RTI International, Research Triangle Park, North Carolina, USA MeSH: HIV,Viral Load,Substance Abuse, intravenous https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000454 The overarching goal of this project is to identify and characterize genetic determinants of HIV 1 susceptibility and resistance in samples of African American (AA) and European American (EA) injection drug users (IDUs) by conducting (1) a case/control genome-wide association (GWA) study of HIV 1 infection (positive/negative); (2) a case-only GWA study of viral load among HIV+ IDUs. The study uses existing samples and data from Urban Health Study (UHS) (PI: Alex Kral), which was the longest-running study of street-recruited IDUs in North America, from 1986-2005. UHS was a serial, cross-sectional sero-epidemiological study. Data were collected every 6 months in communities with a high prevalence of injection drug use in the San Francisco Bay Area. It used targeted sampling in neighborhoods at easily accessible community field sites, such as churches, single room occupancy hotels, and community centers. Eligibility criteria for initial entry to the study were (1) injection drug use in past 30 days; (2) ability to provide informed consent; and (3) age 18 or older. The UHS cohort includes over 9,000 African American and European American IDUs whose serum samples have been stored and data are available on HIV antibody status, HIV risk behaviors, drug abuse and demographics. The current study includes 984 HIV+ cases and 2,243 HIV- controls. Approximately two HIV- controls per case were frequency matched on: (1) self-reported ancestry; (2) sex; (3) age; (4) year of ascertainment; and (5) HIV risk class. This GWAS (DA026141) was funded by the National Institute on Drug Abuse (NIDA; PI: Eric O. Johnson). Funding support for genotyping, which was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR), was provided by NIDA and the NIH contract "High throughput genotyping for studying the genetic contributions to human disease"(HHSN268200782096C).

Länk

dbGaP study = phs000454

Nyckelord

Versioner (1)
  1. 14.12.22 14.12.22 - Adrian Schulz
Rättsinnehavare

Eric O. Johnson, PhD, RTI International, Research Triangle Park, North Carolina, USA

Uppladdad den

14. Dezember 2022

DOI

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Licens

Creative Commons BY 4.0
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    dbGaP phs000454 HIV-1 Host Genetics Among Injection Drug Users

    Engelsk

    The dataset contains data describing participants' case/control status, HIV risk group (Latent Class Analysis, LCA), several LCA indicators (e.g. multiple partners, needle sharing, STD), viral load, and provides basic socio-demographic information. Note that multiple measurements (over time) are reported for some variables.

    6 Formulär  
    pht002650
    Beskrivning

    pht002650

    Alias
    UMLS CUI [1,1]
    C3846158
    Subject ID
    Beskrivning

    subjid

    Datatyp

    string

    Alias
    UMLS CUI [1,1]
    C2348585
    Consent group as determined by DAC
    Beskrivning

    consent

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C0021430
    Case - control status of the subject
    Beskrivning

    affection_status

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C3274646
    HIV status
    Beskrivning

    hivstat

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C0458074
    Viral Load Copies/mL
    Beskrivning

    ViralLoad_cperml

    Datatyp

    float

    Alias
    UMLS CUI [1,1]
    C1168369
    Viral Log 10
    Beskrivning

    ViralLoad_Log10

    Datatyp

    float

    Alias
    UMLS CUI [1,1]
    C1168369
    UMLS CUI [1,2]
    C3873230
    Participant reported sex
    Beskrivning

    sex

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C0079399
    Self-reported ancestry of participant
    Beskrivning

    race

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C0015031
    Reported age of participant
    Beskrivning

    age

    Datatyp

    text

    Måttenheter
    • Years
    Alias
    UMLS CUI [1,1]
    C0001779
    Years
    Age strata used in frequency matching (</=37, 38-45, 46+)
    Beskrivning

    age_cat

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C3846158
    Year participated in UHS (1986-2002)
    Beskrivning

    year

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C3846158
    Year strata used in frequency matching (</= 1994; 1995+)
    Beskrivning

    year_cat

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C3846158
    Latent Class Analysis (LCA) assigned HIV risk group used in frequency matching
    Beskrivning

    lca_group

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C4704739
    UMLS CUI [1,2]
    C0744979
    Multiple sex partners in the past year, indicator used in LCA
    Beskrivning

    mpartners

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C0558265
    UMLS CUI [1,2]
    C4086728
    Ever had sexually transmitted disease (excluding HIV), indicator used in LCA
    Beskrivning

    stis

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C0036916
    UMLS CUI [1,2]
    C0332300
    UMLS CUI [1,3]
    C0019682
    Had receptive anal sex in the past 6 months, indicator used in LCA
    Beskrivning

    anal

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C0282347
    UMLS CUI [1,2]
    C3828652
    Sharing needles in the past 30 days, indicator used in LCA
    Beskrivning

    needleshare

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C0085091
    UMLS CUI [1,2]
    C4331910
    Participant ever traded sex for drugs or money, indicator used in LCA
    Beskrivning

    sexwork

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C0033595
    Blinded site indicator - site 1 vs. 2
    Beskrivning

    site

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C3846158
    Serum Sample ID
    Beskrivning

    sampid

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C5237951
    UMLS CUI [1,2]
    C1550100
    Genotype identified sex
    Beskrivning

    gwassex

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C5236416
    Record identified as individual appearing multiple times as inadvertant duplicate.
    Beskrivning

    cluster

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C0460112
    UMLS CUI [1,2]
    C0679646
    Unique individual who was selected for inclusion in the investigators' final analysis data set, based on passing QC and having complete phenotype and covariate data.
    Beskrivning

    final_analysis

    Datatyp

    text

    Alias
    UMLS CUI [1,1]
    C1512693
    UMLS CUI [1,2]
    C0679646
    Tillbaka till toppen

    Similar models

    The dataset contains data describing participants' case/control status, HIV risk group (Latent Class Analysis, LCA), several LCA indicators (e.g. multiple partners, needle sharing, STD), viral load, and provides basic socio-demographic information. Note that multiple measurements (over time) are reported for some variables.

    6 Formulär
    Name
    Typ
    Description | Question | Decode (Coded Value)
    Datatyp
    Alias
    Item Group
    pht002650
    C3846158 (UMLS CUI [1,1])
    subjid
    Item
    Subject ID
    string
    C2348585 (UMLS CUI [1,1])
    consent
    Item
    Consent group as determined by DAC
    text
    C0021430 (UMLS CUI [1,1])
    affection_status
    Item
    Case - control status of the subject
    text
    C3274646 (UMLS CUI [1,1])
    hivstat
    Item
    HIV status
    text
    C0458074 (UMLS CUI [1,1])
    ViralLoad_cperml
    Item
    Viral Load Copies/mL
    float
    C1168369 (UMLS CUI [1,1])
    ViralLoad_Log10
    Item
    Viral Log 10
    float
    C1168369 (UMLS CUI [1,1])
    C3873230 (UMLS CUI [1,2])
    sex
    Item
    Participant reported sex
    text
    C0079399 (UMLS CUI [1,1])
    race
    Item
    Self-reported ancestry of participant
    text
    C0015031 (UMLS CUI [1,1])
    age
    Item
    Reported age of participant
    text
    C0001779 (UMLS CUI [1,1])
    age_cat
    Item
    Age strata used in frequency matching (</=37, 38-45, 46+)
    text
    C3846158 (UMLS CUI [1,1])
    year
    Item
    Year participated in UHS (1986-2002)
    text
    C3846158 (UMLS CUI [1,1])
    year_cat
    Item
    Year strata used in frequency matching (</= 1994; 1995+)
    text
    C3846158 (UMLS CUI [1,1])
    lca_group
    Item
    Latent Class Analysis (LCA) assigned HIV risk group used in frequency matching
    text
    C4704739 (UMLS CUI [1,1])
    C0744979 (UMLS CUI [1,2])
    mpartners
    Item
    Multiple sex partners in the past year, indicator used in LCA
    text
    C0558265 (UMLS CUI [1,1])
    C4086728 (UMLS CUI [1,2])
    stis
    Item
    Ever had sexually transmitted disease (excluding HIV), indicator used in LCA
    text
    C0036916 (UMLS CUI [1,1])
    C0332300 (UMLS CUI [1,2])
    C0019682 (UMLS CUI [1,3])
    anal
    Item
    Had receptive anal sex in the past 6 months, indicator used in LCA
    text
    C0282347 (UMLS CUI [1,1])
    C3828652 (UMLS CUI [1,2])
    needleshare
    Item
    Sharing needles in the past 30 days, indicator used in LCA
    text
    C0085091 (UMLS CUI [1,1])
    C4331910 (UMLS CUI [1,2])
    sexwork
    Item
    Participant ever traded sex for drugs or money, indicator used in LCA
    text
    C0033595 (UMLS CUI [1,1])
    site
    Item
    Blinded site indicator - site 1 vs. 2
    text
    C3846158 (UMLS CUI [1,1])
    sampid
    Item
    Serum Sample ID
    text
    C5237951 (UMLS CUI [1,1])
    C1550100 (UMLS CUI [1,2])
    gwassex
    Item
    Genotype identified sex
    text
    C5236416 (UMLS CUI [1,1])
    cluster
    Item
    Record identified as individual appearing multiple times as inadvertant duplicate.
    text
    C0460112 (UMLS CUI [1,1])
    C0679646 (UMLS CUI [1,2])
    final_analysis
    Item
    Unique individual who was selected for inclusion in the investigators' final analysis data set, based on passing QC and having complete phenotype and covariate data.
    text
    C1512693 (UMLS CUI [1,1])
    C0679646 (UMLS CUI [1,2])
    Tillbaka till toppen 

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