ID

45722

Description

Principal Investigator: Edward E. Walsh, M.D, University of Rochester Medical Center, Rochester, NY, USA MeSH: Respiratory Syncytial Virus Infections,Infant https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001201 A prospective multi-year clinical translational study including three cohorts of term infants experiencing their first Respiratory Syncytial Virus (RSV) season. All infants are less than or equal to nine months of age at study entry. The three subject cohorts represent the full spectrum of RSV disease severity and include a birth cohort, a cohort of infants hospitalized for RSV disease and infants evaluated at ambulatory settings for RSV infection. All infants are followed longitudinally and evaluated at recognition of acute RSV infection and twice during convalescence. Innate and adaptive immune status are comprehensively measured in association with clinical, environmental, viral, and bacteriologic factors. Genome-wide expression is assessed in the nasal airways, and in sorted peripheral blood lymphocytes. The study goal is to Identify host responses to RSV infection and factors associated with severe disease.

Link

dbGaP-study=phs001201

Keywords

Versions (1)
  1. 5/24/23 5/24/23 - Chiara Middel
Copyright Holder

Edward E. Walsh, M.D, University of Rochester Medical Center, Rochester, NY, USA

Uploaded on

May 24, 2023

DOI

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License

Creative Commons BY 4.0
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dbGaP phs001201 ASsessing and Predicting Infant RSV Effects and Severity (AsPIRES) Study

English

This subject phenotype table contains subject ID, age at time of visit, presence of symptoms (wheezing, rales, retraction, cyanosis, apnea, lethargy, and poor air movement), maximum respiratory rate, worst saturated oxygen score, length of stay, strain of RSV (Respiratory Syncytial Virus), derived RSV severity score, RSV severity label, and antibiotic use.

9 forms  
  1. StudyEvent: SEV1
    1. Eligibility Criteria
    2. The subject consent file includes subject ID and consent information.
    3. This data table contains a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
    4. This subject phenotype table contains subject ID, 12 genes (B2M, CD83, CES1, DNAI2, DNAH5, FOXRED1, GPI, KRT8, OAS1, PPIA, SOCS6, TYROBP) being expressed, and scores tied to gene expression.
    5. This subject phenotype table contains subject ID, delivery method, gestational age, birth weight, breastfeeding, family size, smoke exposure, enrollment season, sex, race, ethnicity, age at enrollment, and derived score for breastfeeding.
    6. This subject phenotype table contains subject ID, and any detected bacteria or virus pathogens including H.influenzae, M.catarrhalis, S.pneumoniae, coronavirus, and rhinovirus.
    7. This sample attribute table contains sample ID, and bacteria taxon including Moraxellaceae, Streptococcaceae, and Pasteurellaceae.
    8. This sample attribute table contains sample ID, body site, analyte type, tumor status, histological type, publication, attribute, sequence number, sample days, presence of bacteria and virus (adenovirus, bocavirus, coronavirus, C. pneumoniae, enterobacteriaceae, Flu A or B, H. influenzae, metapneumovirus, catarrhalis, M. hominis, M. pneumoniae, parechovirus, PIV, rhinovirus, respiratory syncytial virus, S. pneumoniae, and ureaplasma), antibody titer scores of serum (Fa, Ga, Gb, RSV A, RSV B, nasal swab, and nasal wash), and read count.
    9. This subject phenotype table contains subject ID, age at time of visit, presence of symptoms (wheezing, rales, retraction, cyanosis, apnea, lethargy, and poor air movement), maximum respiratory rate, worst saturated oxygen score, length of stay, strain of RSV (Respiratory Syncytial Virus), derived RSV severity score, RSV severity label, and antibiotic use.
pht008325
Description

pht008325

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

SUBJECT_ID

Data type

string

Alias
UMLS CUI [1,1]
C4684638
UMLS CUI [1,2]
C2348585
Subject age at time of visit
Description

VisitAge

Data type

float

Measurement units
  • months
Alias
UMLS CUI [1,1]
C0001779
UMLS CUI [1,2]
C1320304
months
Physician finding - general appearance
Description

phys_find_appearance

Data type

string

Alias
UMLS CUI [1,1]
C0031831
UMLS CUI [1,2]
C1148438
Presence of wheezing
Description

phys_find_wheezing

Data type

string

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0043144
Presence of rales
Description

phys_find_rales

Data type

string

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0034642
Presence of retractions
Description

phys_find_retractions

Data type

string

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0332523
Presence of cyanosis
Description

phys_find_cyanosis

Data type

string

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0010520
Presence of apnea
Description

phys_find_apnea

Data type

string

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0003578
Presence of lethargy
Description

phys_find_lethargy

Data type

string

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0023380
Presence of poor air movement
Description

phys_find_poor_air_movement

Data type

string

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C2700379
UMLS CUI [1,3]
C3536832
UMLS CUI [1,4]
C0026649
Maximum respiratory rate
Description

max_resp_rate

Data type

float

Alias
UMLS CUI [1,1]
C0806909
UMLS CUI [1,2]
C0231832
Worst saturated oxygen score
Description

worst_saO2

Data type

float

Alias
UMLS CUI [1,1]
C1522166
UMLS CUI [1,2]
C0523807
Length of stay
Description

lengthOfStay

Data type

float

Measurement units
  • months
Alias
UMLS CUI [1,1]
C0023303
months
Strain of RSV
Description

rsv_strain

Data type

string

Alias
UMLS CUI [1,1]
C0035236
UMLS CUI [1,2]
C1518614
Derived RSV severity score
Description

severity_score

Data type

float

Alias
UMLS CUI [1,1]
C1441547
UMLS CUI [1,2]
C0035236
UMLS CUI [1,3]
C1319166
RSV severity label
Description

Corrected RSV Severity

Data type

string

Alias
UMLS CUI [1,1]
C0035236
UMLS CUI [1,2]
C1319166
UMLS CUI [1,3]
C0181496
Antibiotic taken at visit 11 or a few days before v11 sample
Description

Antibiotic Use LE v11

Data type

string

Alias
UMLS CUI [1,1]
C0338237
UMLS CUI [1,2]
C1320303
UMLS CUI [1,3]
C0870078
UMLS CUI [2,1]
C0338237
UMLS CUI [2,2]
C0332152
UMLS CUI [2,3]
C1320303
UMLS CUI [2,4]
C0870078
Antibiotic taken at visit 11 or a few days before v11 sample or after v11 but before v13 sample
Description

Antibiotic Use LE v13

Data type

string

Alias
UMLS CUI [1,1]
C0338237
UMLS CUI [1,2]
C1320303
UMLS CUI [1,3]
C0870078
UMLS CUI [2,1]
C0338237
UMLS CUI [2,2]
C0332152
UMLS CUI [2,3]
C1320303
UMLS CUI [2,4]
C0870078
UMLS CUI [3,1]
C0338237
UMLS CUI [3,2]
C0231290
UMLS CUI [3,3]
C1320303
UMLS CUI [3,4]
C0870078
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Similar models

This subject phenotype table contains subject ID, age at time of visit, presence of symptoms (wheezing, rales, retraction, cyanosis, apnea, lethargy, and poor air movement), maximum respiratory rate, worst saturated oxygen score, length of stay, strain of RSV (Respiratory Syncytial Virus), derived RSV severity score, RSV severity label, and antibiotic use.

9 forms
  1. StudyEvent: SEV1
    1. Eligibility Criteria
    2. The subject consent file includes subject ID and consent information.
    3. This data table contains a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
    4. This subject phenotype table contains subject ID, 12 genes (B2M, CD83, CES1, DNAI2, DNAH5, FOXRED1, GPI, KRT8, OAS1, PPIA, SOCS6, TYROBP) being expressed, and scores tied to gene expression.
    5. This subject phenotype table contains subject ID, delivery method, gestational age, birth weight, breastfeeding, family size, smoke exposure, enrollment season, sex, race, ethnicity, age at enrollment, and derived score for breastfeeding.
    6. This subject phenotype table contains subject ID, and any detected bacteria or virus pathogens including H.influenzae, M.catarrhalis, S.pneumoniae, coronavirus, and rhinovirus.
    7. This sample attribute table contains sample ID, and bacteria taxon including Moraxellaceae, Streptococcaceae, and Pasteurellaceae.
    8. This sample attribute table contains sample ID, body site, analyte type, tumor status, histological type, publication, attribute, sequence number, sample days, presence of bacteria and virus (adenovirus, bocavirus, coronavirus, C. pneumoniae, enterobacteriaceae, Flu A or B, H. influenzae, metapneumovirus, catarrhalis, M. hominis, M. pneumoniae, parechovirus, PIV, rhinovirus, respiratory syncytial virus, S. pneumoniae, and ureaplasma), antibody titer scores of serum (Fa, Ga, Gb, RSV A, RSV B, nasal swab, and nasal wash), and read count.
    9. This subject phenotype table contains subject ID, age at time of visit, presence of symptoms (wheezing, rales, retraction, cyanosis, apnea, lethargy, and poor air movement), maximum respiratory rate, worst saturated oxygen score, length of stay, strain of RSV (Respiratory Syncytial Virus), derived RSV severity score, RSV severity label, and antibiotic use.
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
pht008325
C3846158 (UMLS CUI [1,1])
SUBJECT_ID
Item
De-identified Subject ID
string
C4684638 (UMLS CUI [1,1])
C2348585 (UMLS CUI [1,2])
VisitAge
Item
Subject age at time of visit
float
C0001779 (UMLS CUI [1,1])
C1320304 (UMLS CUI [1,2])
phys_find_appearance
Item
Physician finding - general appearance
string
C0031831 (UMLS CUI [1,1])
C1148438 (UMLS CUI [1,2])
phys_find_wheezing
Item
Presence of wheezing
string
C3854307 (UMLS CUI [1,1])
C0043144 (UMLS CUI [1,2])
phys_find_rales
Item
Presence of rales
string
C3854307 (UMLS CUI [1,1])
C0034642 (UMLS CUI [1,2])
phys_find_retractions
Item
Presence of retractions
string
C3854307 (UMLS CUI [1,1])
C0332523 (UMLS CUI [1,2])
phys_find_cyanosis
Item
Presence of cyanosis
string
C3854307 (UMLS CUI [1,1])
C0010520 (UMLS CUI [1,2])
phys_find_apnea
Item
Presence of apnea
string
C3854307 (UMLS CUI [1,1])
C0003578 (UMLS CUI [1,2])
phys_find_lethargy
Item
Presence of lethargy
string
C3854307 (UMLS CUI [1,1])
C0023380 (UMLS CUI [1,2])
phys_find_poor_air_movement
Item
Presence of poor air movement
string
C3854307 (UMLS CUI [1,1])
C2700379 (UMLS CUI [1,2])
C3536832 (UMLS CUI [1,3])
C0026649 (UMLS CUI [1,4])
max_resp_rate
Item
Maximum respiratory rate
float
C0806909 (UMLS CUI [1,1])
C0231832 (UMLS CUI [1,2])
worst_saO2
Item
Worst saturated oxygen score
float
C1522166 (UMLS CUI [1,1])
C0523807 (UMLS CUI [1,2])
lengthOfStay
Item
Length of stay
float
C0023303 (UMLS CUI [1,1])
rsv_strain
Item
Strain of RSV
string
C0035236 (UMLS CUI [1,1])
C1518614 (UMLS CUI [1,2])
severity_score
Item
Derived RSV severity score
float
C1441547 (UMLS CUI [1,1])
C0035236 (UMLS CUI [1,2])
C1319166 (UMLS CUI [1,3])
Corrected RSV Severity
Item
RSV severity label
string
C0035236 (UMLS CUI [1,1])
C1319166 (UMLS CUI [1,2])
C0181496 (UMLS CUI [1,3])
Antibiotic Use LE v11
Item
Antibiotic taken at visit 11 or a few days before v11 sample
string
C0338237 (UMLS CUI [1,1])
C1320303 (UMLS CUI [1,2])
C0870078 (UMLS CUI [1,3])
C0338237 (UMLS CUI [2,1])
C0332152 (UMLS CUI [2,2])
C1320303 (UMLS CUI [2,3])
C0870078 (UMLS CUI [2,4])
Antibiotic Use LE v13
Item
Antibiotic taken at visit 11 or a few days before v11 sample or after v11 but before v13 sample
string
C0338237 (UMLS CUI [1,1])
C1320303 (UMLS CUI [1,2])
C0870078 (UMLS CUI [1,3])
C0338237 (UMLS CUI [2,1])
C0332152 (UMLS CUI [2,2])
C1320303 (UMLS CUI [2,3])
C0870078 (UMLS CUI [2,4])
C0338237 (UMLS CUI [3,1])
C0231290 (UMLS CUI [3,2])
C1320303 (UMLS CUI [3,3])
C0870078 (UMLS CUI [3,4])
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