Trait: respiratory tract infectious disease

Trait Information
Identifier MONDO_0024355
Description Invasion of the host RESPIRATORY SYSTEM by microorganisms, usually leading to pathological processes or diseases. [MESH: D012141]
Trait category
Other disease
Mapped terms 3 mapped terms
  • ICD9:519.8
  • MESH:D012141
  • SCTID:275498002

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS000925
(GBE_HC1020)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Unspecified acute lower respiratory infection (time-to-event) respiratory tract infectious disease 402
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000925/ScoringFiles/PGS000925.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM)
Evaluated Score PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM007452 PGS000925
(GBE_HC1020)
PSS004064|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE unspecified acute lower respiratory infection AUROC: 0.57269 [0.54679, 0.59859] : 0.01184
Incremental AUROC (full-covars): -0.00336
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.50444 [0.47789, 0.53099]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007453 PGS000925
(GBE_HC1020)
PSS004065|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE unspecified acute lower respiratory infection AUROC: 0.60323 [0.54812, 0.65835] : 0.03851
Incremental AUROC (full-covars): -0.00133
PGS R2 (no covariates): 6e-05
PGS AUROC (no covariates): 0.50156 [0.44741, 0.55572]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007454 PGS000925
(GBE_HC1020)
PSS004066|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE unspecified acute lower respiratory infection AUROC: 0.5999 [0.58827, 0.61153] : 0.02334
Incremental AUROC (full-covars): -0.00017
PGS R2 (no covariates): 0.00015
PGS AUROC (no covariates): 0.50839 [0.49651, 0.52027]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007455 PGS000925
(GBE_HC1020)
PSS004067|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE unspecified acute lower respiratory infection AUROC: 0.59639 [0.57815, 0.61463] : 0.02321
Incremental AUROC (full-covars): -0.00306
PGS R2 (no covariates): 0.00104
PGS AUROC (no covariates): 0.47878 [0.46019, 0.49737]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007456 PGS000925
(GBE_HC1020)
PSS004068|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE unspecified acute lower respiratory infection AUROC: 0.58398 [0.57742, 0.59055] : 0.01732
Incremental AUROC (full-covars): 0.00092
PGS R2 (no covariates): 0.00054
PGS AUROC (no covariates): 0.51573 [0.50903, 0.52242]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

Evaluated Samples

PGS Sample Set ID
(PSS)
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS004064
[
  • 485 cases
  • , 6,012 controls
]
African unspecified UKB
PSS004065
[
  • 112 cases
  • , 1,592 controls
]
East Asian UKB
PSS004066
[
  • 2,487 cases
  • , 22,418 controls
]
European non-white British ancestry UKB
PSS004067
[
  • 1,025 cases
  • , 6,806 controls
]
South Asian UKB
PSS004068
[
  • 8,119 cases
  • , 59,306 controls
]
European white British ancestry UKB Testing cohort (heldout set)