Polygenic Score (PGS) ID: PGS000925

Predicted Trait
Reported Trait Unspecified acute lower respiratory infection (time-to-event)
Mapped Trait(s) respiratory tract infectious disorder (MONDO_0024355)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1020
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_HC1020
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 402
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 32,235 cases
  • , 237,469 controls
]
 European UKB — — — white British ancestry —

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) 		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 PSS004064|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE unspecified acute lower respiratory infection — AUROC: 0.57269 [0.54679, 0.59859] R²: 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 PSS004065|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE unspecified acute lower respiratory infection — AUROC: 0.60323 [0.54812, 0.65835] R²: 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 PSS004066|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE unspecified acute lower respiratory infection — AUROC: 0.5999 [0.58827, 0.61153] R²: 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 PSS004067|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE unspecified acute lower respiratory infection — AUROC: 0.59639 [0.57815, 0.61463] R²: 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 PSS004068|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE unspecified acute lower respiratory infection — AUROC: 0.58398 [0.57742, 0.59055] R²: 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)