Polygenic Score (PGS) ID: PGS001251

Predicted Trait
Reported Trait Other interstitial pulmonary diseases (time-to-event)
Mapped Trait(s) interstitial lung disease (EFO_0004244)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1052
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_HC1052
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 57
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
—
[
  • 1,196 cases
  • , 268,508 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
PPM008764 PSS004089|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other interstitial pulmonary diseases — AUROC: 0.76685 [0.68863, 0.84507] R²: 0.06049
Incremental AUROC (full-covars): -0.01407
PGS R2 (no covariates): 0.00442
PGS AUROC (no covariates): 0.4271 [0.31775, 0.53645]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008765 PSS004090|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other interstitial pulmonary diseases — AUROC: 0.64809 [0.35879, 0.93738] R²: 0.00599
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 0.00017
PGS AUROC (no covariates): 0.45824 [0.07908, 0.83739]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008766 PSS004091|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other interstitial pulmonary diseases — AUROC: 0.77039 [0.72659, 0.81418] R²: 0.07337
Incremental AUROC (full-covars): 0.01441
PGS R2 (no covariates): 0.00915
PGS AUROC (no covariates): 0.58668 [0.52852, 0.64484]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008767 PSS004092|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other interstitial pulmonary diseases — AUROC: 0.76583 [0.69953, 0.83214] R²: 0.08099
Incremental AUROC (full-covars): 0.00566
PGS R2 (no covariates): 0.01001
PGS AUROC (no covariates): 0.6044 [0.52353, 0.68526]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008768 PSS004093|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other interstitial pulmonary diseases — AUROC: 0.75237 [0.72682, 0.77791] R²: 0.07255
Incremental AUROC (full-covars): 0.01396
PGS R2 (no covariates): 0.0116
PGS AUROC (no covariates): 0.59358 [0.56068, 0.62648]		 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
PSS004092 — —
[
  • 45 cases
  • , 7,786 controls
]
 — South Asian — UKB —
PSS004093 — —
[
  • 321 cases
  • , 67,104 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004089 — —
[
  • 27 cases
  • , 6,470 controls
]
 — African unspecified — UKB —
PSS004090 — —
[
  • 4 cases
  • , 1,700 controls
]
 — East Asian — UKB —
PSS004091 — —
[
  • 98 cases
  • , 24,807 controls
]
 — European non-white British ancestry UKB —