Polygenic Score (PGS) ID: PGS001030

Predicted Trait
Reported Trait Pulmonary fibrosis
Mapped Trait(s) pulmonary fibrosis (EFO_0009448)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC84
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_HC84
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 51
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
—
[
  • 841 cases
  • , 268,863 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
PPM007913 PSS004652|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Pulmonary fibrosis — AUROC: 0.76432 [0.66152, 0.86711] R²: 0.06337
Incremental AUROC (full-covars): -0.00734
PGS R2 (no covariates): 0.00134
PGS AUROC (no covariates): 0.54418 [0.41387, 0.67449]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007914 PSS004653|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Pulmonary fibrosis — AUROC: 0.78836 [0.4182, 1.0] R²: 0.07327
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 0.01067
PGS AUROC (no covariates): 0.62728 [0.08781, 1.0]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007915 PSS004654|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Pulmonary fibrosis — AUROC: 0.80151 [0.7556, 0.84742] R²: 0.08672
Incremental AUROC (full-covars): 0.01818
PGS R2 (no covariates): 0.0142
PGS AUROC (no covariates): 0.6252 [0.55618, 0.69423]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007916 PSS004655|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Pulmonary fibrosis — AUROC: 0.80812 [0.73923, 0.87701] R²: 0.10725
Incremental AUROC (full-covars): 0.00706
PGS R2 (no covariates): 0.01559
PGS AUROC (no covariates): 0.62171 [0.52443, 0.71899]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007917 PSS004656|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Pulmonary fibrosis — AUROC: 0.76146 [0.73043, 0.79249] R²: 0.07269
Incremental AUROC (full-covars): 0.0067
PGS R2 (no covariates): 0.00735
PGS AUROC (no covariates): 0.57583 [0.53323, 0.61844]		 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
PSS004652 — —
[
  • 19 cases
  • , 6,478 controls
]
 — African unspecified — UKB —
PSS004653 — —
[
  • 3 cases
  • , 1,701 controls
]
 — East Asian — UKB —
PSS004654 — —
[
  • 65 cases
  • , 24,840 controls
]
 — European non-white British ancestry UKB —
PSS004655 — —
[
  • 37 cases
  • , 7,794 controls
]
 — South Asian — UKB —
PSS004656 — —
[
  • 204 cases
  • , 67,221 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)