Polygenic Score (PGS) ID: PGS001132

Predicted Trait
Reported Trait Family history of chronic bronchitis/emphysema
Mapped Trait(s) family history (EFO_0000493)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/FH1113
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_FH1113
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,530
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
—
[
  • 62,798 cases
  • , 206,906 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
PPM008388 PSS004049|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Chronic bronchitis/emphysema (FH) — AUROC: 0.55867 [0.53736, 0.57998] R²: 0.01064
Incremental AUROC (full-covars): -0.00488
PGS R2 (no covariates): 0.00023
PGS AUROC (no covariates): 0.49207 [0.46984, 0.5143]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008389 PSS004050|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Chronic bronchitis/emphysema (FH) — AUROC: 0.59763 [0.55526, 0.63999] R²: 0.03241
Incremental AUROC (full-covars): 0.00659
PGS R2 (no covariates): 0.00372
PGS AUROC (no covariates): 0.53681 [0.49409, 0.57952]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008390 PSS004051|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Chronic bronchitis/emphysema (FH) — AUROC: 0.5885 [0.58009, 0.59692] R²: 0.02565
Incremental AUROC (full-covars): 0.00247
PGS R2 (no covariates): 0.00203
PGS AUROC (no covariates): 0.52356 [0.51492, 0.53221]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008391 PSS004052|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Chronic bronchitis/emphysema (FH) — AUROC: 0.54947 [0.53138, 0.56755] PGS R2 (no covariates): 0.00013
R²: 0.00653
Incremental AUROC (full-covars): -0.00201
PGS AUROC (no covariates): 0.50704 [0.48923, 0.52485]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008392 PSS004053|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Chronic bronchitis/emphysema (FH) — AUROC: 0.58327 [0.57825, 0.58829] R²: 0.02293
Incremental AUROC (full-covars): 0.0012
PGS R2 (no covariates): 0.00095
PGS AUROC (no covariates): 0.51589 [0.51075, 0.52103]		 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
PSS004049 — —
[
  • 743 cases
  • , 5,754 controls
]
 — African unspecified — UKB —
PSS004050 — —
[
  • 200 cases
  • , 1,504 controls
]
 — East Asian — UKB —
PSS004051 — —
[
  • 5,555 cases
  • , 19,350 controls
]
 — European non-white British ancestry UKB —
PSS004052 — —
[
  • 1,151 cases
  • , 6,680 controls
]
 — South Asian — UKB —
PSS004053 — —
[
  • 15,769 cases
  • , 51,656 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)