Polygenic Score (PGS) ID: PGS001332

Predicted Trait
Reported Trait Chronic obstructive pulmonary disease
Mapped Trait(s) chronic obstructive pulmonary disease (EFO_0000341)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC442
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_HC442
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 482
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
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
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
[
  • 7,674 cases
  • , 262,030 controls
]
European white British ancestry UKB

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
PPM009146 PSS004506|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Chronic obstructive airways disease/copd AUROC: 0.75825 [0.69744, 0.81905] : 0.08985
Incremental AUROC (full-covars): 0.00297
PGS R2 (no covariates): 0.00366
PGS AUROC (no covariates): 0.56943 [0.4939, 0.64496]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009147 PSS004507|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Chronic obstructive airways disease/copd AUROC: 0.93404 [0.85456, 1.0] : 0.35918
Incremental AUROC (full-covars): 0.00775
PGS R2 (no covariates): 0.05713
PGS AUROC (no covariates): 0.78102 [0.65685, 0.90519]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009148 PSS004508|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Chronic obstructive airways disease/copd AUROC: 0.75808 [0.74076, 0.77539] : 0.10489
Incremental AUROC (full-covars): 0.0013
PGS R2 (no covariates): 0.00194
PGS AUROC (no covariates): 0.53674 [0.51446, 0.55902]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009149 PSS004509|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Chronic obstructive airways disease/copd AUROC: 0.74266 [0.70089, 0.78443] : 0.08552
Incremental AUROC (full-covars): -0.00028
PGS R2 (no covariates): 0.00048
PGS AUROC (no covariates): 0.51815 [0.46516, 0.57113]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009150 PSS004510|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Chronic obstructive airways disease/copd AUROC: 0.73063 [0.71971, 0.74156] : 0.08401
Incremental AUROC (full-covars): 0.003
PGS R2 (no covariates): 0.00235
PGS AUROC (no covariates): 0.53971 [0.52633, 0.5531]
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
PSS004508
[
  • 671 cases
  • , 24,234 controls
]
European non-white British ancestry UKB
PSS004509
[
  • 130 cases
  • , 7,701 controls
]
South Asian UKB
PSS004510
[
  • 1,860 cases
  • , 65,565 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004506
[
  • 58 cases
  • , 6,439 controls
]
African unspecified UKB
PSS004507
[
  • 6 cases
  • , 1,698 controls
]
East Asian UKB