Polygenic Score (PGS) ID: PGS001333

Predicted Trait
Reported Trait Chronic obstructive pulmonary disease (algorithmically-defined)
Mapped Trait(s) chronic obstructive pulmonary disease (EFO_0000341)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1582
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_HC1582
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 569
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
[
  • 10,255 cases
  • , 259,449 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
PPM009151 PSS004297|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: AD chronic obstructive pulmonary disease AUROC: 0.68968 [0.6281, 0.75125] : 0.05389
Incremental AUROC (full-covars): -0.00542
PGS R2 (no covariates): 5e-05
PGS AUROC (no covariates): 0.49374 [0.43492, 0.55257]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009152 PSS004298|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: AD chronic obstructive pulmonary disease AUROC: 0.77182 [0.67988, 0.86376] : 0.12635
Incremental AUROC (full-covars): -0.00429
PGS R2 (no covariates): 0.00238
PGS AUROC (no covariates): 0.55811 [0.43123, 0.68498]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009153 PSS004299|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: AD chronic obstructive pulmonary disease AUROC: 0.71622 [0.70023, 0.7322] : 0.08141
Incremental AUROC (full-covars): 0.00289
PGS R2 (no covariates): 0.00236
PGS AUROC (no covariates): 0.53939 [0.52155, 0.55723]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009154 PSS004300|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: AD chronic obstructive pulmonary disease AUROC: 0.71121 [0.67474, 0.74767] : 0.06785
Incremental AUROC (full-covars): 0.00468
PGS R2 (no covariates): 0.00251
PGS AUROC (no covariates): 0.53996 [0.49615, 0.58377]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009155 PSS004301|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: AD chronic obstructive pulmonary disease AUROC: 0.70059 [0.69045, 0.71072] : 0.06924
Incremental AUROC (full-covars): 0.0031
PGS R2 (no covariates): 0.00218
PGS AUROC (no covariates): 0.5364 [0.52484, 0.54796]
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
PSS004297
[
  • 89 cases
  • , 6,408 controls
]
African unspecified UKB
PSS004298
[
  • 17 cases
  • , 1,687 controls
]
East Asian UKB
PSS004299
[
  • 1,002 cases
  • , 23,903 controls
]
European non-white British ancestry UKB
PSS004300
[
  • 186 cases
  • , 7,645 controls
]
South Asian UKB
PSS004301
[
  • 2,525 cases
  • , 64,900 controls
]
European white British ancestry UKB Testing cohort (heldout set)