Polygenic Score (PGS) ID: PGS001334

Predicted Trait
Reported Trait Other chronic obstructive pulmonary disease (time-to-event)
Mapped Trait(s) chronic obstructive pulmonary disease (EFO_0000341)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1035
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_HC1035
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 498
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
[
  • 8,718 cases
  • , 260,986 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
PPM009156 PSS004079|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other chronic obstructive pulmonary disease AUROC: 0.75968 [0.69978, 0.81959] : 0.09174
Incremental AUROC (full-covars): -0.0023
PGS R2 (no covariates): 0.00029
PGS AUROC (no covariates): 0.4865 [0.41003, 0.56298]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009157 PSS004080|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other chronic obstructive pulmonary disease AUROC: 0.92777 [0.86245, 0.9931] : 0.33262
Incremental AUROC (full-covars): 0.00135
PGS R2 (no covariates): 0.00048
PGS AUROC (no covariates): 0.52185 [0.32406, 0.71963]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009158 PSS004081|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other chronic obstructive pulmonary disease AUROC: 0.75602 [0.73955, 0.77249] : 0.10564
Incremental AUROC (full-covars): 0.00136
PGS R2 (no covariates): 0.00195
PGS AUROC (no covariates): 0.53598 [0.51506, 0.55689]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009159 PSS004082|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other chronic obstructive pulmonary disease AUROC: 0.74851 [0.70987, 0.78716] : 0.09156
Incremental AUROC (full-covars): 0.00157
PGS R2 (no covariates): 0.00202
PGS AUROC (no covariates): 0.53954 [0.49035, 0.58873]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009160 PSS004083|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other chronic obstructive pulmonary disease AUROC: 0.72542 [0.71492, 0.73591] : 0.0827
Incremental AUROC (full-covars): 0.00368
PGS R2 (no covariates): 0.00314
PGS AUROC (no covariates): 0.54658 [0.5339, 0.55926]
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
PSS004079
[
  • 63 cases
  • , 6,434 controls
]
African unspecified UKB
PSS004080
[
  • 7 cases
  • , 1,697 controls
]
East Asian UKB
PSS004081
[
  • 754 cases
  • , 24,151 controls
]
European non-white British ancestry UKB
PSS004082
[
  • 148 cases
  • , 7,683 controls
]
South Asian UKB
PSS004083
[
  • 2,080 cases
  • , 65,345 controls
]
European white British ancestry UKB Testing cohort (heldout set)