Polygenic Score (PGS) ID: PGS001326

Predicted Trait
Reported Trait Emphysema
Mapped Trait(s) emphysema (EFO_0000464)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC431
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
Terms and Licenses
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Score Details

Score Construction
PGS Name GBE_HC431
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 42
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
[
  • 1,698 cases
  • , 268,006 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
PPM009117 PSS004496|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Emphysema AUROC: 0.79508 [0.66687, 0.92329] : 0.11615
Incremental AUROC (full-covars): -0.00299
PGS R2 (no covariates): 6e-05
PGS AUROC (no covariates): 0.54363 [0.35853, 0.72873]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009118 PSS004497|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Emphysema AUROC: 0.98854 [0.98287, 0.99422] : 0.35967
Incremental AUROC (full-covars): 0.00059
PGS R2 (no covariates): 0.01376
PGS AUROC (no covariates): 0.67098 [0.43987, 0.90208]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009119 PSS004498|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Emphysema AUROC: 0.7867 [0.75313, 0.82026] : 0.09488
Incremental AUROC (full-covars): -0.00065
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.49994 [0.45601, 0.54388]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009120 PSS004499|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Emphysema AUROC: 0.78275 [0.67463, 0.89087] : 0.0813
Incremental AUROC (full-covars): 0.00398
PGS R2 (no covariates): 0.00648
PGS AUROC (no covariates): 0.59809 [0.42688, 0.7693]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009121 PSS004500|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Emphysema AUROC: 0.72797 [0.70437, 0.75156] : 0.05838
Incremental AUROC (full-covars): 0.00547
PGS R2 (no covariates): 0.00531
PGS AUROC (no covariates): 0.56911 [0.54137, 0.59684]
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
PSS004496
[
  • 16 cases
  • , 6,481 controls
]
African unspecified UKB
PSS004497
[
  • 2 cases
  • , 1,702 controls
]
East Asian UKB
PSS004498
[
  • 149 cases
  • , 24,756 controls
]
European non-white British ancestry UKB
PSS004499
[
  • 11 cases
  • , 7,820 controls
]
South Asian UKB
PSS004500
[
  • 429 cases
  • , 66,996 controls
]
European white British ancestry UKB Testing cohort (heldout set)