Polygenic Score (PGS) ID: PGS000923

Predicted Trait
Reported Trait Sarcoidosis (time-to-event)
Mapped Trait(s) Sarcoidosis (Orphanet_797)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC639
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_HC639
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 22
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: 50%
African: 25%
South Asian: 25%
4 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
[
  • 940 cases
  • , 268,764 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
PPM007444 PSS004551|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE sarcoidosis AUROC: 0.70171 [0.64012, 0.7633] : 0.05018
Incremental AUROC (full-covars): 0.03514
PGS R2 (no covariates): 0.02657
PGS AUROC (no covariates): 0.66456 [0.60597, 0.72315]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007445 PSS004552|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE sarcoidosis AUROC: 0.67371 [0.61511, 0.7323] : 0.02923
Incremental AUROC (full-covars): 0.00926
PGS R2 (no covariates): 0.00429
PGS AUROC (no covariates): 0.58898 [0.53125, 0.64671]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007446 PSS004553|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE sarcoidosis AUROC: 0.67148 [0.61146, 0.73151] : 0.0372
Incremental AUROC (full-covars): 0.00677
PGS R2 (no covariates): 0.00103
PGS AUROC (no covariates): 0.52237 [0.45814, 0.58661]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007447 PSS004554|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE sarcoidosis AUROC: 0.65455 [0.6217, 0.6874] : 0.02088
Incremental AUROC (full-covars): 0.09004
PGS R2 (no covariates): 0.018
PGS AUROC (no covariates): 0.64561 [0.61168, 0.67954]
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
PSS004551
[
  • 72 cases
  • , 6,425 controls
]
African unspecified UKB
PSS004552
[
  • 77 cases
  • , 24,828 controls
]
European non-white British ancestry UKB
PSS004553
[
  • 72 cases
  • , 7,759 controls
]
South Asian UKB
PSS004554
[
  • 227 cases
  • , 67,198 controls
]
European white British ancestry UKB Testing cohort (heldout set)