Polygenic Score (PGS) ID: PGS000922

Predicted Trait
Reported Trait Sarcoidosis
Mapped Trait(s) Sarcoidosis (Orphanet_797)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC170
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_HC170
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 12
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
[
  • 734 cases
  • , 268,970 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
PPM007440 PSS004322|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Sarcoidosis AUROC: 0.70759 [0.63998, 0.7752] PGS R2 (no covariates): 0.02057
: 0.05219
Incremental AUROC (full-covars): 0.03111
PGS AUROC (no covariates): 0.64298 [0.57429, 0.71167]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007441 PSS004323|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Sarcoidosis AUROC: 0.67662 [0.6145, 0.73874] : 0.03062
Incremental AUROC (full-covars): 0.02209
PGS R2 (no covariates): 0.00799
PGS AUROC (no covariates): 0.60582 [0.54774, 0.66391]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007442 PSS004324|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Sarcoidosis AUROC: 0.66108 [0.58927, 0.7329] : 0.03112
Incremental AUROC (full-covars): 0.00713
PGS R2 (no covariates): 0.00089
PGS AUROC (no covariates): 0.52621 [0.44905, 0.60338]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007443 PSS004325|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Sarcoidosis AUROC: 0.6486 [0.60932, 0.68789] : 0.01916
Incremental AUROC (full-covars): 0.09187
PGS R2 (no covariates): 0.01741
PGS AUROC (no covariates): 0.64282 [0.60353, 0.68211]
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
PSS004324
[
  • 48 cases
  • , 7,783 controls
]
South Asian UKB
PSS004325
[
  • 176 cases
  • , 67,249 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004322
[
  • 58 cases
  • , 6,439 controls
]
African unspecified UKB
PSS004323
[
  • 67 cases
  • , 24,838 controls
]
European non-white British ancestry UKB