Polygenic Score (PGS) ID: PGS001308

Predicted Trait
Reported Trait Sjogren's syndrome/sicca syndrome
Mapped Trait(s) Sjogren syndrome (EFO_0000699)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC321
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_HC321
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 7
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
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
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 517 cases
  • , 269,187 controls
]
 European UKB — — — white British ancestry —

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
PPM009034 PSS004437|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Sjogren's syndrome/sicca syndrome — AUROC: 0.79846 [0.71474, 0.88218] R²: 0.07345
Incremental AUROC (full-covars): 0.0079
PGS R2 (no covariates): 0.01471
PGS AUROC (no covariates): 0.59027 [0.45551, 0.72504]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009035 PSS004438|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Sjogren's syndrome/sicca syndrome — AUROC: 0.75824 [0.55089, 0.96558] R²: 0.05686
Incremental AUROC (full-covars): 0.00691
PGS R2 (no covariates): 0.0091
PGS AUROC (no covariates): 0.69794 [0.63241, 0.76347]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009036 PSS004439|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Sjogren's syndrome/sicca syndrome — AUROC: 0.77174 [0.71988, 0.82361] R²: 0.07435
Incremental AUROC (full-covars): 0.01461
PGS R2 (no covariates): 0.01453
PGS AUROC (no covariates): 0.65693 [0.58901, 0.72485]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009037 PSS004440|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Sjogren's syndrome/sicca syndrome — AUROC: 0.8014 [0.74455, 0.85826] R²: 0.08893
Incremental AUROC (full-covars): 0.00953
PGS R2 (no covariates): 0.03189
PGS AUROC (no covariates): 0.61034 [0.48809, 0.73259]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009038 PSS004441|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Sjogren's syndrome/sicca syndrome — AUROC: 0.73313 [0.69647, 0.76978] R²: 0.04771
Incremental AUROC (full-covars): 0.01551
PGS R2 (no covariates): 0.01074
PGS AUROC (no covariates): 0.60303 [0.55292, 0.65315]		 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
PSS004437 — —
[
  • 17 cases
  • , 6,480 controls
]
 — African unspecified — UKB —
PSS004438 — —
[
  • 4 cases
  • , 1,700 controls
]
 — East Asian — UKB —
PSS004439 — —
[
  • 58 cases
  • , 24,847 controls
]
 — European non-white British ancestry UKB —
PSS004440 — —
[
  • 29 cases
  • , 7,802 controls
]
 — South Asian — UKB —
PSS004441 — —
[
  • 135 cases
  • , 67,290 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)