Polygenic Score (PGS) ID: PGS001310

Predicted Trait
Reported Trait Rheumatoid arthritis
Mapped Trait(s) rheumatoid arthritis (EFO_0000685)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC430
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_HC430
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 175
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
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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
—
[
  • 5,062 cases
  • , 264,642 controls
]
EuropeanUKB———white British ancestry—
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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.

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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
PPM009044PSS004491|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Rheumatoid arthritis—AUROC: 0.70522 [0.66309, 0.74736]R²: 0.0544
Incremental AUROC (full-covars): 0.00203
PGS R2 (no covariates): 0.00109
PGS AUROC (no covariates): 0.53147 [0.47999, 0.58294]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM009045PSS004492|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Rheumatoid arthritis—AUROC: 0.66116 [0.54578, 0.77655]R²: 0.06929
Incremental AUROC (full-covars): -0.02514
PGS R2 (no covariates): 0.00033
PGS AUROC (no covariates): 0.52178 [0.38366, 0.6599]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM009046PSS004493|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Rheumatoid arthritis—AUROC: 0.68857 [0.6632, 0.71393]R²: 0.04919
Incremental AUROC (full-covars): 0.02092
PGS R2 (no covariates): 0.01316
PGS AUROC (no covariates): 0.58714 [0.55751, 0.61676]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM009047PSS004494|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Rheumatoid arthritis—AUROC: 0.70402 [0.66905, 0.73899]R²: 0.06207
Incremental AUROC (full-covars): -0.0019
PGS R2 (no covariates): 0.00142
PGS AUROC (no covariates): 0.53137 [0.48984, 0.57291]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM009048PSS004495|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Rheumatoid arthritis—AUROC: 0.66508 [0.65049, 0.67967]R²: 0.03894
Incremental AUROC (full-covars): 0.03077
PGS R2 (no covariates): 0.01509
PGS AUROC (no covariates): 0.60018 [0.58428, 0.61607]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
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Evaluated Samples

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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
PSS004491——
[
  • 118 cases
  • , 6,379 controls
]
—African unspecified—UKB—
PSS004492——
[
  • 18 cases
  • , 1,686 controls
]
—East Asian—UKB—
PSS004493——
[
  • 399 cases
  • , 24,506 controls
]
—Europeannon-white British ancestryUKB—
PSS004494——
[
  • 194 cases
  • , 7,637 controls
]
—South Asian—UKB—
PSS004495——
[
  • 1,301 cases
  • , 66,124 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
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