Polygenic Score (PGS) ID: PGS001300

Predicted Trait
Reported Trait Celiac disease or gluten sensitivity, diagnosed
Mapped Trait(s) celiac disease (EFO_0001060)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN21068
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_BIN21068
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9
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%
97,279 individuals (100%)
PGS Evaluation
European: 50%
African: 25%
South Asian: 25%
4 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
—
[
  • 1,826 cases
  • , 95,453 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
PPM008997 PSS003667|
African Ancestry|
969 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — AUROC: 0.77521 [0.67165, 0.87877] R²: 0.10494
Incremental AUROC (full-covars): 0.00391
PGS R2 (no covariates): 0.00465
PGS AUROC (no covariates): 0.54048 [0.39518, 0.68579]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008998 PSS003668|
European Ancestry|
9,024 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — AUROC: 0.67118 [0.63561, 0.70676] R²: 0.04801
Incremental AUROC (full-covars): 0.03638
PGS R2 (no covariates): 0.02217
PGS AUROC (no covariates): 0.58541 [0.54195, 0.62888]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008999 PSS003669|
South Asian Ancestry|
1,145 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — AUROC: 0.78803 [0.69728, 0.87878] R²: 0.09336
Incremental AUROC (full-covars): 0.00365
PGS R2 (no covariates): 0.00127
PGS AUROC (no covariates): 0.56184 [0.43287, 0.6908]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009000 PSS003670|
European Ancestry|
24,310 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — AUROC: 0.6734 [0.64935, 0.69745] R²: 0.04185
Incremental AUROC (full-covars): 0.08398
PGS R2 (no covariates): 0.02957
PGS AUROC (no covariates): 0.62888 [0.60094, 0.65683]		 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
PSS003668 — —
[
  • 213 cases
  • , 8,811 controls
]
 — European non-white British ancestry UKB —
PSS003669 — —
[
  • 16 cases
  • , 1,129 controls
]
 — South Asian — UKB —
PSS003670 — —
[
  • 468 cases
  • , 23,842 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003667 — —
[
  • 18 cases
  • , 951 controls
]
 — African unspecified — UKB —