Polygenic Score (PGS) ID: PGS000997

Predicted Trait
Reported Trait Diverticular disease of intestine (time-to-event)
Mapped Trait(s) diverticular disease (EFO_0009959)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1106
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_HC1106
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 5,757
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
—
[
  • 25,849 cases
  • , 243,855 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
PPM007748 PSS004124|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE diverticular disease of intestine — AUROC: 0.70831 [0.67789, 0.73873] R²: 0.07998
Incremental AUROC (full-covars): -0.0081
PGS R2 (no covariates): 0.00158
PGS AUROC (no covariates): 0.52939 [0.49423, 0.56454]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007749 PSS004125|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE diverticular disease of intestine — AUROC: 0.75551 [0.65982, 0.85119] R²: 0.08781
Incremental AUROC (full-covars): -0.01168
PGS R2 (no covariates): 0.00059
PGS AUROC (no covariates): 0.52785 [0.41459, 0.64111]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007750 PSS004126|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE diverticular disease of intestine — AUROC: 0.7155 [0.70514, 0.72586] R²: 0.10502
Incremental AUROC (full-covars): 0.01733
PGS R2 (no covariates): 0.01777
PGS AUROC (no covariates): 0.59105 [0.57889, 0.60321]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007751 PSS004127|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE diverticular disease of intestine — AUROC: 0.73365 [0.70818, 0.75911] R²: 0.09377
Incremental AUROC (full-covars): 0.01275
PGS R2 (no covariates): 0.01222
PGS AUROC (no covariates): 0.57957 [0.54784, 0.6113]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007752 PSS004128|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE diverticular disease of intestine — AUROC: 0.68053 [0.67412, 0.68694] R²: 0.07483
Incremental AUROC (full-covars): 0.01974
PGS R2 (no covariates): 0.01533
PGS AUROC (no covariates): 0.5794 [0.57219, 0.58662]		 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
PSS004124 — —
[
  • 279 cases
  • , 6,218 controls
]
 — African unspecified — UKB —
PSS004125 — —
[
  • 24 cases
  • , 1,680 controls
]
 — East Asian — UKB —
PSS004126 — —
[
  • 2,245 cases
  • , 22,660 controls
]
 — European non-white British ancestry UKB —
PSS004127 — —
[
  • 330 cases
  • , 7,501 controls
]
 — South Asian — UKB —
PSS004128 — —
[
  • 6,501 cases
  • , 60,924 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)