Polygenic Score (PGS) ID: PGS000996

Predicted Trait
Reported Trait Diverticular disease/diverticulitis
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC262
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_HC262
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 368
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
—
[
  • 3,410 cases
  • , 266,294 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
PPM007743 PSS004389|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diverticular disease/diverticulitis — AUROC: 0.86271 [0.73099, 0.99443] R²: 0.12936
Incremental AUROC (full-covars): 0.00213
PGS R2 (no covariates): 0.00894
PGS AUROC (no covariates): 0.62053 [0.46342, 0.77764]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007744 PSS004390|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diverticular disease/diverticulitis — AUROC: 0.91481 [0.74874, 1.0] R²: 0.2785
Incremental AUROC (full-covars): 0.00029
PGS R2 (no covariates): 0.03618
PGS AUROC (no covariates): 0.74736 [0.4992, 0.99551]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007745 PSS004391|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diverticular disease/diverticulitis — AUROC: 0.70041 [0.67086, 0.72996] R²: 0.04948
Incremental AUROC (full-covars): 0.0039
PGS R2 (no covariates): 0.00095
PGS AUROC (no covariates): 0.52419 [0.48988, 0.55849]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007746 PSS004392|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diverticular disease/diverticulitis — AUROC: 0.80455 [0.70545, 0.90364] R²: 0.1
Incremental AUROC (full-covars): 0.00844
PGS R2 (no covariates): 0.00928
PGS AUROC (no covariates): 0.62862 [0.53202, 0.72522]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007747 PSS004393|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Diverticular disease/diverticulitis — AUROC: 0.67555 [0.65884, 0.69227] R²: 0.03898
Incremental AUROC (full-covars): 0.00841
PGS R2 (no covariates): 0.00372
PGS AUROC (no covariates): 0.55186 [0.53326, 0.57047]		 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
PSS004389 — —
[
  • 11 cases
  • , 6,486 controls
]
 — African unspecified — UKB —
PSS004390 — —
[
  • 2 cases
  • , 1,702 controls
]
 — East Asian — UKB —
PSS004391 — —
[
  • 267 cases
  • , 24,638 controls
]
 — European non-white British ancestry UKB —
PSS004392 — —
[
  • 14 cases
  • , 7,817 controls
]
 — South Asian — UKB —
PSS004393 — —
[
  • 917 cases
  • , 66,508 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)