Polygenic Score (PGS) ID: PGS001306

Predicted Trait
Reported Trait Ulcerative colitis
Mapped Trait(s) ulcerative colitis (EFO_0000729)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC201
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_HC201
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 179
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
—
[
  • 2,682 cases
  • , 267,022 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
PPM009024 PSS004339|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ulcerative colitis — AUROC: 0.62904 [0.5093, 0.74878] R²: 0.04535
Incremental AUROC (full-covars): -0.00864
PGS R2 (no covariates): 0.00044
PGS AUROC (no covariates): 0.51081 [0.37987, 0.64174]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009025 PSS004340|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ulcerative colitis — AUROC: 0.89429 [0.79357, 0.99502] R²: 0.20499
Incremental AUROC (full-covars): -0.0033
PGS R2 (no covariates): 2e-05
PGS AUROC (no covariates): 0.49111 [0.35854, 0.62368]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009026 PSS004341|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ulcerative colitis — AUROC: 0.66162 [0.6277, 0.69554] R²: 0.03336
Incremental AUROC (full-covars): 0.04247
PGS R2 (no covariates): 0.02036
PGS AUROC (no covariates): 0.63006 [0.5958, 0.66432]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009027 PSS004342|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ulcerative colitis — AUROC: 0.67522 [0.62537, 0.72506] R²: 0.03696
Incremental AUROC (full-covars): 0.01011
PGS R2 (no covariates): 0.00545
PGS AUROC (no covariates): 0.56552 [0.50815, 0.62289]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009028 PSS004343|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ulcerative colitis — AUROC: 0.6157 [0.59481, 0.63659] PGS R2 (no covariates): 0.0193
R²: 0.01676
Incremental AUROC (full-covars): 0.08728
PGS AUROC (no covariates): 0.62452 [0.60374, 0.6453]		 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
PSS004339 — —
[
  • 27 cases
  • , 6,470 controls
]
 — African unspecified — UKB —
PSS004340 — —
[
  • 5 cases
  • , 1,699 controls
]
 — East Asian — UKB —
PSS004341 — —
[
  • 239 cases
  • , 24,666 controls
]
 — European non-white British ancestry UKB —
PSS004342 — —
[
  • 103 cases
  • , 7,728 controls
]
 — South Asian — UKB —
PSS004343 — —
[
  • 720 cases
  • , 66,705 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)