Polygenic Score (PGS) ID: PGS004253

Predicted Trait
Reported Trait Ulcerative colitis
Mapped Trait(s) ulcerative colitis (EFO_0000729)
Released in PGS Catalog: March 28, 2024
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Score Details

Score Construction
PGS Name uc_ldpred2
Development Method
Name LDpred2-auto
Parameters NR
Variants
Original Genome Build hg19
Number of Variants 744,575
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000545
Citation (link to publication) Middha P et al. Nat Commun (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • European
  • Not Reported
45,975 individuals (100%)
Score Development/Training
European: 100%
13,382 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004133
Europe PMC: 28067908
 45,975 individuals European, NR NR
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
—
[
  • 1,970 cases
  • , 11,412 controls
]
 European UKB — — — — —

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
PPM020320 PSS011334|
European Ancestry|
21,335 individuals
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Reported Trait: Ulcerative colitis OR: 1.75 [1.59, 1.92] AUROC: 0.65 [0.62, 0.68] — age, sex, 10 PCs —
PPM020319 PSS011335|
European Ancestry|
5,735 individuals
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Reported Trait: Ulcerative colitis OR: 1.84 [1.76, 1.93] AUROC: 0.66 [0.64, 0.68] — age at diagnosis/enrollment, sex, genotyping array, 10 PCs —

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
PSS011334 — —
[
  • 459 cases
  • , 20,876 controls
]
 — European — BioVU —
PSS011335 — —
[
  • 844 cases
  • , 4,891 controls
]
 — European — UKB —