Polygenic Score (PGS) ID: PGS004254

Predicted Trait
Reported Trait Crohn's disease
Mapped Trait(s) Crohn's disease (EFO_0000384)
Released in PGS Catalog: March 28, 2024
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Score Details

Score Construction
PGS Name cd_ldpred2
Development Method
Name LDpred2-auto
Parameters NR
Variants
Original Genome Build hg19
Number of Variants 744,682
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
40,266 individuals (100%)
Score Development/Training
European: 100%
12,331 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: GCST004132
Europe PMC: 28067908
 40,266 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
—
[
  • 918 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
PPM020321 PSS011333|
European Ancestry|
5,285 individuals
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Reported Trait: Crohn's disease OR: 1.83 [1.72, 1.95] AUROC: 0.72 [0.69, 0.74] — age at diagnosis/enrollment, sex, genotyping array, 10 PCs —
PPM020322 PSS011332|
European Ancestry|
22,296 individuals
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Reported Trait: Crohn's disease OR: 2.18 [2.05, 2.32] AUROC: 0.72 [0.7, 0.73] — age, sex, 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
PSS011332 — —
[
  • 1,420 cases
  • , 20,876 controls
]
 — European — BioVU —
PSS011333 — —
[
  • 394 cases
  • , 4,891 controls
]
 — European — UKB —