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(Variants and weights)

Polygenic Score (PGS) ID: PGS000017

Predicted Trait

Reported Trait: Inflammatory bowel disease
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): inflammatory bowel disease

Score Details

Name: GPS_IBD

Original Genome Build: hg19
Number of Variants: 6,907,112

PGS Development Method: LDPred
PGS Development Details/Relevant Parameters: ρ = 0.1; LD panel = 503 1000G Europeans

Citation: Khera AV et al. Nat Genet (2018) | PGS Catalog Publication ID: PGP000006

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003043
PubMed: 26192919
34,652 individuals European
Score Development/Training
Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
Inflammatory bowel disease ascertainment was based on report in an interview with a trained nurse, or an ICD-9 code of 555.X or ICD-10 code of K51.X in hospitalization records. 120,280 individuals
[ 1,360 cases, 121,640 controls]
European UKB UKB Phase 1

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000026 PSS000016 Khera AV et al. (2018) Reported Trait: Inflammatory bowel disease cases AUROC: 0.63 [0.62 - 0.64] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.021 age; sex; Ancestry PC 1-4; genotyping chip

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000016 Inflammatory bowel disease ascertainment was based on report in an interview with a trained nurse, or an ICD-9 code of 555.X or ICD-10 code of K51.X in hospitalization records. 288,978 individuals
[ 5,853 cases, 294,831 controls]
European UKB UKB Phase 2