Polygenic Score (PGS) ID: PGS000017

Predicted Trait
Reported Trait Inflammatory bowel disease
Mapped Trait(s) inflammatory bowel disease (EFO_0003767)
Released in PGS Catalog: Oct. 14, 2019
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Terms and Licenses
Freely available to the academic community for research use. Parties interested in using the scores for commercial purposes should contact the Broad Office of Strategic Alliances and Partnering (partnering@broadinstitute.org).

Score Details

Score Construction
PGS Name GPS_IBD
Development Method
Name LDpred
Parameters ρ = 0.1; LD panel = 503 1000G Europeans
Variants
Original Genome Build hg19
Number of Variants 6,907,112
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000006
Citation (link to publication) Khera AV et al. Nat Genet (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
34,652 individuals (100%)
Score Development/Training
European: 100%
120,280 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: GCST003043
Europe PMC: 26192919
 34,652 individuals European 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
—
[
  • 1,360 cases
  • , 118,920 controls
]
 European UKB 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. — — — 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 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
PPM000026 PSS000016|
European Ancestry|
288,978 individuals
 PGP000006 |
Khera AV et al. Nat Genet (2018)
 Reported Trait: Inflammatory bowel disease — 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 —
PPM012874 PSS009588|
European Ancestry|
1,433 individuals
 PGP000288 |
Garcia-Etxebarria K et al. Sci Rep (2022)
|Ext.		 Reported Trait: Inflammatory Bowel Disease — AUROC: 0.69 [0.66, 0.72] — — —

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
PSS009588 — —
[
  • 498 cases
  • , 935 controls
]
 — European — BV —
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. —
[
  • 5,853 cases
  • , 283,125 controls
]
 — European — UKB UKB Phase 2