Polygenic Score (PGS) ID: PGS004051

Predicted Trait
Reported Trait Inflammatory bowel disease (IBD)
Mapped Trait(s) inflammatory bowel disease (EFO_0003767)
Released in PGS Catalog: Dec. 19, 2023
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Score Details

Score Construction
PGS Name megaprs.auto.GCST004131.IBD
Development Method
Name megaprs.auto
Parameters Model:Model186,Type:bayesr,Her_Scaling:1,Lasso_lambda:NA,Lasso_s:NA,Bolt_p:NA,Bolt_f2:NA,BayesR_p1:0.975,BayesR_p2:0.01,BayesR_p3:0.01,BayesR_p4:0.005
Variants
Original Genome Build GRCh38
Number of Variants 784,928
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000517
Citation (link to publication) Monti R et al. Am J Hum Genet (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • Not Reported
  • European
59,957 individuals (100%)
Score Development/Training
European: 100%
5,340 individuals (100%)
PGS Evaluation
European: 66.7%
South Asian: 33.3%
6 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004131
Europe PMC: 28067908
 59,957 individuals NR, 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
— 5,340 individuals 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
PPM019257 PSS011220|
European Ancestry|
199,274 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Inflammatory bowel disease β: 0.314 [0.27094623, 0.3570459]
OR: 1.36888 [1.31120456, 1.42910147]		 AUROC: 0.58489 [0.57210995, 0.59766877] R²: 0.01549 [0.01126134, 0.02041918] 0 beta = log(or)/sd_pgs
PPM019258 PSS011231|
European Ancestry|
396,819 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Inflammatory bowel disease OR: 2.00653 [1.96129353, 2.05281389]
β: 0.69641 [0.67360422, 0.71921148]		 AUROC: 0.6875 [0.68162312, 0.69338152] R²: 0.07485 [0.07002551, 0.07988684] 0 beta = log(or)/sd_pgs
PPM019259 PSS011244|
South Asian Ancestry|
44,057 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Inflammatory bowel disease OR: 1.90388 [1.74000795, 2.08318936]
β: 0.64389 [0.55388968, 0.73390007]		 AUROC: 0.68195 [0.6575792, 0.70632398] R²: 0.06418 [0.04826446, 0.08480071] 0 beta = log(or)/sd_pgs
PPM019260 PSS011260|
European Ancestry|
66,865 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Inflammatory bowel disease OR: 1.53763 [1.4663408, 1.61237934]
β: 0.43024 [0.38277005, 0.47771094]		 AUROC: 0.61658 [0.60284816, 0.63032177] R²: 0.02901 [0.02229249, 0.03588211] 0 beta = log(or)/sd_pgs
PPM019261 PSS011288|
South Asian Ancestry|
9,326 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Inflammatory bowel disease OR: 1.63845 [1.40628747, 1.90892925]
β: 0.49375 [0.34095323, 0.64654248]		 AUROC: 0.63419 [0.59012677, 0.6782445] R²: 0.03667 [0.01631785, 0.06339845] 0 beta = log(or)/sd_pgs
PPM019262 PSS011273|
European Ancestry|
90,274 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Inflammatory bowel disease OR: 1.9624 [1.85716399, 2.07360018]
β: 0.67417 [0.61905059, 0.72928631]		 AUROC: 0.68392 [0.669613, 0.69822212] R²: 0.06945 [0.05902191, 0.08200647] 0 beta = log(or)/sd_pgs

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
PSS011273 — —
[
  • 1,335 cases
  • , 88,939 controls
]
 — European — UKB —
PSS011244 — —
[
  • 43,591 cases
  • , 466 controls
]
 — South Asian — G&H —
PSS011220 — —
[
  • 197,177 cases
  • , 2,097 controls
]
 — European — EB —
PSS011288 — —
[
  • 168 cases
  • , 9,158 controls
]
 — South Asian — UKB —
PSS011260 — —
[
  • 65,096 cases
  • , 1,769 controls
]
 — European — HUNT —
PSS011231 K11_IBD_STRICT, ICD10: K50|K51, ICD9: 555|556 —
[
  • 389,004 cases
  • , 7,815 controls
]
 — European — FinnGen —