Polygenic Score (PGS) ID: PGS002066

Predicted Trait
Reported Trait Ulcerative colitis
Mapped Trait(s) ulcerative colitis (EFO_0000729)
Additional Trait Information digestive
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_555.2
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 566,637
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 Sample Sets

Development Samples

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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM011390 PSS009330|
European Ancestry|
16,188 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0641 [0.0487, 0.0794] sex, age, birth date, deprivation index, 16 PCs —
PPM011391 PSS009104|
European Ancestry|
3,520 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0466 [0.0135, 0.0796] sex, age, birth date, deprivation index, 16 PCs —
PPM011392 PSS008658|
European Ancestry|
5,477 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0426 [0.0161, 0.0691] sex, age, birth date, deprivation index, 16 PCs —
PPM011393 PSS008432|
Greater Middle Eastern Ancestry|
1,007 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0056 [-0.0568, 0.068] sex, age, birth date, deprivation index, 16 PCs —
PPM011395 PSS007994|
East Asian Ancestry|
1,630 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0398 [-0.009, 0.0885] sex, age, birth date, deprivation index, 16 PCs —
PPM011396 PSS007777|
African Ancestry|
2,105 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0272 [-0.0157, 0.0701] sex, age, birth date, deprivation index, 16 PCs —
PPM011397 PSS008881|
African Ancestry|
3,465 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0058 [-0.0276, 0.0392] sex, age, birth date, deprivation index, 16 PCs —
PPM011394 PSS008212|
South Asian Ancestry|
5,337 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ulcerative colitis — — Partial Correlation (partial-r): 0.0388 [0.0119, 0.0656] sex, age, birth date, deprivation index, 16 PCs —
PPM021728 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
|Ext.		 Reported Trait: Ulcerative colitis OR: 1.11 [0.97, 1.28] AUROC: 0.57 — — —

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
PSS009104 — — 3,520 individuals — European Poland (NE Europe) UKB —
PSS008432 — — 1,007 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009330 — — 16,188 individuals — European UK (+ Ireland) UKB —
PSS008658 — — 5,477 individuals — European Italy (South Europe) UKB —
PSS008881 — — 3,465 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008212 — — 5,337 individuals — South Asian India (South Asia) UKB —
PSS011762 — — 8,417 individuals — European — BBofA —
PSS007994 — — 1,630 individuals — East Asian China (East Asia) UKB —
PSS007777 — — 2,105 individuals — African American or Afro-Caribbean Carribean UKB —