Polygenic Score (PGS) ID: PGS002069

Predicted Trait
Reported Trait Functional digestive disorders
Mapped Trait(s) digestive system disease (EFO_0000405)
Additional Trait Information digestive
Released in PGS Catalog: Jan. 10, 2022
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name portability-ldpred2_564
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 747,820
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: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
PPM011413 PSS009333|
European Ancestry|
17,355 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Functional digestive disorders — — Partial Correlation (partial-r): 0.0432 [0.0283, 0.0581] sex, age, birth date, deprivation index, 16 PCs —
PPM011414 PSS009107|
European Ancestry|
3,730 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Functional digestive disorders — — Partial Correlation (partial-r): 0.0616 [0.0295, 0.0936] sex, age, birth date, deprivation index, 16 PCs —
PPM011415 PSS008661|
European Ancestry|
5,869 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Functional digestive disorders — — Partial Correlation (partial-r): 0.0273 [0.0017, 0.0529] sex, age, birth date, deprivation index, 16 PCs —
PPM011416 PSS008435|
Greater Middle Eastern Ancestry|
1,070 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Functional digestive disorders — — Partial Correlation (partial-r): -0.0128 [-0.0733, 0.0477] sex, age, birth date, deprivation index, 16 PCs —
PPM011417 PSS008215|
South Asian Ancestry|
5,621 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Functional digestive disorders — — Partial Correlation (partial-r): 0.0375 [0.0114, 0.0637] sex, age, birth date, deprivation index, 16 PCs —
PPM011418 PSS007996|
East Asian Ancestry|
1,694 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Functional digestive disorders — — Partial Correlation (partial-r): 0.039 [-0.009, 0.0867] sex, age, birth date, deprivation index, 16 PCs —
PPM011420 PSS008884|
African Ancestry|
3,630 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Functional digestive disorders — — Partial Correlation (partial-r): 0.0257 [-0.0069, 0.0583] sex, age, birth date, deprivation index, 16 PCs —
PPM011419 PSS007780|
African Ancestry|
2,227 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Functional digestive disorders — — Partial Correlation (partial-r): 0.0063 [-0.0354, 0.048] sex, age, birth date, deprivation index, 16 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
PSS007780 — — 2,227 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008435 — — 1,070 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009107 — — 3,730 individuals — European Poland (NE Europe) UKB —
PSS009333 — — 17,355 individuals — European UK (+ Ireland) UKB —
PSS008661 — — 5,869 individuals — European Italy (South Europe) UKB —
PSS008215 — — 5,621 individuals — South Asian India (South Asia) UKB —
PSS008884 — — 3,630 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007996 — — 1,694 individuals — East Asian China (East Asia) UKB —