Polygenic Score (PGS) ID: PGS001858

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
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Score Details

Score Construction
PGS Name portability-PLR_564
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 764
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
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
391,124 individuals European UK (+ Ireland) 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
PPM009754 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): 0.0383 [0.0061, 0.0704] sex, age, birth date, deprivation index, 16 PCs
PPM009757 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): 0.0139 [-0.0123, 0.0401] sex, age, birth date, deprivation index, 16 PCs
PPM009758 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): 0.0307 [-0.0172, 0.0785] sex, age, birth date, deprivation index, 16 PCs
PPM009759 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): 0.0283 [-0.0135, 0.0699] sex, age, birth date, deprivation index, 16 PCs
PPM009760 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): -0.0057 [-0.0383, 0.0269] sex, age, birth date, deprivation index, 16 PCs
PPM009753 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): 0.02 [0.0051, 0.0349] sex, age, birth date, deprivation index, 16 PCs
PPM009755 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): 0.0006 [-0.025, 0.0263] sex, age, birth date, deprivation index, 16 PCs
PPM009756 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): -0.0144 [-0.0748, 0.0462] 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
PSS009107 3,730 individuals European Poland (NE Europe) UKB
PSS008884 3,630 individuals African unspecified Nigeria (West Africa) 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
PSS008435 1,070 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS007996 1,694 individuals East Asian China (East Asia) UKB