Polygenic Score (PGS) ID: PGS002223

Predicted Trait
Reported Trait Sensitive stomach
Mapped Trait(s) health trait (EFO_0007652)
Additional Trait Information digestive
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_sensitive_stomach
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 795,614
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
PPM012630 PSS009489|
European Ancestry|
6,619 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sensitive stomach — — Partial Correlation (partial-r): 0.0922 [0.0682, 0.116] sex, age, birth date, deprivation index, 16 PCs —
PPM012631 PSS009263|
European Ancestry|
1,216 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sensitive stomach — — Partial Correlation (partial-r): 0.0905 [0.034, 0.1465] sex, age, birth date, deprivation index, 16 PCs —
PPM012632 PSS008817|
European Ancestry|
2,231 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sensitive stomach — — Partial Correlation (partial-r): 0.0032 [-0.0385, 0.0449] sex, age, birth date, deprivation index, 16 PCs —
PPM012633 PSS008591|
Greater Middle Eastern Ancestry|
196 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sensitive stomach — — Partial Correlation (partial-r): -0.0138 [-0.1614, 0.1344] sex, age, birth date, deprivation index, 16 PCs —
PPM012634 PSS008369|
South Asian Ancestry|
842 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sensitive stomach — — Partial Correlation (partial-r): 0.1276 [0.0597, 0.1942] sex, age, birth date, deprivation index, 16 PCs —
PPM012635 PSS008145|
East Asian Ancestry|
413 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sensitive stomach — — Partial Correlation (partial-r): 0.0012 [-0.0977, 0.1001] sex, age, birth date, deprivation index, 16 PCs —
PPM012636 PSS007933|
African Ancestry|
355 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sensitive stomach — — Partial Correlation (partial-r): 0.0978 [-0.0094, 0.2029] sex, age, birth date, deprivation index, 16 PCs —
PPM012637 PSS009037|
African Ancestry|
479 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sensitive stomach — — Partial Correlation (partial-r): 0.0343 [-0.0574, 0.1254] 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
PSS009037 — — 479 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009263 — — 1,216 individuals — European Poland (NE Europe) UKB —
PSS008591 — — 196 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008369 — — 842 individuals — South Asian India (South Asia) UKB —
PSS009489 — — 6,619 individuals — European UK (+ Ireland) UKB —
PSS008817 — — 2,231 individuals — European Italy (South Europe) UKB —
PSS008145 — — 413 individuals — East Asian China (East Asia) UKB —
PSS007933 — — 355 individuals — African American or Afro-Caribbean Carribean UKB —