Polygenic Score (PGS) ID: PGS002182

Predicted Trait
Reported Trait Gamma-glutamyl transferase
Mapped Trait(s) serum gamma-glutamyl transferase measurement (EFO_0004532)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_log_log_gammaGT
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 713,481
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
PPM012303 PSS009453|
European Ancestry|
18,990 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Gamma glutamyltransferase — — Partial Correlation (partial-r): 0.3999 [0.3879, 0.4118] sex, age, birth date, deprivation index, 16 PCs —
PPM012304 PSS009227|
European Ancestry|
3,948 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Gamma glutamyltransferase — — Partial Correlation (partial-r): 0.3606 [0.3331, 0.3875] sex, age, birth date, deprivation index, 16 PCs —
PPM012305 PSS008781|
European Ancestry|
6,321 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Gamma glutamyltransferase — — Partial Correlation (partial-r): 0.3639 [0.3423, 0.3851] sex, age, birth date, deprivation index, 16 PCs —
PPM012306 PSS008555|
Greater Middle Eastern Ancestry|
1,124 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Gamma glutamyltransferase — — Partial Correlation (partial-r): 0.4225 [0.3728, 0.4698] sex, age, birth date, deprivation index, 16 PCs —
PPM012307 PSS008333|
South Asian Ancestry|
6,000 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Gamma glutamyltransferase — — Partial Correlation (partial-r): 0.3609 [0.3387, 0.3828] sex, age, birth date, deprivation index, 16 PCs —
PPM012308 PSS008110|
East Asian Ancestry|
1,716 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Gamma glutamyltransferase — — Partial Correlation (partial-r): 0.3316 [0.2886, 0.3733] sex, age, birth date, deprivation index, 16 PCs —
PPM012309 PSS007897|
African Ancestry|
2,344 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Gamma glutamyltransferase — — Partial Correlation (partial-r): 0.1412 [0.1011, 0.1808] sex, age, birth date, deprivation index, 16 PCs —
PPM012310 PSS009001|
African Ancestry|
3,654 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Gamma glutamyltransferase — — Partial Correlation (partial-r): 0.1247 [0.0926, 0.1566] 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
PSS009001 — — 3,654 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008555 — — 1,124 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009227 — — 3,948 individuals — European Poland (NE Europe) UKB —
PSS009453 — — 18,990 individuals — European UK (+ Ireland) UKB —
PSS008781 — — 6,321 individuals — European Italy (South Europe) UKB —
PSS008333 — — 6,000 individuals — South Asian India (South Asia) UKB —
PSS008110 — — 1,716 individuals — East Asian China (East Asia) UKB —
PSS007897 — — 2,344 individuals — African American or Afro-Caribbean Carribean UKB —