Polygenic Score (PGS) ID: PGS001964

Predicted Trait
Reported Trait Gamma glutamyltransferase
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-PLR_log_log_gammaGT
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 76,069
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
PPM010587 PSS009453|
European Ancestry|
18,990 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Gamma glutamyltransferase Partial Correlation (partial-r): 0.4046 [0.3926, 0.4164] sex, age, birth date, deprivation index, 16 PCs
PPM010589 PSS008781|
European Ancestry|
6,321 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Gamma glutamyltransferase Partial Correlation (partial-r): 0.3709 [0.3494, 0.392] sex, age, birth date, deprivation index, 16 PCs
PPM010590 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): 0.4245 [0.3749, 0.4717] sex, age, birth date, deprivation index, 16 PCs
PPM010591 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): 0.3621 [0.3399, 0.3839] sex, age, birth date, deprivation index, 16 PCs
PPM010592 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): 0.3412 [0.2984, 0.3825] sex, age, birth date, deprivation index, 16 PCs
PPM010593 PSS007897|
African Ancestry|
2,344 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Gamma glutamyltransferase Partial Correlation (partial-r): 0.1377 [0.0976, 0.1774] sex, age, birth date, deprivation index, 16 PCs
PPM010594 PSS009001|
African Ancestry|
3,654 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Gamma glutamyltransferase Partial Correlation (partial-r): 0.1235 [0.0913, 0.1554] sex, age, birth date, deprivation index, 16 PCs
PPM010588 PSS009227|
European Ancestry|
3,948 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Gamma glutamyltransferase Partial Correlation (partial-r): 0.3675 [0.3401, 0.3942] 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