PGS Catalog - PGS001964 / Gamma-glutamyl transferase (Polygenic Score)

Polygenic Score (PGS) ID: PGS001964

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-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

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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)	—

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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.

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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	—
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	—
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	—

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Evaluated Samples

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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
PSS007897	—	—	2,344 individuals	—	African American or Afro-Caribbean	Carribean	UKB	—
PSS008110	—	—	1,716 individuals	—	East Asian	China (East Asia)	UKB	—
PSS008333	—	—	6,000 individuals	—	South Asian	India (South Asia)	UKB	—
PSS008555	—	—	1,124 individuals	—	Greater Middle Eastern (Middle Eastern, North African or Persian)	Iran (Middle East)	UKB	—
PSS008781	—	—	6,321 individuals	—	European	Italy (South Europe)	UKB	—
PSS009001	—	—	3,654 individuals	—	African unspecified	Nigeria (West Africa)	UKB	—
PSS009227	—	—	3,948 individuals	—	European	Poland (NE Europe)	UKB	—
PSS009453	—	—	18,990 individuals	—	European	UK (+ Ireland)	UKB	—

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