PGS Catalog - PGS001836 / Glaucoma (Polygenic Score)

Polygenic Score (PGS) ID: PGS001836

Predicted Trait
Reported Trait	Glaucoma
Mapped Trait(s)	glaucoma (MONDO_0005041)
Additional Trait Information	sense organs

Released in PGS Catalog: Jan. 10, 2022

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Score Details

Score Construction
PGS Name	portability-PLR_365
Development Method
Name	Penalized regression (bigstatsr)
Parameters	HapMap3 variants
Variants
Original Genome Build	GRCh37
Number of Variants	7,052
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
PPM009578	PSS009306\| European Ancestry\| 19,592 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Glaucoma	—	—	Partial Correlation (partial-r): 0.0419 [0.0279, 0.0558]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009579	PSS009080\| European Ancestry\| 4,066 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Glaucoma	—	—	Partial Correlation (partial-r): 0.0404 [0.0096, 0.0711]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009580	PSS008634\| European Ancestry\| 6,540 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Glaucoma	—	—	Partial Correlation (partial-r): 0.0301 [0.0059, 0.0544]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009581	PSS008408\| Greater Middle Eastern Ancestry\| 1,181 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Glaucoma	—	—	Partial Correlation (partial-r): 0.0631 [0.0056, 0.1202]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009582	PSS008188\| South Asian Ancestry\| 6,176 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Glaucoma	—	—	Partial Correlation (partial-r): 0.0232 [-0.0018, 0.0481]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009583	PSS007971\| East Asian Ancestry\| 1,783 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Glaucoma	—	—	Partial Correlation (partial-r): 0.0002 [-0.0465, 0.0469]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009584	PSS007753\| African Ancestry\| 2,447 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Glaucoma	—	—	Partial Correlation (partial-r): 0.0282 [-0.0116, 0.0679]	sex, age, birth date, deprivation index, 16 PCs	—
PPM009585	PSS008858\| African Ancestry\| 3,854 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Glaucoma	—	—	Partial Correlation (partial-r): 0.0257 [-0.0059, 0.0573]	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
PSS007753	—	—	2,447 individuals	—	African American or Afro-Caribbean	Carribean	UKB	—
PSS007971	—	—	1,783 individuals	—	East Asian	China (East Asia)	UKB	—
PSS008188	—	—	6,176 individuals	—	South Asian	India (South Asia)	UKB	—
PSS008408	—	—	1,181 individuals	—	Greater Middle Eastern (Middle Eastern, North African or Persian)	Iran (Middle East)	UKB	—
PSS008634	—	—	6,540 individuals	—	European	Italy (South Europe)	UKB	—
PSS008858	—	—	3,854 individuals	—	African unspecified	Nigeria (West Africa)	UKB	—
PSS009080	—	—	4,066 individuals	—	European	Poland (NE Europe)	UKB	—
PSS009306	—	—	19,592 individuals	—	European	UK (+ Ireland)	UKB	—

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