PGS Catalog - PGS002041 / Macular degeneration (senile) of retina NOS (Polygenic Score)

Polygenic Score (PGS) ID: PGS002041

Predicted Trait
Reported Trait	Macular degeneration (senile) of retina NOS
Mapped Trait(s)	age-related macular degeneration (EFO_0001365)
Additional Trait Information	sense organs

Released in PGS Catalog: Jan. 10, 2022

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Score Details

Score Construction
PGS Name	portability-ldpred2_362.29
Development Method
Name	LDpred2 (bigsnpr)
Parameters	LDpred2-auto using HapMap3 variants
Variants
Original Genome Build	GRCh37
Number of Variants	116,538
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
PPM011194	PSS009304\| European Ancestry\| 19,413 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Macular degeneration (senile) of retina NOS	—	—	Partial Correlation (partial-r): 0.0159 [0.0018, 0.0299]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011195	PSS009078\| European Ancestry\| 4,043 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Macular degeneration (senile) of retina NOS	—	—	Partial Correlation (partial-r): 0.0248 [-0.0061, 0.0556]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011196	PSS008632\| European Ancestry\| 6,470 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Macular degeneration (senile) of retina NOS	—	—	Partial Correlation (partial-r): 0.0179 [-0.0065, 0.0423]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011197	PSS008406\| Greater Middle Eastern Ancestry\| 1,165 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Macular degeneration (senile) of retina NOS	—	—	Partial Correlation (partial-r): -0.0344 [-0.0921, 0.0236]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011198	PSS008186\| South Asian Ancestry\| 6,037 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Macular degeneration (senile) of retina NOS	—	—	Partial Correlation (partial-r): 0.0372 [0.0119, 0.0624]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011199	PSS007970\| East Asian Ancestry\| 1,775 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Macular degeneration (senile) of retina NOS	—	—	Partial Correlation (partial-r): -0.0312 [-0.0779, 0.0156]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011200	PSS007752\| African Ancestry\| 2,374 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Macular degeneration (senile) of retina NOS	—	—	Partial Correlation (partial-r): 0.0038 [-0.0366, 0.0442]	sex, age, birth date, deprivation index, 16 PCs	—
PPM011201	PSS008856\| African Ancestry\| 3,723 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Macular degeneration (senile) of retina NOS	—	—	Partial Correlation (partial-r): 0.018 [-0.0143, 0.0501]	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
PSS007752	—	—	2,374 individuals	—	African American or Afro-Caribbean	Carribean	UKB	—
PSS007970	—	—	1,775 individuals	—	East Asian	China (East Asia)	UKB	—
PSS008186	—	—	6,037 individuals	—	South Asian	India (South Asia)	UKB	—
PSS008406	—	—	1,165 individuals	—	Greater Middle Eastern (Middle Eastern, North African or Persian)	Iran (Middle East)	UKB	—
PSS008632	—	—	6,470 individuals	—	European	Italy (South Europe)	UKB	—
PSS008856	—	—	3,723 individuals	—	African unspecified	Nigeria (West Africa)	UKB	—
PSS009078	—	—	4,043 individuals	—	European	Poland (NE Europe)	UKB	—
PSS009304	—	—	19,413 individuals	—	European	UK (+ Ireland)	UKB	—

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