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
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
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 —
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 —

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
PSS007752 — — 2,374 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009078 — — 4,043 individuals — European Poland (NE Europe) 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 —
PSS008186 — — 6,037 individuals — South Asian India (South Asia) UKB —
PSS009304 — — 19,413 individuals — European UK (+ Ireland) UKB —
PSS007970 — — 1,775 individuals — East Asian China (East Asia) UKB —