Polygenic Score (PGS) ID: PGS003493

Predicted Trait
Reported Trait avMSE
Mapped Trait(s) visual acuity measurement (EFO_0008385)
Released in PGS Catalog: April 12, 2023
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name cont-decay-avMSE
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
79,207 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 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
— 79,207 individuals,
0.47 % Male samples
 European UKB — Mean = 57.4 years
Sd = 7.9 years		 — white British —

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
PPM017421 PSS010892|
European Ancestry|
4,334 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017505 PSS010808|
European Ancestry|
1,138 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017589 PSS010640|
European Ancestry|
1,952 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017673 PSS010556|
Greater Middle Eastern Ancestry|
432 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM017757 PSS010220|
European Ancestry|
467 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM017841 PSS010472|
South Asian Ancestry|
2,604 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM017925 PSS010388|
East Asian Ancestry|
631 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018009 PSS010304|
African Ancestry|
1,322 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM018093 PSS010724|
African Ancestry|
1,891 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —

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
PSS010304 — — 1,322 individuals,
37.0 % Male samples
 Mean = 52.8 years
Sd = 7.9 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010724 — — 1,891 individuals,
43.0 % Male samples
 Mean = 52.2 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010472 — — 2,604 individuals,
54.0 % Male samples
 Mean = 53.6 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010220 — — 467 individuals,
43.0 % Male samples
 Mean = 58.9 years
Sd = 6.9 years		 European Ashkenazi UKB —
PSS010892 — — 4,334 individuals,
48.0 % Male samples
 Mean = 57.1 years
Sd = 8.0 years		 European white British UKB —
PSS010640 — — 1,952 individuals,
44.0 % Male samples
 Mean = 54.5 years
Sd = 8.6 years		 European Italian UKB —
PSS010388 — — 631 individuals,
31.0 % Male samples
 Mean = 53.8 years
Sd = 8.1 years		 East Asian Chinese UKB —
PSS010808 — — 1,138 individuals,
36.0 % Male samples
 Mean = 54.7 years
Sd = 8.0 years		 European Polish UKB —
PSS010556 — — 432 individuals,
56.0 % Male samples
 Mean = 52.8 years
Sd = 8.2 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —