Polygenic Score (PGS) ID: PGS003564

Predicted Trait
Reported Trait Myopia diagnosis
Mapped Trait(s) Myopia (HP_0000545)
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-myopia
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%
79,733 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
— 79,733 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
PPM017492 PSS010931|
European Ancestry|
4,366 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Myopia diagnosis — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM017576 PSS010847|
European Ancestry|
1,145 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Myopia diagnosis — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM017660 PSS010679|
European Ancestry|
1,967 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Myopia diagnosis — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM017744 PSS010595|
Greater Middle Eastern Ancestry|
433 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Myopia diagnosis — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM017828 PSS010259|
European Ancestry|
480 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Myopia diagnosis — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017912 PSS010511|
South Asian Ancestry|
2,626 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Myopia diagnosis — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM017996 PSS010427|
East Asian Ancestry|
646 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Myopia diagnosis — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM018080 PSS010343|
African Ancestry|
1,335 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Myopia diagnosis — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM018164 PSS010763|
African Ancestry|
1,897 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Myopia diagnosis — — 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
PSS010847 — — 1,145 individuals,
36.0 % Male samples
 Mean = 54.7 years
Sd = 8.0 years		 European Polish UKB —
PSS010595 — — 433 individuals,
55.0 % Male samples
 Mean = 52.8 years
Sd = 8.2 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010343 — — 1,335 individuals,
37.0 % Male samples
 Mean = 52.8 years
Sd = 7.9 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010763 — — 1,897 individuals,
43.0 % Male samples
 Mean = 52.2 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010511 — — 2,626 individuals,
54.0 % Male samples
 Mean = 53.6 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010259 — — 480 individuals,
43.0 % Male samples
 Mean = 58.9 years
Sd = 6.9 years		 European Ashkenazi UKB —
PSS010931 — — 4,366 individuals,
48.0 % Male samples
 Mean = 57.1 years
Sd = 8.0 years		 European white British UKB —
PSS010679 — — 1,967 individuals,
44.0 % Male samples
 Mean = 54.5 years
Sd = 8.6 years		 European Italian UKB —
PSS010427 — — 646 individuals,
31.0 % Male samples
 Mean = 53.8 years
Sd = 8.1 years		 East Asian Chinese UKB —