PGS Catalog - PGS003860 / Refractive error (Polygenic Score)

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
GWAS Catalog: GCST90275204 Europe PMC: 37055258	468,769 individuals	European	24 cohorts ALIENOR ,ANZRAG ,AREDS ,B58C ,BATS ,BMES ,CROATIA-KORCULA ,CROATIA-VIS ,DCCT ,EGCUT ,EPIC-Norfolk ,ERF ,FECD ,FES ,GERA ,GHS ,KORA ,OGP ,ORCADES ,RS ,TwinsUK ,UKB ,WESDR ,YFS

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
—	4,000 individuals	European	UKB	—	—	—	—	—

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
PPM018722	PSS011080\| European Ancestry\| 6,000 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Low myopia	—	AUROC: 0.728 [0.715, 0.741]	—	—	—
PPM018736	PSS011083\| South Asian Ancestry\| 4,641 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: High myopia (HM6)	—	AUROC: 0.706 [0.668, 0.743]	—	—	—
PPM018723	PSS011078\| African Ancestry\| 4,089 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Low myopia	—	AUROC: 0.582 [0.563, 0.601]	—	—	—
PPM018725	PSS011079\| East Asian Ancestry\| 978 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Low myopia	—	AUROC: 0.653 [0.619, 0.687]	—	—	—
PPM018726	PSS011080\| European Ancestry\| 6,000 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Moderate myopia	—	AUROC: 0.754 [0.738, 0.77]	—	—	—
PPM018727	PSS011078\| African Ancestry\| 4,089 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Moderate myopia	—	AUROC: 0.596 [0.566, 0.626]	—	—	—
PPM018728	PSS011083\| South Asian Ancestry\| 4,641 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Moderate myopia	—	AUROC: 0.686 [0.664, 0.708]	—	—	—
PPM018737	PSS011079\| East Asian Ancestry\| 978 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: High myopia (HM6)	—	AUROC: 0.672 [0.619, 0.724]	—	—	—
PPM018739	PSS011081\| European Ancestry\| 1,649 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Refractive error	—	—	R²: 0.141 [0.112, 0.171]	—	—
PPM018729	PSS011079\| East Asian Ancestry\| 978 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Moderate myopia	—	AUROC: 0.66 [0.621, 0.699]	—	—	—
PPM018731	PSS011078\| African Ancestry\| 4,089 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: High myopia (HM5)	—	AUROC: 0.586 [0.542, 0.629]	—	—	—
PPM018740	PSS011082\| European Ancestry\| 1,277 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Moderate hyperopia	—	AUROC: 0.765 [0.695, 0.825]	—	—	—
PPM018741	PSS011081\| European Ancestry\| 1,649 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Moderate hyperopia	—	AUROC: 0.774 [0.698, 0.845]	—	—	—
PPM018732	PSS011083\| South Asian Ancestry\| 4,641 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: High myopia (HM5)	—	AUROC: 0.695 [0.664, 0.726]	—	—	—
PPM018735	PSS011078\| African Ancestry\| 4,089 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: High myopia (HM6)	—	AUROC: 0.584 [0.53, 0.639]	—	—	—
PPM018714	PSS011080\| European Ancestry\| 6,000 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Refractive error	—	—	R²: 0.19 [0.172, 0.208]	—	—
PPM018715	PSS011078\| African Ancestry\| 4,089 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Refractive error	—	—	R²: 0.02 [0.012, 0.029]	—	—
PPM018716	PSS011083\| South Asian Ancestry\| 4,641 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Refractive error	—	—	R²: 0.08 [0.066, 0.096]	—	—
PPM018717	PSS011079\| East Asian Ancestry\| 978 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Refractive error	—	—	R²: 0.06 [0.034, 0.092]	—	—
PPM018718	PSS011080\| European Ancestry\| 6,000 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Moderate hyperopia	—	AUROC: 0.742 [0.718, 0.766]	—	—	—
PPM018719	PSS011078\| African Ancestry\| 4,089 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Moderate hyperopia	—	AUROC: 0.61 [0.543, 0.677]	—	—	—
PPM018720	PSS011083\| South Asian Ancestry\| 4,641 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Moderate hyperopia	—	AUROC: 0.676 [0.631, 0.721]	—	—	—
PPM018721	PSS011079\| East Asian Ancestry\| 978 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Moderate hyperopia	—	AUROC: 0.61 [0.415, 0.805]	—	—	—
PPM018733	PSS011079\| East Asian Ancestry\| 978 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: High myopia (HM5)	—	AUROC: 0.648 [0.601, 0.694]	—	—	—
PPM018734	PSS011080\| European Ancestry\| 6,000 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: High myopia (HM6)	—	AUROC: 0.783 [0.754, 0.812]	—	—	—
PPM018724	PSS011083\| South Asian Ancestry\| 4,641 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Low myopia	—	AUROC: 0.647 [0.631, 0.664]	—	—	—
PPM018730	PSS011080\| European Ancestry\| 6,000 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: High myopia (HM5)	—	AUROC: 0.774 [0.75, 0.798]	—	—	—
PPM018738	PSS011082\| European Ancestry\| 1,277 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Refractive error	—	—	R²: 0.116 [0.079, 0.153]	—	—
PPM018742	PSS011082\| European Ancestry\| 1,277 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Low myopia	—	AUROC: 0.703 [0.654, 0.751]	—	—	—
PPM018743	PSS011081\| European Ancestry\| 1,649 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Low myopia	—	AUROC: 0.691 [0.659, 0.722]	—	—	—
PPM018744	PSS011082\| European Ancestry\| 1,277 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Moderate myopia	—	AUROC: 0.735 [0.6, 0.854]	—	—	—
PPM018745	PSS011081\| European Ancestry\| 1,649 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Moderate myopia	—	AUROC: 0.691 [0.624, 0.754]	—	—	—
PPM018746	PSS011082\| European Ancestry\| 1,277 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: High myopia (HM5)	—	AUROC: 0.579 [0.567, 0.592]	—	—	—
PPM018747	PSS011081\| European Ancestry\| 1,649 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: High myopia (HM6)	—	AUROC: 0.739 [0.619, 0.851]	—	—	—
PPM018748	PSS011081\| European Ancestry\| 1,649 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: High myopia (HM6)	—	AUROC: 0.783 [0.754, 0.812]	—	—	—
PPM018749	PSS011089\| Ancestry Not Reported\| 6,119 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Refractive error	—	—	R²: 0.05 [0.04, 0.06]	—	—
PPM018750	PSS011088\| Ancestry Not Reported\| 4,037 individuals	PGP000498 \| Clark R et al. EBioMedicine (2023)	Reported Trait: Refractive error	—	—	R²: 0.12 [0.1, 0.14]	—	—

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
PSS011078	—	—	4,089 individuals	—	African unspecified	—	UKB	—
PSS011079	—	—	978 individuals	—	East Asian	—	UKB	—
PSS011080	—	—	6,000 individuals	—	European	—	UKB	—
PSS011081	—	—	1,649 individuals, 48.7 % Male samples	Mean = 13.62 years Sd = 0.36 years	European	—	Generation_R	—
PSS011082	—	—	1,277 individuals, 50.4 % Male samples	Mean = 9.83 years Sd = 0.35 years	European	—	Generation_R	—
PSS011083	—	—	4,641 individuals	—	South Asian	—	UKB	—
PSS011088	—	—	4,037 individuals, 47.2 % Male samples	Mean = 15.43 years Sd = 0.28 years	Not reported	—	ALSPAC	—
PSS011089	—	—	6,119 individuals, 50.7 % Male samples	Mean = 7.53 years Sd = 0.31 years	Not reported	—	ALSPAC	—

Predicted Trait
Reported Trait	Refractive error
Mapped Trait(s)	refractive error measurement (EFO_0007814)

Score Construction
PGS Name	PGS_RE
Development Method
Name	LDpred2
Parameters	NR
Variants
Original Genome Build	NR
Number of Variants	767,867
Effect Weight Type	beta

PGS Source
PGS Catalog Publication (PGP) ID	PGP000498
Citation (link to publication)	Clark R et al. EBioMedicine (2023)

Ancestry Distribution
Source of Variant Associations (GWAS)	European: 100% 468,769 individuals (100%)
Score Development/Training	European: 100% 4,000 individuals (100%)
PGS Evaluation	European: 37.5% Not Reported: 25% African: 12.5% East Asian: 12.5% South Asian: 12.5% 8 Sample Sets

Polygenic Score (PGS) ID: PGS003860

Score Details

Development Samples

Source of Variant Associations (GWAS)

Score Development/Training

Performance Metrics

Evaluated Samples