Polygenic Score (PGS) ID: PGS000137

Predicted Trait
Reported Trait Glaucoma
Mapped Trait(s) glaucoma (MONDO_0005041)
Released in PGS Catalog: March 27, 2020
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Score Details

Score Construction
PGS Name MTAG_glaucoma
Development Method
Name Clumping and Thresholding (C+T)
Parameters r2 = 0.1; p < 0.001
Variants
Original Genome Build NR
Number of Variants 2,673
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000066
Citation (link to publication) Craig JE et al. Nat Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
351,696 individuals (100%)
Score Development/Training
European: 100%
8,004 individuals (100%)
PGS Evaluation
European: 75%
Multi-ancestry (including European): 12.5%
  • European
  • Additional Asian Ancestries
  • Greater Middle Eastern
  • Hispanic or Latin American
  • Not Reported
South Asian: 12.5%
8 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST009722
Europe PMC: 31959993
 351,696 individuals European NR
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
—
[
  • 1,734 cases
  • , 2,938 controls
]
 European ANZRAG Advanced glaucoma — — — Used to select the optimal p-value threshold. Adjusted for sex and first four PCs
—
[
  • 332 cases
  • , 3,000 controls
]
,
47.0 % Male samples
 European NR Advanced glaucoma Mean = 59.0 years
Sd = 10.16 years		 — — Used to replicate OR seen in ANZRAG on UK cases from Southhampton and Liverpool

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
PPM000422 PSS000245|
European Ancestry|
1,795 individuals
 PGP000066 |
Craig JE et al. Nat Genet (2020)
 Reported Trait: Primary open-angle glaucoma (POAG) — AUROC: 0.8 — age, sex, self-reported family history —
PPM000426 PSS000249|
South Asian Ancestry|
7,033 individuals
 PGP000066 |
Craig JE et al. Nat Genet (2020)
 Reported Trait: Glaucoma — AUROC: 0.76 [0.73, 0.79] — age, sex Model 3
PPM000424 PSS000248|
European Ancestry|
3,112 individuals
 PGP000066 |
Craig JE et al. Nat Genet (2020)
 Reported Trait: Glaucoma — AUROC: 0.75 [0.73, 0.76] — age, sex Model 3
PPM000429 PSS000247|
European Ancestry|
3,112 individuals
 PGP000066 |
Craig JE et al. Nat Genet (2020)
 Reported Trait: Primary open-angle glaucoma (POAG) — AUROC: 0.76 [0.72, 0.81] — age, sex Model 3
PPM000425 PSS000249|
South Asian Ancestry|
7,033 individuals
 PGP000066 |
Craig JE et al. Nat Genet (2020)
 Reported Trait: Glaucoma — AUROC: 0.64 [0.59, 0.68] — — Model 1
PPM000423 PSS000248|
European Ancestry|
3,112 individuals
 PGP000066 |
Craig JE et al. Nat Genet (2020)
 Reported Trait: Glaucoma — AUROC: 0.66 [0.64, 0.68] — — Model 1
PPM000428 PSS000247|
European Ancestry|
3,112 individuals
 PGP000066 |
Craig JE et al. Nat Genet (2020)
 Reported Trait: Primary open-angle glaucoma (POAG) — AUROC: 0.67 [0.63, 0.72] — — Model 1
PPM000427 PSS000246|
European Ancestry|
965 individuals
 PGP000066 |
Craig JE et al. Nat Genet (2020)
 Reported Trait: Glaucoma in MYOC p.Gln368Ter carriers — — HR (Hazard Ratio; highest vs. lowest tertile of PRS): 3.4 [1.7, 6.6] sex, PCs 1-6 —
PPM000421 PSS000245|
European Ancestry|
1,795 individuals
 PGP000066 |
Craig JE et al. Nat Genet (2020)
 Reported Trait: Primary open-angle glaucoma (POAG) — AUROC: 0.71 [0.66, 0.77] — — —
PPM016165 PSS010053|
European Ancestry|
1,103 individuals
 PGP000403 |
Siggs OM et al. JAMA Ophthalmol (2022)
|Ext.		 Reported Trait: Visual field worsening — — Hazard ratio (HR, top 5% vs bottom 95%): 1.5 [1.13, 1.97]
Hazard ratio (HR, bottom 20% vs intermediate risk): 0.52 [0.28, 0.96]		 — —
PPM020780 PSS011408|
European Ancestry|
903 individuals
 PGP000588 |
Marshall HN et al. Ophthalmol Glaucoma (2022)
|Ext.		 Reported Trait: Age at first trabeculectomy in individuals with primary open-angle glaucoma β: -1.94 [-3.47, -0.41] — — Sex, family history of glaucoma —
PPM020781 PSS011408|
European Ancestry|
903 individuals
 PGP000588 |
Marshall HN et al. Ophthalmol Glaucoma (2022)
|Ext.		 Reported Trait: Requirement for bilateral trabeculectomy in individuals with primary open-angle glaucoma — — Odds ratio (OR, top vs bottom PRS decile): 1.41 [1.06, 1.91] — —
PPM022190 PSS011837|
Multi-ancestry (including European)|
455 individuals
 PGP000688 |
Saks DG et al. Acta Ophthalmol (2023)
|Ext.		 Reported Trait: Vascular wedge presence in individuals with glaucoma — — p: 0.007 Age, sex, optic disc haemorrhage —
PPM022191 PSS011837|
Multi-ancestry (including European)|
455 individuals
 PGP000688 |
Saks DG et al. Acta Ophthalmol (2023)
|Ext.		 Reported Trait: Retinal nerve fibre layer wedge presence in individuals with glaucoma — — p: 0.07 Age, sex, optic disc haemorrhage —

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
PSS010053 — — 1,103 individuals — European — PROGRESSA Ancestrally matched normative population cohort (n = 17 642) was used for PRS reference
PSS000245 — —
[
  • 74 cases
  • , 1,721 controls
]
,
43.0 % Male samples
 Mean = 64.02 years
Sd = 8.24 years		 European — BMES —
PSS000246 MYOC p.Gln368Ter (rs74315329) carriers using imputation. Glaucoma cases were defined as those who (i) had an ICD-10 diagnosis of ‘primary open angle glaucoma’, ‘other glaucoma’ or ‘glaucoma, unspecified’; (ii) responded ‘glaucoma’ to the question ‘Has a doctor told you that you have any of the following problems with your eyes?’; or (iii) responded ‘glaucoma’ to the question ‘In the touch screen you selected that you have been told by a doctor that you have other serious illnesses or disabilities, could you now tell me what they are? (non-cancer illness). —
[
  • 72 cases
  • , 893 controls
]
 — European — UKB —
PSS000247 ICD-10 defined Primary open-angle glaucoma (POAG) —
[
  • 112 cases
  • , 3,000 controls
]
 — European — UKB —
PSS000248 Glaucoma cases were defined as those who (i) had an ICD-10 diagnosis of ‘primary open angle glaucoma’, ‘other glaucoma’ or ‘glaucoma, unspecified’; (ii) responded ‘glaucoma’ to the question ‘Has a doctor told you that you have any of the following problems with your eyes?’; or (iii) responded ‘glaucoma’ to the question ‘In the touch screen you selected that you have been told by a doctor that you have other serious illnesses or disabilities, could you now tell me what they are? (non-cancer illness). —
[
  • 112 cases
  • , 3,000 controls
]
 — European — UKB —
PSS000249 Glaucoma cases were defined as those who (i) had an ICD-10 diagnosis of ‘primary open angle glaucoma’, ‘other glaucoma’ or ‘glaucoma, unspecified’; (ii) responded ‘glaucoma’ to the question ‘Has a doctor told you that you have any of the following problems with your eyes?’; or (iii) responded ‘glaucoma’ to the question ‘In the touch screen you selected that you have been told by a doctor that you have other serious illnesses or disabilities, could you now tell me what they are? (non-cancer illness). —
[
  • 192 cases
  • , 6,841 controls
]
 — South Asian — UKB —
PSS011837 — — 429 individuals — European — PROGRESSA —
PSS011837 — — 5 individuals — Asian unspecified — PROGRESSA —
PSS011837 — — 1 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) — PROGRESSA —
PSS011837 — — 1 individuals — Hispanic or Latin American — PROGRESSA —
PSS011837 — — 19 individuals — Not reported — PROGRESSA —
PSS011408 — — 903 individuals,
42.7 % Male samples
 — European — ANZRAG —