Polygenic Score (PGS) ID: PGS000137

Predicted Trait
Reported Trait Glaucoma
Mapped Trait(s) glaucoma (EFO_0000516)
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: 80%
South Asian: 20%
5 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
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]
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
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
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
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
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
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
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
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

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
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