PGS Publication: PGP000066

Publication Information (EuropePMC)
Title Multitrait analysis of glaucoma identifies new risk loci and enables polygenic prediction of disease susceptibility and progression.
PubMed ID 31959993(Europe PMC)
doi 10.1038/s41588-019-0556-y
Publication Date Jan. 20, 2020
Journal Nat Genet
Author(s) Craig JE, Han X, Qassim A, Hassall M, Cooke Bailey JN, Kinzy TG, Khawaja AP, An J, Marshall H, Gharahkhani P, Igo RP, Graham SL, Healey PR, Ong JS, Zhou T, Siggs O, Law MH, Souzeau E, Ridge B, Hysi PG, Burdon KP, Mills RA, Landers J, Ruddle JB, Agar A, Galanopoulos A, White AJR, Willoughby CE, Andrew NH, Best S, Vincent AL, Goldberg I, Radford-Smith G, Martin NG, Montgomery GW, Vitart V, Hoehn R, Wojciechowski R, Jonas JB, Aung T, Pasquale LR, Cree AJ, Sivaprasad S, Vallabh NA, NEIGHBORHOOD consortium, UK Biobank Eye and Vision Consortium, Viswanathan AC, Pasutto F, Haines JL, Klaver CCW, van Duijn CM, Casson RJ, Foster PJ, Khaw PT, Hammond CJ, Mackey DA, Mitchell P, Lotery AJ, Wiggs JL, Hewitt AW, MacGregor S.
Released in PGS Catalog: March 27, 2020

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Additional Asian Ancestries
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Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000137
(MTAG_glaucoma)
 PGP000066 |
Craig JE et al. Nat Genet (2020)
 Glaucoma glaucoma 2,673
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000137/ScoringFiles/PGS000137.txt.gz

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) 		Evaluated Score 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 PGS000137
(MTAG_glaucoma)
 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 PGS000137
(MTAG_glaucoma)
 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 PGS000137
(MTAG_glaucoma)
 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 PGS000137
(MTAG_glaucoma)
 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 PGS000137
(MTAG_glaucoma)
 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 PGS000137
(MTAG_glaucoma)
 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 PGS000137
(MTAG_glaucoma)
 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 PGS000137
(MTAG_glaucoma)
 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 PGS000137
(MTAG_glaucoma)
 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] — — —

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 —