Predicted Trait | |
Reported Trait | Glaucoma |
Mapped Trait(s) | glaucoma (EFO_0000516) |
Score Construction | |
PGS Name | MTAG_glaucoma |
Variants | |
Original Genome Build | NR |
Number of Variants | 2,673 |
Development Method | |
Name | Clumping + Thresholding |
Parameters | r2 = 0.1; p < 0.001 |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000066 |
Citation (link to publication) | Craig JE et al. Nat Genet (2020) |
Study Identifiers | Sample Numbers | Sample Ancestry |
---|---|---|
GWAS Catalog: GCST009722 EuropePMC: 31959993 |
351,696 individuals | European |
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 |
---|---|---|---|---|---|---|---|
Advanced glaucoma | — | [
|
— | European | — | ANZRAG | Used to select the optimal p-value threshold. Adjusted for sex and first four PCs |
Advanced glaucoma | — | [ ,
47.0 % Male samples |
Mean = 59.0 years Sd = 10.16 years |
European | — | Used to replicate OR seen in ANZRAG on UK cases from Southhampton and Liverpool |
PGS Performance Metric ID (PPM ID) |
PGS Sample Set ID (PSS ID) |
Performance Source | Trait |
PGS Effect Sizes (per SD change) |
PGS Classification Metrics | Other Metrics | Covariates Included in the Model | PGS Performance: Other Relevant Information |
---|---|---|---|---|---|---|---|---|
PPM000422 | PSS000245 | PGP000066 Craig JE et al. (2020) | Reported Trait: Primary open-angle glaucoma (POAG) | — | AUROC: 0.8 | — | age, sex, self-reported family history | — |
PPM000426 | PSS000249 | PGP000066 Craig JE et al. (2020) | Reported Trait: Glaucoma | — | AUROC: 0.76 [0.73, 0.79] | — | age, sex | Model 3 |
PPM000424 | PSS000248 | PGP000066 Craig JE et al. (2020) | Reported Trait: Glaucoma | — | AUROC: 0.75 [0.73, 0.76] | — | age, sex | Model 3 |
PPM000429 | PSS000247 | PGP000066 Craig JE et al. (2020) | Reported Trait: Primary open-angle glaucoma (POAG) | — | AUROC: 0.76 [0.72, 0.81] | — | age, sex | Model 3 |
PPM000425 | PSS000249 | PGP000066 Craig JE et al. (2020) | Reported Trait: Glaucoma | — | AUROC: 0.64 [0.59, 0.68] | — | — | Model 1 |
PPM000423 | PSS000248 | PGP000066 Craig JE et al. (2020) | Reported Trait: Glaucoma | — | AUROC: 0.66 [0.64, 0.68] | — | — | Model 1 |
PPM000428 | PSS000247 | PGP000066 Craig JE et al. (2020) | Reported Trait: Primary open-angle glaucoma (POAG) | — | AUROC: 0.67 [0.63, 0.72] | — | — | Model 1 |
PPM000427 | PSS000246 | PGP000066 Craig JE et al. (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 | PGP000066 Craig JE et al. (2020) | Reported Trait: Primary open-angle glaucoma (POAG) | — | AUROC: 0.71 [0.66, 0.77] | — | — | — |
PGS Sample Set ID (PSS ID) |
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 | — | — | [ ,
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). | — | [
|
— | European | — | UKB | — |
PSS000247 | ICD-10 defined Primary open-angle glaucoma (POAG) | — | [
|
— | 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). | — | [
|
— | 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). | — | [
|
— | South Asian | — | UKB | — |