| Predicted Trait | |
| Reported Trait | Type 2 diabetes |
| Mapped Trait(s) | type 2 diabetes mellitus (MONDO_0005148) |
| Additional Trait Information | UK Biobank codes: non-cancer codes: 1223; ICD9: 25000, 25002, 25010, 25012, 25020, 25022, 25030, 25032, 25040, 25042, 25050, 25052, 25060, 25062, 25070, 25072, 25080, 25082, 25090, 25092; ICD10: E11,E110-E119 |
| Score Construction | |
| PGS Name | t2d_5 |
| Development Method | |
| Name | LASSO |
| Parameters | To reduce the number of candidate SNPs to a computationally feasible set, a gwas was performed on the raw phenotype and the 50,000 snps with smallest p-value were retained. The raw phenotype was regressed on age, sex, and the top 20 UK Biobank PCs and a residual phenotype was then built. The LASSO model was trained using these 50k SNPs and the adjusted phenotype. |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 3,277 |
| Effect Weight Type | beta |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000520 |
| Citation (link to publication) | Raben TG et al. Sci Rep (2023) |
| Ancestry Distribution | |
| Score Development/Training | European: 100% 200,000 individuals (100%) |
| PGS Evaluation | Greater Middle Eastern: 66.7% European: 33.3% 3 Sample Sets |
| 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 |
|---|---|---|---|---|---|---|---|---|
| — | [ ,
47.1 % Male samples |
European | NR | UK Biobank codes: non-cancer codes: 1223; ICD9: 25000, 25002, 25010, 25012, 25020, 25022, 25030, 25032, 25040, 25042, 25050, 25052, 25060, 25062, 25070, 25072, 25080, 25082, 25090, 25092; ICD10: E11,E110-E119 | — | used UK self report 'white' category and then used an adjusted phenotype that includes a regression on the top 20 PCs | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PPM020118 | PSS011296| European Ancestry| 45,334 individuals |
PGP000520 | Raben TG et al. Sci Rep (2023) |
Reported Trait: Type 2 diabetes | — | AUROC: 0.69924 | — | year of birth, sex | — |
| PPM022855 | PSS012080| Greater Middle Eastern Ancestry| 4,534 individuals |
PGP000753 | Aliyu U et al. Diabetes Obes Metab (2025) |Ext. |
Reported Trait: Prediabetes | OR: 1.21 [1.137, 1.289] | AUROC: 0.65 [0.634, 0.666] | R²: 0.086 | sex, baseline age, BMI, PCs1-10 | — |
| PPM022879 | PSS012081| Greater Middle Eastern Ancestry| 2,143 individuals |
PGP000753 | Aliyu U et al. Diabetes Obes Metab (2025) |Ext. |
Reported Trait: Incident T2D in prediabetics | HR: 1.684 [1.462, 1.941] | AUROC: 0.785 [0.754, 0.816] | — | sex, baseline age, BMI, PCs1-10 | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS012080 | age-matched cohort | — | [
|
— | Greater Middle Eastern (Middle Eastern, North African or Persian) (Qatari) |
— | QBB | — |
| PSS012081 | — | Median = 6.0 years | [ ,
54.22 % Male samples |
— | Greater Middle Eastern (Middle Eastern, North African or Persian) (Qatari) |
— | QBB | — |
| PSS011296 | 22,667 sibling pairs | — | 45,334 individuals | — | European | — | UKB | — |