| Predicted Trait | |
| Reported Trait | Coeliac disease |
| Mapped Trait(s) | celiac disease (EFO_0001060) |
| Score Construction | |
| PGS Name | GRS-DQ2.5-CeD |
| Variants | |
| Original Genome Build | hg18 |
| Number of Variants | 2,513 |
| Development Method | |
| Name | SparSNP |
| Parameters | Lasso penalised linear SVM on SNPs, 10-fold cross-validation |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000029 |
| Citation (link to publication) | Abraham G et al. Genome Med (2015) |
| Detailed Phenotype Description | Participant Follow-up Time | Sample Numbers | Age of Study Participants | Sample Ancestry | Additional Ancestry Description | Cohort(s) | Additional Sample/Cohort Information |
|---|---|---|---|---|---|---|---|
| — | — | 11,912 individuals | — | European (British, Dutch, Italian, Finnish) |
— | Four cohorts (UK2, NL, IT, Finn) combined into one, SNPs |
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 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 |
|---|---|---|---|---|---|---|---|---|
| PPM000100 | PSS000065 | PGP000029 Abraham G et al. (2015) |
Reported Trait: Coeliac disease in HLA-DQ2.5 carriers | — | AUROC: 0.718[0.676, 0.761] | — | — | — |
|
PGS Sample Set ID (PSS ID) |
Detailed Phenotype Description | Participant Follow-up Time | Sample Numbers | Age of Study Participants | Sample Ancestry | Additional Ancestry Description | Cohort(s) | Additional Sample/Cohort Information |
|---|---|---|---|---|---|---|---|---|
| PSS000065 | The HLA-DQ2.5-positive subset of NIDDK-CIDR | — | [
|
— | European | — | NIDDK | HLA alleles were imputed using SNP2HLA |