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) |
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 |
---|---|---|---|---|---|---|---|
— | — | 11,912 individuals | — | European (British, Dutch, Italian, Finnish) |
— | Four cohorts (UK2, NL, IT, Finn) combined into one, SNPs |
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) |
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 |
---|---|---|---|---|---|---|---|---|
PSS000065 | The HLA-DQ2.5-positive subset of NIDDK-CIDR | — | [
|
— | European | — | NIDDK | HLA alleles were imputed using SNP2HLA |