Predicted Trait | |
Reported Trait | Celiac disease or gluten sensitivity, diagnosed |
Mapped Trait(s) | celiac disease (EFO_0001060) |
Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN21068 |
Score Construction | |
PGS Name | GBE_BIN21068 |
Development Method | |
Name | snpnet |
Parameters | NR |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 9 |
Effect Weight Type | NR |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000244 |
Citation (link to publication) | Tanigawa Y et al. PLoS Genet (2022) |
Ancestry Distribution | |
Score Development/Training | European: 100% 97,279 individuals (100%) |
PGS Evaluation | European: 50% African: 25% South Asian: 25% 4 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 |
---|---|---|---|---|---|---|---|---|
— | [
|
European | UKB | — | — | — | white British ancestry | — |
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 |
---|---|---|---|---|---|---|---|---|
PPM008997 | PSS003667| African Ancestry| 969 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Diagnosed with coeliac disease or gluten sensitivity | — | AUROC: 0.77521 [0.67165, 0.87877] | R²: 0.10494 Incremental AUROC (full-covars): 0.00391 PGS R2 (no covariates): 0.00465 PGS AUROC (no covariates): 0.54048 [0.39518, 0.68579] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008998 | PSS003668| European Ancestry| 9,024 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Diagnosed with coeliac disease or gluten sensitivity | — | AUROC: 0.67118 [0.63561, 0.70676] | R²: 0.04801 Incremental AUROC (full-covars): 0.03638 PGS R2 (no covariates): 0.02217 PGS AUROC (no covariates): 0.58541 [0.54195, 0.62888] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008999 | PSS003669| South Asian Ancestry| 1,145 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Diagnosed with coeliac disease or gluten sensitivity | — | AUROC: 0.78803 [0.69728, 0.87878] | R²: 0.09336 Incremental AUROC (full-covars): 0.00365 PGS R2 (no covariates): 0.00127 PGS AUROC (no covariates): 0.56184 [0.43287, 0.6908] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM009000 | PSS003670| European Ancestry| 24,310 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Diagnosed with coeliac disease or gluten sensitivity | — | AUROC: 0.6734 [0.64935, 0.69745] | R²: 0.04185 Incremental AUROC (full-covars): 0.08398 PGS R2 (no covariates): 0.02957 PGS AUROC (no covariates): 0.62888 [0.60094, 0.65683] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
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 |
---|---|---|---|---|---|---|---|---|
PSS003668 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS003669 | — | — | [
|
— | South Asian | — | UKB | — |
PSS003670 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |
PSS003667 | — | — | [
|
— | African unspecified | — | UKB | — |