Experimental Factor Ontology (EFO) Information | |
Identifier | EFO_0007149 |
Description | Acute inflammation of the vermiform appendix. [NCIT: P378] | Trait categories |
Digestive system disorder
Immune system disorder
|
Synonyms |
9 synonyms
|
Mapped terms |
13 mapped terms
|
Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | Ancestry distribution | Scoring File (FTP Link) |
---|---|---|---|---|---|---|
PGS001369 (GBE_HC1090) |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Acute appendicitis (time-to-event) | appendicitis | 4 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001369/ScoringFiles/PGS001369.txt.gz |
PGS001785 (1kgeur_gbmi_leaveUKBBout_AcApp_pst_eff_a1_b0.5_phiauto) |
PGP000262 | Wang Y et al. Cell Genom (2023) |
Acute appendicitis | appendicitis | 911,334 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001785/ScoringFiles/PGS001785.txt.gz |
PGS Performance Metric ID (PPM) |
Evaluated Score |
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 |
---|---|---|---|---|---|---|---|---|---|
PPM005205 | PGS001369 (GBE_HC1090) |
PSS004099| African Ancestry| 6,497 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE acute appendicitis | — | AUROC: 0.62041 [0.53518, 0.70564] | R²: 0.03016 Incremental AUROC (full-covars): -0.00198 PGS R2 (no covariates): 0.00105 PGS AUROC (no covariates): 0.47489 [0.37525, 0.57453] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM005206 | PGS001369 (GBE_HC1090) |
PSS004100| East Asian Ancestry| 1,704 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE acute appendicitis | — | AUROC: 0.8493 [0.77779, 0.9208] | R²: 0.14577 Incremental AUROC (full-covars): 0.00105 PGS R2 (no covariates): 0.00332 PGS AUROC (no covariates): 0.51032 [0.33889, 0.68176] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM005207 | PGS001369 (GBE_HC1090) |
PSS004101| European Ancestry| 24,905 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE acute appendicitis | — | AUROC: 0.56849 [0.52835, 0.60862] | R²: 0.00702 Incremental AUROC (full-covars): -0.00219 PGS R2 (no covariates): 0.0 PGS AUROC (no covariates): 0.49616 [0.45378, 0.53854] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM005208 | PGS001369 (GBE_HC1090) |
PSS004102| South Asian Ancestry| 7,831 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE acute appendicitis | — | AUROC: 0.72977 [0.65912, 0.80042] | Incremental AUROC (full-covars): 0.00039 PGS R2 (no covariates): 0.00096 R²: 0.05613 PGS AUROC (no covariates): 0.5334 [0.44427, 0.62254] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM005209 | PGS001369 (GBE_HC1090) |
PSS004103| European Ancestry| 67,425 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE acute appendicitis | — | AUROC: 0.57413 [0.55138, 0.59688] | R²: 0.00617 Incremental AUROC (full-covars): 0.00987 PGS R2 (no covariates): 0.00332 PGS AUROC (no covariates): 0.55036 [0.52746, 0.57326] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM009289 | PGS001785 (1kgeur_gbmi_leaveUKBBout_AcApp_pst_eff_a1_b0.5_phiauto) |
PSS007708| European Ancestry| 359,031 individuals |
PGP000262 | Wang Y et al. Cell Genom (2023) |
Reported Trait: Acute appendicitis | — | AUROC: 0.584 | Nagelkerke's R2 (covariates regressed out): 0.00406 | sex,age,age2,age*sex,age^2*sex, 20PCs | — |
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 |
---|---|---|---|---|---|---|---|---|
PSS007708 | — | — | [
|
— | European | — | UKB | — |
PSS004099 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS004100 | — | — | [
|
— | East Asian | — | UKB | — |
PSS004101 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS004102 | — | — | [
|
— | South Asian | — | UKB | — |
PSS004103 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |