Experimental Factor Ontology (EFO) Information | |
Identifier | EFO_0009959 |
Description | A complex disorder characterised by mucosal outpouchings (diverticulae) of the colonic wall which can become infected and inflamed leading to diverticulitis, perforation and bleeding. | Trait category |
Digestive system disorder
|
Mapped term | MedDRA:10013534 |
Child trait(s) | 2 child traits |
Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | Ancestry distribution | Scoring File (FTP Link) |
---|---|---|---|---|---|---|
PGS000996 (GBE_HC262) |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Diverticular disease/diverticulitis | diverticular disease, diverticulitis |
368 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000996/ScoringFiles/PGS000996.txt.gz |
PGS000996 (GBE_HC262) |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Diverticular disease/diverticulitis | diverticular disease, diverticulitis |
368 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000996/ScoringFiles/PGS000996.txt.gz |
PGS000997 (GBE_HC1106) |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Diverticular disease of intestine (time-to-event) | diverticular disease | 5,757 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000997/ScoringFiles/PGS000997.txt.gz |
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 |
---|---|---|---|---|---|---|---|---|---|
PPM007743 | PGS000996 (GBE_HC262) |
PSS004389| African Ancestry| 6,497 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Diverticular disease/diverticulitis | — | AUROC: 0.86271 [0.73099, 0.99443] | R²: 0.12936 Incremental AUROC (full-covars): 0.00213 PGS R2 (no covariates): 0.00894 PGS AUROC (no covariates): 0.62053 [0.46342, 0.77764] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007744 | PGS000996 (GBE_HC262) |
PSS004390| East Asian Ancestry| 1,704 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Diverticular disease/diverticulitis | — | AUROC: 0.91481 [0.74874, 1.0] | R²: 0.2785 Incremental AUROC (full-covars): 0.00029 PGS R2 (no covariates): 0.03618 PGS AUROC (no covariates): 0.74736 [0.4992, 0.99551] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007745 | PGS000996 (GBE_HC262) |
PSS004391| European Ancestry| 24,905 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Diverticular disease/diverticulitis | — | AUROC: 0.70041 [0.67086, 0.72996] | R²: 0.04948 Incremental AUROC (full-covars): 0.0039 PGS R2 (no covariates): 0.00095 PGS AUROC (no covariates): 0.52419 [0.48988, 0.55849] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007746 | PGS000996 (GBE_HC262) |
PSS004392| South Asian Ancestry| 7,831 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Diverticular disease/diverticulitis | — | AUROC: 0.80455 [0.70545, 0.90364] | R²: 0.1 Incremental AUROC (full-covars): 0.00844 PGS R2 (no covariates): 0.00928 PGS AUROC (no covariates): 0.62862 [0.53202, 0.72522] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007747 | PGS000996 (GBE_HC262) |
PSS004393| European Ancestry| 67,425 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Diverticular disease/diverticulitis | — | AUROC: 0.67555 [0.65884, 0.69227] | R²: 0.03898 Incremental AUROC (full-covars): 0.00841 PGS R2 (no covariates): 0.00372 PGS AUROC (no covariates): 0.55186 [0.53326, 0.57047] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007748 | PGS000997 (GBE_HC1106) |
PSS004124| African Ancestry| 6,497 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE diverticular disease of intestine | — | AUROC: 0.70831 [0.67789, 0.73873] | R²: 0.07998 Incremental AUROC (full-covars): -0.0081 PGS R2 (no covariates): 0.00158 PGS AUROC (no covariates): 0.52939 [0.49423, 0.56454] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007749 | PGS000997 (GBE_HC1106) |
PSS004125| East Asian Ancestry| 1,704 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE diverticular disease of intestine | — | AUROC: 0.75551 [0.65982, 0.85119] | R²: 0.08781 Incremental AUROC (full-covars): -0.01168 PGS R2 (no covariates): 0.00059 PGS AUROC (no covariates): 0.52785 [0.41459, 0.64111] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007750 | PGS000997 (GBE_HC1106) |
PSS004126| European Ancestry| 24,905 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE diverticular disease of intestine | — | AUROC: 0.7155 [0.70514, 0.72586] | R²: 0.10502 Incremental AUROC (full-covars): 0.01733 PGS R2 (no covariates): 0.01777 PGS AUROC (no covariates): 0.59105 [0.57889, 0.60321] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007751 | PGS000997 (GBE_HC1106) |
PSS004127| South Asian Ancestry| 7,831 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE diverticular disease of intestine | — | AUROC: 0.73365 [0.70818, 0.75911] | R²: 0.09377 Incremental AUROC (full-covars): 0.01275 PGS R2 (no covariates): 0.01222 PGS AUROC (no covariates): 0.57957 [0.54784, 0.6113] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM007752 | PGS000997 (GBE_HC1106) |
PSS004128| European Ancestry| 67,425 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: TTE diverticular disease of intestine | — | AUROC: 0.68053 [0.67412, 0.68694] | R²: 0.07483 Incremental AUROC (full-covars): 0.01974 PGS R2 (no covariates): 0.01533 PGS AUROC (no covariates): 0.5794 [0.57219, 0.58662] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
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 |
---|---|---|---|---|---|---|---|---|
PSS004124 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS004125 | — | — | [
|
— | East Asian | — | UKB | — |
PSS004126 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS004127 | — | — | [
|
— | South Asian | — | UKB | — |
PSS004128 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |
PSS007708 | — | — | [
|
— | European | — | UKB | — |
PSS004099 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS004100 | — | — | [
|
— | East Asian | — | UKB | — |
PSS004389 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS004390 | — | — | [
|
— | East Asian | — | UKB | — |
PSS004391 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS004392 | — | — | [
|
— | South Asian | — | UKB | — |
PSS004393 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |
PSS004101 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS004102 | — | — | [
|
— | South Asian | — | UKB | — |
PSS004103 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |