Trait: appendicitis

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 10 synonyms
  • Appendicitis
  • acute appendicitis
  • acute appendicitis with generalised peritonitis
  • acute appendicitis with generalized peritonitis
  • acute appendicitis with generalized peritonitis (disorder)
  • acute appendicitis with peritoneal abscess
  • acute appendicitis with peritoneal abscess (disorder)
  • appendicitis
  • inflammation of vermiform appendix
  • vermiform appendix inflammation
Mapped terms 13 mapped terms
  • DOID:8337
  • ICD10:K35
  • ICD10:K37
  • ICD9:540-543.99
  • ICD9:541
  • MESH:D001064
  • MONDO:0005649
  • MeSH:D001064
  • MedDRA:10003011
  • MedDRA:10003014
  • NCIT:C35145
  • SCTID:74400008
  • UMLS:C0003615

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
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

Performance Metrics

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) 		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 —

Evaluated Samples

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 — —
[
  • 2,985 cases
  • , 356,045 controls
]
 — European — UKB —
PSS004099 — —
[
  • 35 cases
  • , 6,462 controls
]
 — African unspecified — UKB —
PSS004100 — —
[
  • 9 cases
  • , 1,695 controls
]
 — East Asian — UKB —
PSS004101 — —
[
  • 190 cases
  • , 24,715 controls
]
 — European non-white British ancestry UKB —
PSS004102 — —
[
  • 37 cases
  • , 7,794 controls
]
 — South Asian — UKB —
PSS004103 — —
[
  • 612 cases
  • , 66,813 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)