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 13 synonyms
  • Appendicitis
  • acute appendicitis
  • acute appendicitis
  • acute appendicitis with generalised peritonitis
  • acute appendicitis with generalized peritonitis
  • acute appendicitis with generalized peritonitis
  • acute appendicitis with generalized peritonitis (disorder)
  • acute appendicitis with peritoneal abscess
  • acute appendicitis with peritoneal abscess
  • acute appendicitis with peritoneal abscess (disorder)
  • appendicitis
  • inflammation of vermiform appendix
  • vermiform appendix inflammation
Mapped terms 15 mapped terms
  • DOID:8337
  • ICD10:K35
  • ICD10:K37
  • ICD9:540-543.99
  • ICD9:541
  • MEDGEN:1630
  • MESH:D001064
  • MONDO:0005649
  • MeSH:D001064
  • MedDRA:10003011
  • MedDRA:10003014
  • NCIT:C35145
  • SCTID:74400008
  • UMLS:C0003615
  • icd11.foundation:1881255733

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
GWAS
Dev
Eval
 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
PGS004876
(INTERVENE_MegaPRS_Appendicitis)
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Appendicitis appendicitis 601,835
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004876/ScoringFiles/PGS004876.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 —
PPM021188 PGS004876
(INTERVENE_MegaPRS_Appendicitis)
 PSS011551|
European Ancestry|
38,191 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Appendicitis HR: 1.04 [0.96, 1.14] C-index: 0.58 [0.55, 0.61] — PCs 1-10 —
PPM021189 PGS004876
(INTERVENE_MegaPRS_Appendicitis)
 PSS011550|
European Ancestry|
69,715 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Appendicitis HR: 1.07 [1.02, 1.12] C-index: 0.54 [0.53, 0.56] — PCs 1-10 —
PPM021190 PGS004876
(INTERVENE_MegaPRS_Appendicitis)
 PSS011549|
European Ancestry|
29,427 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Appendicitis HR: 1.1 [1.01, 1.19] C-index: 0.56 [0.53, 0.58] — PCs 1-10 —
PPM021191 PGS004876
(INTERVENE_MegaPRS_Appendicitis)
 PSS011547|
European Ancestry|
44,188 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Appendicitis HR: 1.06 [0.97, 1.16] — — PCs 1-10 —
PPM021192 PGS004876
(INTERVENE_MegaPRS_Appendicitis)
 PSS011548|
European Ancestry|
7,018 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Appendicitis HR: 1.1 [1.01, 1.2] C-index: 0.57 [0.54, 0.59] — PCs 1-10 —
PPM021193 PGS004876
(INTERVENE_MegaPRS_Appendicitis)
 PSS011546|
European Ancestry|
412,090 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Appendicitis HR: 1.07 [1.06, 1.08] C-index: 0.53 [0.52, 0.53] — PCs 1-10 —
PPM021194 PGS004876
(INTERVENE_MegaPRS_Appendicitis)
 PSS011545|
European Ancestry|
199,868 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Appendicitis HR: 1.05 [1.03, 1.07] C-index: 0.54 [0.53, 0.54] — PCs 1-10 —

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
PSS011549 — —
[
  • 586 cases
  • , 28,841 controls
]
 — European — GEL —
PSS011550 — —
[
  • 1,768 cases
  • , 67,947 controls
]
 — European — HUNT —
PSS011551 — —
[
  • 527 cases
  • , 37,664 controls
]
 — European — MGBB —
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)
PSS011545 — —
[
  • 13,442 cases
  • , 186,426 controls
]
 — European — EB —
PSS011546 — —
[
  • 31,397 cases
  • , 380,693 controls
]
 — European — FinnGen —
PSS011547 — —
[
  • 453 cases
  • , 43,735 controls
]
 — European — G&H —
PSS011548 — —
[
  • 519 cases
  • , 6,499 controls
]
 — European — GS:SFHS —