Trait: disorder of appendix

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009542
Description A disease or disorder that involves the vermiform appendix. [MONDO: patterns/location]
Trait category
Digestive system disorder
Synonyms 9 synonyms
  • appendiceal disease
  • appendix disease
  • disease of appendix
  • disease of vermiform appendix
  • disease or disorder of vermiform appendix
  • disorder of appendix
  • disorder of vermiform appendix
  • vermiform appendix disease
  • vermiform appendix disease or disorder
Mapped terms 6 mapped terms
  • DOID:60000
  • ICD10:K38
  • ICD9:543.9
  • MONDO:0056798
  • SCTID:18526009
  • UMLS:C0267613
Child trait(s) appendicitis

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
Note: This table shows all PGS for "disorder of appendix" and any child terms of this trait in the EFO hierarchy by default.
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. medRxiv (2021)
|Pre
Acute appendicitis (time-to-event) appendicitis 4
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001369/ScoringFiles/PGS001369.txt.gz
PGS001853
(portability-PLR_540)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Appendiceal conditions disorder of appendix 19
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001853/ScoringFiles/PGS001853.txt.gz
PGS002064
(portability-ldpred2_540)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Appendiceal conditions disorder of appendix 497,422
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002064/ScoringFiles/PGS002064.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. medRxiv (2021)
|Pre
Reported Trait: TTE acute appendicitis AUROC: 0.62041 [0.53518, 0.70564] : 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. medRxiv (2021)
|Pre
Reported Trait: TTE acute appendicitis AUROC: 0.8493 [0.77779, 0.9208] : 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. medRxiv (2021)
|Pre
Reported Trait: TTE acute appendicitis AUROC: 0.56849 [0.52835, 0.60862] : 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. medRxiv (2021)
|Pre
Reported Trait: TTE acute appendicitis AUROC: 0.72977 [0.65912, 0.80042] : 0.05613
Incremental AUROC (full-covars): 0.00039
PGS R2 (no covariates): 0.00096
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. medRxiv (2021)
|Pre
Reported Trait: TTE acute appendicitis AUROC: 0.57413 [0.55138, 0.59688] : 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
PPM009715 PGS001853
(portability-PLR_540)
PSS009102|
European Ancestry|
4,136 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0345 [0.0039, 0.0649] sex, age, birth date, deprivation index, 16 PCs
PPM009716 PGS001853
(portability-PLR_540)
PSS008656|
European Ancestry|
6,660 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0198 [-0.0043, 0.0438] sex, age, birth date, deprivation index, 16 PCs
PPM009717 PGS001853
(portability-PLR_540)
PSS008430|
Greater Middle Eastern Ancestry|
1,200 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): -0.0243 [-0.0813, 0.0328] sex, age, birth date, deprivation index, 16 PCs
PPM009718 PGS001853
(portability-PLR_540)
PSS008210|
South Asian Ancestry|
6,331 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0024 [-0.0223, 0.0271] sex, age, birth date, deprivation index, 16 PCs
PPM009719 PGS001853
(portability-PLR_540)
PSS007992|
East Asian Ancestry|
1,810 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0008 [-0.0455, 0.0471] sex, age, birth date, deprivation index, 16 PCs
PPM009720 PGS001853
(portability-PLR_540)
PSS007775|
African Ancestry|
2,484 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): -0.0062 [-0.0457, 0.0333] sex, age, birth date, deprivation index, 16 PCs
PPM009721 PGS001853
(portability-PLR_540)
PSS008879|
African Ancestry|
3,924 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): -0.0204 [-0.0517, 0.011] sex, age, birth date, deprivation index, 16 PCs
PPM009714 PGS001853
(portability-PLR_540)
PSS009328|
European Ancestry|
20,000 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0242 [0.0104, 0.0381] sex, age, birth date, deprivation index, 16 PCs
PPM011374 PGS002064
(portability-ldpred2_540)
PSS009328|
European Ancestry|
20,000 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0149 [0.0011, 0.0288] sex, age, birth date, deprivation index, 16 PCs
PPM011375 PGS002064
(portability-ldpred2_540)
PSS009102|
European Ancestry|
4,136 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): -0.0011 [-0.0317, 0.0294] sex, age, birth date, deprivation index, 16 PCs
PPM011376 PGS002064
(portability-ldpred2_540)
PSS008656|
European Ancestry|
6,660 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0284 [0.0043, 0.0524] sex, age, birth date, deprivation index, 16 PCs
PPM011377 PGS002064
(portability-ldpred2_540)
PSS008430|
Greater Middle Eastern Ancestry|
1,200 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): -0.0502 [-0.1069, 0.0069] sex, age, birth date, deprivation index, 16 PCs
PPM011378 PGS002064
(portability-ldpred2_540)
PSS008210|
South Asian Ancestry|
6,331 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0161 [-0.0085, 0.0408] sex, age, birth date, deprivation index, 16 PCs
PPM011379 PGS002064
(portability-ldpred2_540)
PSS007992|
East Asian Ancestry|
1,810 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0333 [-0.0131, 0.0795] sex, age, birth date, deprivation index, 16 PCs
PPM011380 PGS002064
(portability-ldpred2_540)
PSS007775|
African Ancestry|
2,484 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): -0.0115 [-0.051, 0.028] sex, age, birth date, deprivation index, 16 PCs
PPM011381 PGS002064
(portability-ldpred2_540)
PSS008879|
African Ancestry|
3,924 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0213 [-0.0101, 0.0526] sex, age, birth date, deprivation index, 16 PCs

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
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)
PSS009102 4,136 individuals European Poland (NE Europe) UKB
PSS008656 6,660 individuals European Italy (South Europe) UKB
PSS008430 1,200 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008210 6,331 individuals South Asian India (South Asia) UKB
PSS008879 3,924 individuals African unspecified Nigeria (West Africa) UKB
PSS009328 20,000 individuals European UK (+ Ireland) UKB
PSS007992 1,810 individuals East Asian China (East Asia) UKB
PSS007775 2,484 individuals African American or Afro-Caribbean Carribean UKB