Trait: cholelithiasis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004799
Description The presence of calculi in the gallbladder. [NCIT: C122822]
Trait category
Digestive system disorder
Synonyms 3 synonyms
  • cholelithiasis
  • gallbladder disease type 4
  • gallstones
Mapped terms 13 mapped terms
  • DOID:10211
  • ICD10:K80
  • ICD9:574
  • ICD9:574.20
  • ICD9:574.5
  • MESH:D002769
  • MONDO:0012672
  • MeSH:D002769
  • MedDRA:10008629
  • NCIT:C122822
  • OMIM:611465
  • SCTID:266474003
  • UMLS:C0008350

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)
PGS001174
(GBE_HC1125)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Cholelithiasis (time-to-event) cholelithiasis 970
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001174/ScoringFiles/PGS001174.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
PPM008580 PGS001174
(GBE_HC1125)
PSS004139|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE cholelithiasis AUROC: 0.69202 [0.6517, 0.73234] : 0.05473
Incremental AUROC (full-covars): 0.01651
PGS R2 (no covariates): 0.00765
PGS AUROC (no covariates): 0.56963 [0.52438, 0.61487]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008581 PGS001174
(GBE_HC1125)
PSS004140|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE cholelithiasis AUROC: 0.69749 [0.6348, 0.76018] : 0.06838
Incremental AUROC (full-covars): 0.01442
PGS R2 (no covariates): 0.00347
PGS AUROC (no covariates): 0.557 [0.48585, 0.62815]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008582 PGS001174
(GBE_HC1125)
PSS004141|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE cholelithiasis AUROC: 0.66706 [0.6514, 0.68272] : 0.05295
Incremental AUROC (full-covars): 0.04311
PGS R2 (no covariates): 0.02808
PGS AUROC (no covariates): 0.62342 [0.60688, 0.63996]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008583 PGS001174
(GBE_HC1125)
PSS004142|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE cholelithiasis AUROC: 0.68516 [0.65563, 0.7147] : 0.05864
Incremental AUROC (full-covars): 0.01084
PGS R2 (no covariates): 0.00661
PGS AUROC (no covariates): 0.55746 [0.52498, 0.58993]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008584 PGS001174
(GBE_HC1125)
PSS004143|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE cholelithiasis AUROC: 0.67421 [0.66558, 0.68284] : 0.05848
Incremental AUROC (full-covars): 0.04052
PGS R2 (no covariates): 0.02571
PGS AUROC (no covariates): 0.61632 [0.60704, 0.62561]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004139
[
  • 158 cases
  • , 6,339 controls
]
African unspecified UKB
PSS004140
[
  • 65 cases
  • , 1,639 controls
]
East Asian UKB
PSS004141
[
  • 1,175 cases
  • , 23,730 controls
]
European non-white British ancestry UKB
PSS004142
[
  • 312 cases
  • , 7,519 controls
]
South Asian UKB
PSS004143
[
  • 3,753 cases
  • , 63,672 controls
]
European white British ancestry UKB Testing cohort (heldout set)