Trait: gallstones

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004210
Description Solid crystalline precipitates in the biliary tract, usually formed in the gallbladder, resulting in the condition of cholelithiasis. Gallstones, derived from the bile, consist mainly of calcium, cholesterol, or bilirubin. [MESH: D042882]
Trait category
Digestive system disorder
Synonyms 4 synonyms
  • Biliary Calculi
  • Gall Stone
  • Gall Stones
  • gallstones
Mapped term(s) 5 mapped terms
  • ICD9:574.20
  • MESH:D042882
  • MONDO:0005346
  • MeSH:D042882
  • SCTID:235919008

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution PGS Scoring File (FTP Link)
PGS000705
(HC188)
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Gallstones gallstones 183,458
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000705/ScoringFiles/PGS000705.txt.gz - Check Terms/Licenses

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
PPM001597 PGS000705
(HC188)
PSS000811|
European Ancestry|
87,413 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Gallstones AUROC: 0.62164 Age, sex, PCs(1-10)
PPM001613 PGS000705
(HC188)
PSS000812|
European Ancestry|
135,300 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Gallstones HR: 1.34 [1.32, 1.37] C-index: 0.605 Age as time scale, sex, batch, 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
PSS000811 87,413 individuals European UKB
PSS000812
[
  • 11,629 cases
  • , 123,671 controls
]
European
(Finnish)
FinnGen