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 terms 8 mapped terms
  • ICD9:574.20
  • MEDGEN:66850
  • MESH:D042882
  • MONDO:0005346
  • MeSH:D042882
  • MedDRA:10017650
  • SCTID:235919008
  • UMLS:C0242216

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)
PGS000705
(HC188)
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Gallstones gallstones 183,458
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000705/ScoringFiles/PGS000705.txt.gz - Check Terms/Licenses
PGS001256
(GBE_HC188)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Gallstones gallstones 876
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001256/ScoringFiles/PGS001256.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
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) —
PPM008785 PGS001256
(GBE_HC188)
 PSS004334|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Gallstones — AUROC: 0.68692 [0.64329, 0.73056] R²: 0.04974
Incremental AUROC (full-covars): 0.02029
PGS R2 (no covariates): 0.00785
PGS AUROC (no covariates): 0.56814 [0.51821, 0.61807]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008786 PGS001256
(GBE_HC188)
 PSS004335|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Gallstones — AUROC: 0.67793 [0.60585, 0.75001] R²: 0.06195
Incremental AUROC (full-covars): 0.00834
PGS R2 (no covariates): 0.00064
PGS AUROC (no covariates): 0.52583 [0.44852, 0.60314]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008787 PGS001256
(GBE_HC188)
 PSS004336|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Gallstones — AUROC: 0.66809 [0.65163, 0.68454] R²: 0.05165
Incremental AUROC (full-covars): 0.04397
PGS R2 (no covariates): 0.0275
PGS AUROC (no covariates): 0.62496 [0.60759, 0.64234]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008788 PGS001256
(GBE_HC188)
 PSS004337|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Gallstones — AUROC: 0.68743 [0.65645, 0.71841] R²: 0.0581
Incremental AUROC (full-covars): 0.01295
PGS R2 (no covariates): 0.00775
PGS AUROC (no covariates): 0.56733 [0.53369, 0.60096]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008789 PGS001256
(GBE_HC188)
 PSS004338|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Gallstones — AUROC: 0.67227 [0.66315, 0.68138] R²: 0.05484
Incremental AUROC (full-covars): 0.04156
PGS R2 (no covariates): 0.02494
PGS AUROC (no covariates): 0.6171 [0.6073, 0.6269]		 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
PSS000811 — — 87,413 individuals — European — UKB —
PSS000812 — —
[
  • 11,629 cases
  • , 123,671 controls
]
 — European
(Finnish)		 — FinnGen —
PSS004334 — —
[
  • 136 cases
  • , 6,361 controls
]
 — African unspecified — UKB —
PSS004335 — —
[
  • 55 cases
  • , 1,649 controls
]
 — East Asian — UKB —
PSS004336 — —
[
  • 1,055 cases
  • , 23,850 controls
]
 — European non-white British ancestry UKB —
PSS004337 — —
[
  • 278 cases
  • , 7,553 controls
]
 — South Asian — UKB —
PSS004338 — —
[
  • 3,344 cases
  • , 64,081 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)