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 5 synonyms
  • GBD4
  • cholelithiasis
  • gallbladder disease 4
  • gallbladder disease type 4
  • gallstones
Mapped terms 15 mapped terms
  • DOID:10211
  • ICD10:K80
  • ICD9:574
  • ICD9:574.20
  • ICD9:574.5
  • MEDGEN:3039
  • MESH:D002769
  • MONDO:0012672
  • MeSH:D002769
  • MedDRA:10008629
  • NCIT:C122822
  • OMIM:611465
  • SCTID:266474003
  • UMLS:C0008350
  • icd11.foundation:1268183934

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)
PGS001174
(GBE_HC1125)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Cholelithiasis (time-to-event) cholelithiasis 970
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001174/ScoringFiles/PGS001174.txt.gz
PGS001861
(portability-PLR_574)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Cholelithiasis and cholecystitis cholelithiasis,
Cholecystitis		 2,059
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001861/ScoringFiles/PGS001861.txt.gz
PGS002072
(portability-ldpred2_574)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Cholelithiasis and cholecystitis cholelithiasis,
Cholecystitis		 428,587
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002072/ScoringFiles/PGS002072.txt.gz
PGS004476
(disease.K80.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 K80 (Cholelithiasis) cholelithiasis 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004476/ScoringFiles/PGS004476.txt.gz
PGS004546
(meta.K80.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 K80 (Cholelithiasis) cholelithiasis 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004546/ScoringFiles/PGS004546.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. PLoS Genet (2022)
 Reported Trait: TTE cholelithiasis — AUROC: 0.69202 [0.6517, 0.73234] R²: 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. PLoS Genet (2022)
 Reported Trait: TTE cholelithiasis — AUROC: 0.69749 [0.6348, 0.76018] R²: 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. PLoS Genet (2022)
 Reported Trait: TTE cholelithiasis — AUROC: 0.66706 [0.6514, 0.68272] R²: 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. PLoS Genet (2022)
 Reported Trait: TTE cholelithiasis — AUROC: 0.68516 [0.65563, 0.7147] R²: 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. PLoS Genet (2022)
 Reported Trait: TTE cholelithiasis — AUROC: 0.67421 [0.66558, 0.68284] R²: 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
PPM009777 PGS001861
(portability-PLR_574)
 PSS009336|
European Ancestry|
19,908 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0948 [0.081, 0.1085] sex, age, birth date, deprivation index, 16 PCs —
PPM009778 PGS001861
(portability-PLR_574)
 PSS009110|
European Ancestry|
4,121 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0809 [0.0504, 0.1112] sex, age, birth date, deprivation index, 16 PCs —
PPM009779 PGS001861
(portability-PLR_574)
 PSS008664|
European Ancestry|
6,631 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0769 [0.0529, 0.1008] sex, age, birth date, deprivation index, 16 PCs —
PPM009780 PGS001861
(portability-PLR_574)
 PSS008438|
Greater Middle Eastern Ancestry|
1,197 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0684 [0.0113, 0.1251] sex, age, birth date, deprivation index, 16 PCs —
PPM009781 PGS001861
(portability-PLR_574)
 PSS008218|
South Asian Ancestry|
6,310 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0422 [0.0175, 0.0668] sex, age, birth date, deprivation index, 16 PCs —
PPM009782 PGS001861
(portability-PLR_574)
 PSS007999|
East Asian Ancestry|
1,806 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.041 [-0.0054, 0.0872] sex, age, birth date, deprivation index, 16 PCs —
PPM009783 PGS001861
(portability-PLR_574)
 PSS007783|
African Ancestry|
2,477 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0362 [-0.0033, 0.0757] sex, age, birth date, deprivation index, 16 PCs —
PPM009784 PGS001861
(portability-PLR_574)
 PSS008887|
African Ancestry|
3,912 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0251 [-0.0063, 0.0565] sex, age, birth date, deprivation index, 16 PCs —
PPM011437 PGS002072
(portability-ldpred2_574)
 PSS009336|
European Ancestry|
19,908 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.098 [0.0842, 0.1117] sex, age, birth date, deprivation index, 16 PCs —
PPM011439 PGS002072
(portability-ldpred2_574)
 PSS008664|
European Ancestry|
6,631 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0805 [0.0565, 0.1044] sex, age, birth date, deprivation index, 16 PCs —
PPM011440 PGS002072
(portability-ldpred2_574)
 PSS008438|
Greater Middle Eastern Ancestry|
1,197 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0663 [0.0092, 0.123] sex, age, birth date, deprivation index, 16 PCs —
PPM011441 PGS002072
(portability-ldpred2_574)
 PSS008218|
South Asian Ancestry|
6,310 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0503 [0.0256, 0.0749] sex, age, birth date, deprivation index, 16 PCs —
PPM011442 PGS002072
(portability-ldpred2_574)
 PSS007999|
East Asian Ancestry|
1,806 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0441 [-0.0023, 0.0903] sex, age, birth date, deprivation index, 16 PCs —
PPM011443 PGS002072
(portability-ldpred2_574)
 PSS007783|
African Ancestry|
2,477 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0336 [-0.0059, 0.0731] sex, age, birth date, deprivation index, 16 PCs —
PPM011444 PGS002072
(portability-ldpred2_574)
 PSS008887|
African Ancestry|
3,912 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.033 [0.0016, 0.0643] sex, age, birth date, deprivation index, 16 PCs —
PPM011438 PGS002072
(portability-ldpred2_574)
 PSS009110|
European Ancestry|
4,121 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholelithiasis and cholecystitis — — Partial Correlation (partial-r): 0.0792 [0.0487, 0.1096] sex, age, birth date, deprivation index, 16 PCs —
PPM020591 PGS004476
(disease.K80.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: K80 (Cholelithiasis) OR: 1.21943 — — — —
PPM020661 PGS004546
(meta.K80.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: K80 (Cholelithiasis) OR: 1.29862 — — — —

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
PSS011364 — — 56,192 individuals — European — UKB —
PSS007783 — — 2,477 individuals — African American or Afro-Caribbean Carribean UKB —
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)
PSS009336 — — 19,908 individuals — European UK (+ Ireland) UKB —
PSS009110 — — 4,121 individuals — European Poland (NE Europe) UKB —
PSS008664 — — 6,631 individuals — European Italy (South Europe) UKB —
PSS008438 — — 1,197 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008218 — — 6,310 individuals — South Asian India (South Asia) UKB —
PSS008887 — — 3,912 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007999 — — 1,806 individuals — East Asian China (East Asia) UKB —