Polygenic Score (PGS) ID: PGS002072

Predicted Trait
Reported Trait Cholelithiasis and cholecystitis
Mapped Trait(s)
Additional Trait Information digestive
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_574
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 428,587
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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) 		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
PPM011437 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 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 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 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 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 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 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 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 —

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