Polygenic Score (PGS) ID: PGS001861

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-PLR_574
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 2,059
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM009777 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 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 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 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 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 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 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 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

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
PSS009110 4,121 individuals European Poland (NE Europe) UKB
PSS008438 1,197 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) 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
PSS008887 3,912 individuals African unspecified Nigeria (West Africa) UKB
PSS007999 1,806 individuals East Asian China (East Asia) UKB