Polygenic Score (PGS) ID: PGS001862

Predicted Trait
Reported Trait Other biliary tract disease
Mapped Trait(s) biliary tract disease (EFO_0009534)
Additional Trait Information digestive
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_575
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 151
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
PPM009785 PSS009337|
European Ancestry|
19,288 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other biliary tract disease Partial Correlation (partial-r): 0.0221 [0.008, 0.0362] sex, age, birth date, deprivation index, 16 PCs
PPM009786 PSS009111|
European Ancestry|
3,998 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other biliary tract disease Partial Correlation (partial-r): 0.0485 [0.0174, 0.0795] sex, age, birth date, deprivation index, 16 PCs
PPM009787 PSS008665|
European Ancestry|
6,436 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other biliary tract disease Partial Correlation (partial-r): -0.0029 [-0.0274, 0.0215] sex, age, birth date, deprivation index, 16 PCs
PPM009788 PSS008439|
Greater Middle Eastern Ancestry|
1,170 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other biliary tract disease Partial Correlation (partial-r): 0.0133 [-0.0445, 0.0711] sex, age, birth date, deprivation index, 16 PCs
PPM009789 PSS008219|
South Asian Ancestry|
6,142 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other biliary tract disease Partial Correlation (partial-r): 0.0217 [-0.0033, 0.0468] sex, age, birth date, deprivation index, 16 PCs
PPM009790 PSS008000|
East Asian Ancestry|
1,775 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other biliary tract disease Partial Correlation (partial-r): 0.03 [-0.0168, 0.0767] sex, age, birth date, deprivation index, 16 PCs
PPM009792 PSS008888|
African Ancestry|
3,852 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other biliary tract disease Partial Correlation (partial-r): -0.0004 [-0.0321, 0.0312] sex, age, birth date, deprivation index, 16 PCs
PPM009791 PSS007784|
African Ancestry|
2,432 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Other biliary tract disease Partial Correlation (partial-r): 0.0111 [-0.0288, 0.051] 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
PSS007784 2,432 individuals African American or Afro-Caribbean Carribean UKB
PSS008439 1,170 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009111 3,998 individuals European Poland (NE Europe) UKB
PSS008665 6,436 individuals European Italy (South Europe) UKB
PSS009337 19,288 individuals European UK (+ Ireland) UKB
PSS008219 6,142 individuals South Asian India (South Asia) UKB
PSS008888 3,852 individuals African unspecified Nigeria (West Africa) UKB
PSS008000 1,775 individuals East Asian China (East Asia) UKB