Polygenic Score (PGS) ID: PGS002073

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-ldpred2_575
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 363,801
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
PPM011445 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): 0.0215 [0.0074, 0.0356] sex, age, birth date, deprivation index, 16 PCs —
PPM011446 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): 0.0453 [0.0142, 0.0762] sex, age, birth date, deprivation index, 16 PCs —
PPM011447 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): -0.0067 [-0.0311, 0.0178] sex, age, birth date, deprivation index, 16 PCs —
PPM011448 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): -0.0075 [-0.0653, 0.0503] sex, age, birth date, deprivation index, 16 PCs —
PPM011449 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): 0.029 [0.004, 0.054] sex, age, birth date, deprivation index, 16 PCs —
PPM011450 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): 0.053 [0.0062, 0.0995] sex, age, birth date, deprivation index, 16 PCs —
PPM011452 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): 0.0035 [-0.0281, 0.0352] sex, age, birth date, deprivation index, 16 PCs —
PPM011451 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): 0.0039 [-0.036, 0.0438] 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 —