Polygenic Score (PGS) ID: PGS002102

Predicted Trait
Reported Trait Apolipoprotein B
Mapped Trait(s) apolipoprotein B measurement (EFO_0004615)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_apoB
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 315,483
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
PPM011672 PSS009385|
European Ancestry|
18,910 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein B Partial Correlation (partial-r): 0.391 [0.3789, 0.4031] sex, age, birth date, deprivation index, 16 PCs
PPM011673 PSS009159|
European Ancestry|
3,935 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein B Partial Correlation (partial-r): 0.3949 [0.3682, 0.4211] sex, age, birth date, deprivation index, 16 PCs
PPM011674 PSS008713|
European Ancestry|
6,296 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein B Partial Correlation (partial-r): 0.3557 [0.3339, 0.3771] sex, age, birth date, deprivation index, 16 PCs
PPM011675 PSS008487|
Greater Middle Eastern Ancestry|
1,115 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein B Partial Correlation (partial-r): 0.3441 [0.2908, 0.3953] sex, age, birth date, deprivation index, 16 PCs
PPM011676 PSS008265|
South Asian Ancestry|
5,953 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein B Partial Correlation (partial-r): 0.2734 [0.2497, 0.2968] sex, age, birth date, deprivation index, 16 PCs
PPM011677 PSS008043|
East Asian Ancestry|
1,705 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein B Partial Correlation (partial-r): 0.3092 [0.2654, 0.3518] sex, age, birth date, deprivation index, 16 PCs
PPM011678 PSS007829|
African Ancestry|
2,325 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein B Partial Correlation (partial-r): 0.3289 [0.292, 0.3648] sex, age, birth date, deprivation index, 16 PCs
PPM011679 PSS008933|
African Ancestry|
3,626 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Apolipoprotein B Partial Correlation (partial-r): 0.2593 [0.2286, 0.2895] 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
PSS008933 3,626 individuals African unspecified Nigeria (West Africa) UKB
PSS008487 1,115 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009159 3,935 individuals European Poland (NE Europe) UKB
PSS008713 6,296 individuals European Italy (South Europe) UKB
PSS009385 18,910 individuals European UK (+ Ireland) UKB
PSS008265 5,953 individuals South Asian India (South Asia) UKB
PSS008043 1,705 individuals East Asian China (East Asia) UKB
PSS007829 2,325 individuals African American or Afro-Caribbean Carribean UKB