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
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

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 —