Polygenic Score (PGS) ID: PGS002101

Predicted Trait
Reported Trait Apolipoprotein A
Mapped Trait(s) apolipoprotein A 1 measurement (EFO_0004614)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_apoA
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 681,234
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
PPM011664 PSS009384|
European Ancestry|
17,339 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein A — — Partial Correlation (partial-r): 0.4018 [0.3893, 0.4143] sex, age, birth date, deprivation index, 16 PCs —
PPM011665 PSS009158|
European Ancestry|
3,563 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein A — — Partial Correlation (partial-r): 0.4015 [0.3735, 0.4288] sex, age, birth date, deprivation index, 16 PCs —
PPM011666 PSS008712|
European Ancestry|
5,765 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein A — — Partial Correlation (partial-r): 0.4118 [0.3901, 0.433] sex, age, birth date, deprivation index, 16 PCs —
PPM011667 PSS008486|
Greater Middle Eastern Ancestry|
1,033 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein A — — Partial Correlation (partial-r): 0.3567 [0.3017, 0.4093] sex, age, birth date, deprivation index, 16 PCs —
PPM011668 PSS008264|
South Asian Ancestry|
5,470 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein A — — Partial Correlation (partial-r): 0.3678 [0.3447, 0.3906] sex, age, birth date, deprivation index, 16 PCs —
PPM011670 PSS007828|
African Ancestry|
2,151 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein A — — Partial Correlation (partial-r): 0.2377 [0.1973, 0.2774] sex, age, birth date, deprivation index, 16 PCs —
PPM011671 PSS008932|
African Ancestry|
3,389 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein A — — Partial Correlation (partial-r): 0.2133 [0.1808, 0.2453] sex, age, birth date, deprivation index, 16 PCs —
PPM011669 PSS008042|
East Asian Ancestry|
1,543 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Apolipoprotein A — — Partial Correlation (partial-r): 0.353 [0.3082, 0.3962] 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
PSS008932 — — 3,389 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009158 — — 3,563 individuals — European Poland (NE Europe) UKB —
PSS008486 — — 1,033 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008264 — — 5,470 individuals — South Asian India (South Asia) UKB —
PSS009384 — — 17,339 individuals — European UK (+ Ireland) UKB —
PSS008712 — — 5,765 individuals — European Italy (South Europe) UKB —
PSS008042 — — 1,543 individuals — East Asian China (East Asia) UKB —
PSS007828 — — 2,151 individuals — African American or Afro-Caribbean Carribean UKB —