Polygenic Score (PGS) ID: PGS002108

Predicted Trait
Reported Trait Cholesterol
Mapped Trait(s) total cholesterol measurement (EFO_0004574)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_cholesterol
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 451,160
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
PPM011719 PSS009391|
European Ancestry|
19,002 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholesterol — — Partial Correlation (partial-r): 0.3292 [0.3165, 0.3418] sex, age, birth date, deprivation index, 16 PCs —
PPM011720 PSS009165|
European Ancestry|
3,952 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholesterol — — Partial Correlation (partial-r): 0.3416 [0.3137, 0.3689] sex, age, birth date, deprivation index, 16 PCs —
PPM011721 PSS008719|
European Ancestry|
6,326 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholesterol — — Partial Correlation (partial-r): 0.3064 [0.2839, 0.3286] sex, age, birth date, deprivation index, 16 PCs —
PPM011722 PSS008493|
Greater Middle Eastern Ancestry|
1,126 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholesterol — — Partial Correlation (partial-r): 0.2983 [0.2437, 0.3511] sex, age, birth date, deprivation index, 16 PCs —
PPM011723 PSS008271|
South Asian Ancestry|
6,001 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholesterol — — Partial Correlation (partial-r): 0.215 [0.1907, 0.239] sex, age, birth date, deprivation index, 16 PCs —
PPM011724 PSS008048|
East Asian Ancestry|
1,717 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholesterol — — Partial Correlation (partial-r): 0.2733 [0.2287, 0.3168] sex, age, birth date, deprivation index, 16 PCs —
PPM011725 PSS007835|
African Ancestry|
2,343 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholesterol — — Partial Correlation (partial-r): 0.266 [0.2278, 0.3034] sex, age, birth date, deprivation index, 16 PCs —
PPM011726 PSS008939|
African Ancestry|
3,656 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cholesterol — — Partial Correlation (partial-r): 0.1947 [0.1632, 0.2258] 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
PSS008939 — — 3,656 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008493 — — 1,126 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009165 — — 3,952 individuals — European Poland (NE Europe) UKB —
PSS008719 — — 6,326 individuals — European Italy (South Europe) UKB —
PSS009391 — — 19,002 individuals — European UK (+ Ireland) UKB —
PSS008271 — — 6,001 individuals — South Asian India (South Asia) UKB —
PSS008048 — — 1,717 individuals — East Asian China (East Asia) UKB —
PSS007835 — — 2,343 individuals — African American or Afro-Caribbean Carribean UKB —