Polygenic Score (PGS) ID: PGS001895

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-PLR_cholesterol
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 16,576
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM010043 PSS009391|
European Ancestry|
19,002 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cholesterol Partial Correlation (partial-r): 0.3271 [0.3143, 0.3397] sex, age, birth date, deprivation index, 16 PCs
PPM010044 PSS009165|
European Ancestry|
3,952 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cholesterol Partial Correlation (partial-r): 0.343 [0.3152, 0.3703] sex, age, birth date, deprivation index, 16 PCs
PPM010045 PSS008719|
European Ancestry|
6,326 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cholesterol Partial Correlation (partial-r): 0.3093 [0.2868, 0.3314] sex, age, birth date, deprivation index, 16 PCs
PPM010046 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): 0.2914 [0.2365, 0.3444] sex, age, birth date, deprivation index, 16 PCs
PPM010047 PSS008271|
South Asian Ancestry|
6,001 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cholesterol Partial Correlation (partial-r): 0.2092 [0.1848, 0.2333] sex, age, birth date, deprivation index, 16 PCs
PPM010048 PSS008048|
East Asian Ancestry|
1,717 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cholesterol Partial Correlation (partial-r): 0.2781 [0.2336, 0.3215] sex, age, birth date, deprivation index, 16 PCs
PPM010049 PSS007835|
African Ancestry|
2,343 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cholesterol Partial Correlation (partial-r): 0.2749 [0.2369, 0.3121] sex, age, birth date, deprivation index, 16 PCs
PPM010050 PSS008939|
African Ancestry|
3,656 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cholesterol Partial Correlation (partial-r): 0.203 [0.1716, 0.234] 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