Polygenic Score (PGS) ID: PGS001954

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
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-PLR_log_HDL
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 85,429
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
PPM010507 PSS009432|
European Ancestry|
17,454 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: HDL cholesterol Partial Correlation (partial-r): 0.4605 [0.4488, 0.4721] sex, age, birth date, deprivation index, 16 PCs
PPM010508 PSS009206|
European Ancestry|
3,590 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: HDL cholesterol Partial Correlation (partial-r): 0.4525 [0.4261, 0.4782] sex, age, birth date, deprivation index, 16 PCs
PPM010509 PSS008760|
European Ancestry|
5,800 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: HDL cholesterol Partial Correlation (partial-r): 0.4564 [0.4357, 0.4765] sex, age, birth date, deprivation index, 16 PCs
PPM010510 PSS008534|
Greater Middle Eastern Ancestry|
1,034 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: HDL cholesterol Partial Correlation (partial-r): 0.4038 [0.351, 0.4541] sex, age, birth date, deprivation index, 16 PCs
PPM010511 PSS008312|
South Asian Ancestry|
5,476 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: HDL cholesterol Partial Correlation (partial-r): 0.409 [0.3867, 0.4309] sex, age, birth date, deprivation index, 16 PCs
PPM010513 PSS007876|
African Ancestry|
2,160 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: HDL cholesterol Partial Correlation (partial-r): 0.3126 [0.2739, 0.3504] sex, age, birth date, deprivation index, 16 PCs
PPM010514 PSS008980|
African Ancestry|
3,401 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: HDL cholesterol Partial Correlation (partial-r): 0.2509 [0.219, 0.2822] sex, age, birth date, deprivation index, 16 PCs
PPM010512 PSS008089|
East Asian Ancestry|
1,562 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: HDL cholesterol Partial Correlation (partial-r): 0.3656 [0.3215, 0.408] 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
PSS007876 2,160 individuals African American or Afro-Caribbean Carribean UKB
PSS008980 3,401 individuals African unspecified Nigeria (West Africa) UKB
PSS009206 3,590 individuals European Poland (NE Europe) UKB
PSS008534 1,034 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008760 5,800 individuals European Italy (South Europe) UKB
PSS008312 5,476 individuals South Asian India (South Asia) UKB
PSS009432 17,454 individuals European UK (+ Ireland) UKB
PSS008089 1,562 individuals East Asian China (East Asia) UKB