Polygenic Score (PGS) ID: PGS001933

Predicted Trait
Reported Trait LDL direct
Mapped Trait(s) low density lipoprotein cholesterol measurement (EFO_0004611)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_LDL
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 25,604
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
PPM010339 PSS009376|
European Ancestry|
18,968 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: LDL direct Partial Correlation (partial-r): 0.3331 [0.3204, 0.3457] sex, age, birth date, deprivation index, 16 PCs
PPM010340 PSS009150|
European Ancestry|
3,946 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: LDL direct Partial Correlation (partial-r): 0.3496 [0.3219, 0.3768] sex, age, birth date, deprivation index, 16 PCs
PPM010341 PSS008704|
European Ancestry|
6,312 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: LDL direct Partial Correlation (partial-r): 0.3177 [0.2953, 0.3397] sex, age, birth date, deprivation index, 16 PCs
PPM010342 PSS008478|
Greater Middle Eastern Ancestry|
1,122 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: LDL direct Partial Correlation (partial-r): 0.297 [0.2422, 0.3499] sex, age, birth date, deprivation index, 16 PCs
PPM010343 PSS008256|
South Asian Ancestry|
5,987 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: LDL direct Partial Correlation (partial-r): 0.2086 [0.1842, 0.2327] sex, age, birth date, deprivation index, 16 PCs
PPM010344 PSS008034|
East Asian Ancestry|
1,716 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: LDL direct Partial Correlation (partial-r): 0.2593 [0.2144, 0.3032] sex, age, birth date, deprivation index, 16 PCs
PPM010345 PSS007820|
African Ancestry|
2,338 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: LDL direct Partial Correlation (partial-r): 0.2864 [0.2486, 0.3234] sex, age, birth date, deprivation index, 16 PCs
PPM010346 PSS008924|
African Ancestry|
3,651 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: LDL direct Partial Correlation (partial-r): 0.2203 [0.1891, 0.251] 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
PSS007820 2,338 individuals African American or Afro-Caribbean Carribean UKB
PSS008478 1,122 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009376 18,968 individuals European UK (+ Ireland) UKB
PSS008034 1,716 individuals East Asian China (East Asia) UKB
PSS008924 3,651 individuals African unspecified Nigeria (West Africa) UKB
PSS009150 3,946 individuals European Poland (NE Europe) UKB
PSS008256 5,987 individuals South Asian India (South Asia) UKB
PSS008704 6,312 individuals European Italy (South Europe) UKB