Polygenic Score (PGS) ID: PGS001963

Predicted Trait
Reported Trait Lipoprotein A
Mapped Trait(s) lipoprotein A measurement (EFO_0006925)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_log_lipoA
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 7,887
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
PPM010579 PSS009452|
European Ancestry|
15,154 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lipoprotein A Partial Correlation (partial-r): 0.6002 [0.5899, 0.6103] sex, age, birth date, deprivation index, 16 PCs
PPM010580 PSS009226|
European Ancestry|
3,133 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lipoprotein A Partial Correlation (partial-r): 0.5621 [0.5376, 0.5856] sex, age, birth date, deprivation index, 16 PCs
PPM010581 PSS008780|
European Ancestry|
5,176 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lipoprotein A Partial Correlation (partial-r): 0.4772 [0.4558, 0.498] sex, age, birth date, deprivation index, 16 PCs
PPM010582 PSS008554|
Greater Middle Eastern Ancestry|
925 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lipoprotein A Partial Correlation (partial-r): 0.2941 [0.2334, 0.3525] sex, age, birth date, deprivation index, 16 PCs
PPM010583 PSS008332|
South Asian Ancestry|
5,230 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lipoprotein A Partial Correlation (partial-r): 0.3014 [0.2766, 0.3259] sex, age, birth date, deprivation index, 16 PCs
PPM010584 PSS008109|
East Asian Ancestry|
1,541 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lipoprotein A Partial Correlation (partial-r): 0.1975 [0.1487, 0.2453] sex, age, birth date, deprivation index, 16 PCs
PPM010585 PSS007896|
African Ancestry|
1,926 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lipoprotein A Partial Correlation (partial-r): 0.1097 [0.0651, 0.1539] sex, age, birth date, deprivation index, 16 PCs
PPM010586 PSS009000|
African Ancestry|
3,050 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lipoprotein A Partial Correlation (partial-r): 0.0348 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
PSS009000 3,050 individuals African unspecified Nigeria (West Africa) UKB
PSS008554 925 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009226 3,133 individuals European Poland (NE Europe) UKB
PSS009452 15,154 individuals European UK (+ Ireland) UKB
PSS008780 5,176 individuals European Italy (South Europe) UKB
PSS008332 5,230 individuals South Asian India (South Asia) UKB
PSS008109 1,541 individuals East Asian China (East Asia) UKB
PSS007896 1,926 individuals African American or Afro-Caribbean Carribean UKB