Polygenic Score (PGS) ID: PGS002029

Predicted Trait
Reported Trait Disorders of lipoid metabolism
Mapped Trait(s) Abnormal circulating lipid concentration (HP_0003119)
Additional Trait Information endocrine/metabolic
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_272
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 764,390
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
PPM011106 PSS009291|
European Ancestry|
20,000 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0996 [0.0858, 0.1133] sex, age, birth date, deprivation index, 16 PCs
PPM011108 PSS008619|
European Ancestry|
6,660 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0952 [0.0713, 0.119] sex, age, birth date, deprivation index, 16 PCs
PPM011109 PSS008395|
Greater Middle Eastern Ancestry|
1,200 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0977 [0.0409, 0.1539] sex, age, birth date, deprivation index, 16 PCs
PPM011110 PSS008173|
South Asian Ancestry|
6,331 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0926 [0.0681, 0.117] sex, age, birth date, deprivation index, 16 PCs
PPM011111 PSS007960|
East Asian Ancestry|
1,810 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0539 [0.0075, 0.0999] sex, age, birth date, deprivation index, 16 PCs
PPM011113 PSS008844|
African Ancestry|
3,924 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.05 [0.0186, 0.0812] sex, age, birth date, deprivation index, 16 PCs
PPM011107 PSS009065|
European Ancestry|
4,136 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.1035 [0.0732, 0.1337] sex, age, birth date, deprivation index, 16 PCs
PPM011112 PSS007741|
African Ancestry|
2,484 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Disorders of lipoid metabolism Partial Correlation (partial-r): 0.0769 [0.0375, 0.116] 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
PSS009065 4,136 individuals European Poland (NE Europe) UKB
PSS008619 6,660 individuals European Italy (South Europe) UKB
PSS008395 1,200 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008173 6,331 individuals South Asian India (South Asia) UKB
PSS009291 20,000 individuals European UK (+ Ireland) UKB
PSS008844 3,924 individuals African unspecified Nigeria (West Africa) UKB
PSS007960 1,810 individuals East Asian China (East Asia) UKB
PSS007741 2,484 individuals African American or Afro-Caribbean Carribean UKB