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: 33.3%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
Multi-ancestry (including European): 11.1%
  • European
  • Not Reported
South Asian: 11.1%
9 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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 —
PPM022464 PSS011950|
Multi-ancestry (including European)|
151 individuals
 PGP000716 |
Ying S et al. BMC Med Genomics (2023)
|Ext.		 Reported Trait: LDLC in 22q11.2 microdeletion carriers β: 0.2524 (0.0839) — — sex, age, BMI, T2D, Psychotic illness, Originating ascertainment cohort, Sequencing platform, PC1-4 —

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 —
PSS011950 Cohort of adults with a 22q11.2 microdeletion — 151 individuals,
50.0 % Male samples
 Median = 34.0 years European, Not reported — NR —
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 —