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
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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: 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
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 —
PPM022463 PSS011950|
Multi-ancestry (including European)|
151 individuals
 PGP000716 |
Ying S et al. BMC Med Genomics (2023)
|Ext.		 Reported Trait: HDLC in 22q11.2 microdeletion carriers β: 0.3818 (0.0667) — — 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
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 —
PSS011950 Cohort of adults with a 22q11.2 microdeletion — 151 individuals,
50.0 % Male samples
 Median = 34.0 years European, Not reported — NR —