PGS Publication: PGP000330

Publication Information (EuropePMC)
Title LDL-C Concentrations and the 12-SNP LDL-C Score for Polygenic Hypercholesterolaemia in Self-Reported South Asian, Black and Caribbean Participants of the UK Biobank.
PubMed ID 35432461(Europe PMC)
doi 10.3389/fgene.2022.845498
Publication Date March 31, 2022
Journal Front Genet
Author(s) Gratton J, Finan C, Hingorani AD, Humphries SE, Futema M.
Released in PGS Catalog: June 9, 2022

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000814
(GRS12_LDLc)
 PGP000200 |
Talmud PJ et al. Lancet (2013)
 LDL cholesterol low density lipoprotein cholesterol measurement 16
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000814/ScoringFiles/PGS000814.txt.gz

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) 		Evaluated Score 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
PPM013054 PGS000814
(GRS12_LDLc)
 PSS009666|
South Asian Ancestry|
7,016 individuals
 PGP000330 |
Gratton J et al. Front Genet (2022)
|Ext.		 Reported Trait: LDL-C concentration — — R²: 0.049 [0.035, 0.063] Age, sex —
PPM013055 PGS000814
(GRS12_LDLc)
 PSS009668|
European Ancestry|
353,166 individuals
 PGP000330 |
Gratton J et al. Front Genet (2022)
|Ext.		 Reported Trait: LDL-C concentration >4.9 mmol/L OR: 11.01 [10.08, 12.04] — — — —
PPM013056 PGS000814
(GRS12_LDLc)
 PSS009667|
African Ancestry|
7,082 individuals
 PGP000330 |
Gratton J et al. Front Genet (2022)
|Ext.		 Reported Trait: LDL-C concentration >4.9 mmol/L OR: 10.54 [5.29, 21.67] — — — —
PPM013057 PGS000814
(GRS12_LDLc)
 PSS009666|
South Asian Ancestry|
7,016 individuals
 PGP000330 |
Gratton J et al. Front Genet (2022)
|Ext.		 Reported Trait: LDL-C concentration >4.9 mmol/L OR: 6.64 [2.98, 15.22] — — — —
PPM013058 PGS000814
(GRS12_LDLc)
 PSS009668|
European Ancestry|
353,166 individuals
 PGP000330 |
Gratton J et al. Front Genet (2022)
|Ext.		 Reported Trait: Coronary heart disease OR: 1.76 [1.56, 1.99] — — — —
PPM013059 PGS000814
(GRS12_LDLc)
 PSS009667|
African Ancestry|
7,082 individuals
 PGP000330 |
Gratton J et al. Front Genet (2022)
|Ext.		 Reported Trait: Coronary heart disease OR: 2.26 [0.78, 7.22] — — — —
PPM013060 PGS000814
(GRS12_LDLc)
 PSS009666|
South Asian Ancestry|
7,016 individuals
 PGP000330 |
Gratton J et al. Front Genet (2022)
|Ext.		 Reported Trait: Coronary heart disease OR: 1.24 [0.62, 2.53] — — — —
PPM013061 PGS000814
(GRS12_LDLc)
 PSS009668|
European Ancestry|
353,166 individuals
 PGP000330 |
Gratton J et al. Front Genet (2022)
|Ext.		 Reported Trait: Coronary heart disease OR: 1.25 [1.13, 1.39] — — — —
PPM013062 PGS000814
(GRS12_LDLc)
 PSS009667|
African Ancestry|
7,082 individuals
 PGP000330 |
Gratton J et al. Front Genet (2022)
|Ext.		 Reported Trait: Coronary heart disease OR: 1.09 [0.48, 2.58] — — — —
PPM013063 PGS000814
(GRS12_LDLc)
 PSS009666|
South Asian Ancestry|
7,016 individuals
 PGP000330 |
Gratton J et al. Front Genet (2022)
|Ext.		 Reported Trait: Coronary heart disease OR: 1.98 [0.95, 4.25] — — — —
PPM013052 PGS000814
(GRS12_LDLc)
 PSS009668|
European Ancestry|
353,166 individuals
 PGP000330 |
Gratton J et al. Front Genet (2022)
|Ext.		 Reported Trait: LDL-C concentration — — R²: 0.108 [0.105, 0.111] Age, sex —
PPM013053 PGS000814
(GRS12_LDLc)
 PSS009667|
African Ancestry|
7,082 individuals
 PGP000330 |
Gratton J et al. Front Genet (2022)
|Ext.		 Reported Trait: LDL-C concentration — — R²: 0.105 [0.086, 0.124] Age, sex —

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
PSS009666 — — 7,016 individuals,
54.3 % Male samples
 Median = 53.0 years
IQR = [46.0, 60.0] years		 South Asian — UKB —
PSS009667 — — 7,082 individuals,
43.3 % Male samples
 Median = 59.0 years
IQR = [45.0, 58.0] years		 African American or Afro-Caribbean Black/Caribbean UKB —
PSS009668 — — 353,166 individuals,
46.2 % Male samples
 Median = 58.0 years
IQR = [51.0, 63.0] years		 European White UKB —