PGS Publication: PGP000313

Publication Information (EuropePMC)
Title Transferability of genetic risk scores in African populations.
PubMed ID 35654908(Europe PMC)
doi 10.1038/s41591-022-01835-x
Publication Date June 2, 2022
Journal Nat Med
Author(s) Kamiza AB, Toure SM, Vujkovic M, Machipisa T, Soremekun OS, Kintu C, Corpas M, Pirie F, Young E, Gill D, Sandhu MS, Kaleebu P, Nyirenda M, Motala AA, Chikowore T, Fatumo S.
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:
Display options:
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

PGS Developed 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)
PGS002286
(GRS_286_TC)
 PGP000313 |
Kamiza AB et al. Nat Med (2022)
 Total cholesterol total cholesterol measurement 286
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002286/ScoringFiles/PGS002286.txt.gz
PGS002285
(GRS_286_LDL)
 PGP000313 |
Kamiza AB et al. Nat Med (2022)
 LDL cholesterol low density lipoprotein cholesterol measurement 286
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002285/ScoringFiles/PGS002285.txt.gz
PGS002284
(GRS_286_HDL)
 PGP000313 |
Kamiza AB et al. Nat Med (2022)
 HDL cholesterol high density lipoprotein cholesterol measurement 286
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002284/ScoringFiles/PGS002284.txt.gz
PGS002287
(GRS_286_TG)
 PGP000313 |
Kamiza AB et al. Nat Med (2022)
 Triglyceride triglyceride measurement 286
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002287/ScoringFiles/PGS002287.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
PPM012983 PGS002285
(GRS_286_LDL)
 PSS009639|
African Ancestry|
2,569 individuals
 PGP000313 |
Kamiza AB et al. Nat Med (2022)
 Reported Trait: Low density lipoprotein cholesterol levels — — R²: 0.0814 age, sex, type 2 diabetes, PC1, PC2, PC3, PC4, PC5 Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment)
PPM012984 PGS002287
(GRS_286_TG)
 PSS009639|
African Ancestry|
2,569 individuals
 PGP000313 |
Kamiza AB et al. Nat Med (2022)
 Reported Trait: Triglyceride levels — — R²: 0.0087 age, sex, type 2 diabetes, PC1, PC2, PC3, PC4, PC5 Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment)
PPM012982 PGS002284
(GRS_286_HDL)
 PSS009639|
African Ancestry|
2,569 individuals
 PGP000313 |
Kamiza AB et al. Nat Med (2022)
 Reported Trait: High density lipoprotein cholesterol levels — — R²: 0.0213 age, sex, type 2 diabetes, PC1, PC2, PC3, PC4, PC5 Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment)
PPM012985 PGS002286
(GRS_286_TC)
 PSS009639|
African Ancestry|
2,569 individuals
 PGP000313 |
Kamiza AB et al. Nat Med (2022)
 Reported Trait: Total cholesterol levels — AUROC: 0.651 [0.631, 0.671] R²: 0.0693 age, sex, type 2 diabetes, PC1, PC2, PC3, PC4, PC5 Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment)

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
PSS009639 Non-fasting serum lipid levels were measured using the Cobas Integra 400 Plus Chemistry analyser, an automated analyser that employs four different technologies: absorption photometry, fluorescence polarization immunoassay, immune-turbidimetry, and potentiometry for accurate analysis. LDL-C were measured using the homogeneous enzymatic colorimetric assays — 2,569 individuals,
42.9 % Male samples
 Mean = 33.1 years
Ci = [18.0, 48.2] years		 Sub-Saharan African
(South Africans)		 — SAZ —