PGS Publication: PGP000046

Publication Information (EuropePMC)
Title The transferability of lipid loci across African, Asian and European cohorts.
PubMed ID 31551420(Europe PMC)
doi 10.1038/s41467-019-12026-7
Publication Date Sept. 24, 2019
Journal Nat Commun
Author(s) Kuchenbaecker K, Telkar N, Reiker T, Walters RG, Lin K, Eriksson A, Gurdasani D, Gilly A, Southam L, Tsafantakis E, Karaleftheri M, Seeley J, Kamali A, Asiki G, Millwood IY, Holmes M, Du H, Guo Y, Kumari M, Dedoussis G, Li L, Chen Z, Sandhu MS, Zeggini E, Understanding Society Scientific Group.
Released in PGS: Feb. 12, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000064 GLGC2017_HDL PGP000046 Kuchenbaecker K et al. Nat Commun (2019) High density lipoprotein (HDL) cholesterol high density lipoprotein cholesterol measurement 120 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000064/ScoringFiles/PGS000064.txt.gz
PGS000065 GLGC2017_LDL PGP000046 Kuchenbaecker K et al. Nat Commun (2019) Low density lipoprotein (HDL) cholesterol low density lipoprotein cholesterol measurement 103 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000065/ScoringFiles/PGS000065.txt.gz
PGS000066 GLGC2017_TG PGP000046 Kuchenbaecker K et al. Nat Commun (2019) Triglycerides (TG) triglyceride measurement 101 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000066/ScoringFiles/PGS000066.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000167 PGS000064 (GLGC2017_HDL) PSS000104 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum high-density lipoprotein (HDL) levels correlation (r): 0.285[0.265, 0.305] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000168 PGS000065 (GLGC2017_LDL) PSS000104 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum low-density lipoprotein (LDL) levels correlation (r): 0.274[0.254, 0.294] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000169 PGS000066 (GLGC2017_TG) PSS000104 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum triglyceride (TG) levels correlation (r): 0.204[0.183, 0.223] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000170 PGS000064 (GLGC2017_HDL) PSS000102 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum high-density lipoprotein (HDL) levels correlation (r): 0.279[0.222, 0.336] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000171 PGS000065 (GLGC2017_LDL) PSS000102 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum low-density lipoprotein (LDL) levels correlation (r): 0.229[0.172, 0.286] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000172 PGS000066 (GLGC2017_TG) PSS000102 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum triglyceride (TG) levels correlation (r): 0.235[0.176, 0.294] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000173 PGS000064 (GLGC2017_HDL) PSS000103 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum high-density lipoprotein (HDL) levels correlation (r): 0.268[0.209, 0.327] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000174 PGS000065 (GLGC2017_LDL) PSS000103 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum low-density lipoprotein (LDL) levels correlation (r): 0.29[0.231, 0.349] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000175 PGS000066 (GLGC2017_TG) PSS000103 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum triglyceride (TG) levels correlation (r): 0.234[0.175, 0.293] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000176 PGS000064 (GLGC2017_HDL) PSS000100 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum high-density lipoprotein (HDL) levels correlation (r): 0.121[0.098, 0.145] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000177 PGS000065 (GLGC2017_LDL) PSS000100 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum low-density lipoprotein (LDL) levels correlation (r): 0.28[0.257, 0.304] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000178 PGS000066 (GLGC2017_TG) PSS000100 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum triglyceride (TG) levels correlation (r): 0.063[0.038, 0.089] age, sex Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000179 PGS000064 (GLGC2017_HDL) PSS000101 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum high-density lipoprotein (HDL) levels correlation (r): 0.18[0.145, 0.215] age, sex, region, 20 PCs of genetic ancestry Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000180 PGS000065 (GLGC2017_LDL) PSS000101 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum low-density lipoprotein (LDL) levels correlation (r): 0.198[0.161, 0.235] age, sex, region, 20 PCs of genetic ancestry Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA
PPM000181 PGS000066 (GLGC2017_TG) PSS000101 PGP000046
Kuchenbaecker K et al. (2019)
Reported Trait: Serum triglyceride (TG) levels correlation (r): 0.139[0.1, 0.178] age, sex, region, 20 PCs of genetic ancestry Relatedness and population structure were accounted for using a linear mixed model with random polygenic effect implemented in GEMMA

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000100 Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) 6,407 individuals,
44.0 % Male samples
Mean = 34.0 years Sub-Saharan African APCDR APCDR-Uganda study
PSS000101 Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) 21,295 individuals,
38.0 % Male samples
Mean = 60.0 years East Asian
(Chinese)
CKB - 20810 samples had HDL measurements - 17662 samples had LDL measurements - 20222 samples had triglyceride measurements
PSS000102 Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) 1,641 individuals,
58.0 % Male samples
Mean = 62.0 years European
(Greek)
Population isolate from the Pomak villages in the North of Greece HELIC - 1186 samples had HDL measurements - 1186 samples had LDL measurements - 1176 samples had triglyceride measurements
PSS000103 Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) 1,945 individuals,
66.0 % Male samples
Mean = 45.0 years European
(Greek)
Population isolate from the Mylopotamos villages in Crete HELIC - 1078 samples had HDL measurements - 1075 samples had LDL measurements - 1066 samples had triglyceride measurements
PSS000104 Serum levels of high-density lipoprotein (HDL), low-density lipoprotein (LDL) cholesterol and triglycerides (TG) 9,962 individuals,
56.0 % Male samples
Mean = 52.0 years European UKHLS - 9706 samples had HDL measurements - 9767 samples had LDL measurements - 9635 samples had triglyceride measurements