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 Catalog: Feb. 12, 2020

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)
PGS000066
(GLGC2017_TG)
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (2019)
 Triglycerides (TG) triglyceride measurement 101
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000066/ScoringFiles/PGS000066.txt.gz
PGS000064
(GLGC2017_HDL)
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (2019)
 HDL cholesterol high density lipoprotein cholesterol measurement 120
-
 https://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)
 LDL cholesterol low density lipoprotein cholesterol measurement 103
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000065/ScoringFiles/PGS000065.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
PPM000167 PGS000064
(GLGC2017_HDL)
 PSS000104|
European Ancestry|
9,962 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
European Ancestry|
9,962 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
European Ancestry|
9,962 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
European Ancestry|
1,641 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
European Ancestry|
1,641 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
European Ancestry|
1,641 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
European Ancestry|
1,945 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
European Ancestry|
1,945 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
European Ancestry|
1,945 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
African Ancestry|
6,407 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
African Ancestry|
6,407 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
African Ancestry|
6,407 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
East Asian Ancestry|
21,295 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
East Asian Ancestry|
21,295 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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|
East Asian Ancestry|
21,295 individuals
 PGP000046 |
Kuchenbaecker K et al. Nat Commun (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) 		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