PGS Publication: PGP000045

Publication Information (EuropePMC)
Title An Examination of the Relationship between Lipid Levels and Associated Genetic Markers across Racial/Ethnic Populations in the Multi-Ethnic Study of Atherosclerosis.
PubMed ID 25951326(Europe PMC)
doi 10.1371/journal.pone.0126361
Publication Date May 7, 2015
Journal PLoS One
Author(s) Johnson L, Zhu J, Scott ER, Wineinger NE.
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)
PGS000061
(GRS_LDL)
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Low-density lipoprotein (LDL) cholesterol low density lipoprotein cholesterol measurement 37
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000061/ScoringFiles/PGS000061.txt.gz
PGS000060
(GRS_HDL)
 PGP000045 |
Johnson L et al. PLoS One (2015)
 HDL cholesterol high density lipoprotein cholesterol measurement 46
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000060/ScoringFiles/PGS000060.txt.gz
PGS000062
(GRS_TC)
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Total cholesterol total cholesterol measurement 52
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000062/ScoringFiles/PGS000062.txt.gz
PGS000063
(GRS_TG)
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Triglycerides triglyceride measurement 32
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000063/ScoringFiles/PGS000063.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
PPM000151 PGS000060
(GRS_HDL)
 PSS000098|
European Ancestry|
2,063 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum high-density lipoprotein (HDL) levels β: 8.39 — Beta (p-value): 2.76e-06 age, age^2, sex, GRS_LDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000152 PGS000060
(GRS_HDL)
 PSS000097|
East Asian Ancestry|
666 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum high-density lipoprotein (HDL) levels β: 15.58 — Beta (p-value): 2.17e-07 age, age^2, sex, GRS_LDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000153 PGS000060
(GRS_HDL)
 PSS000096|
African Ancestry|
1,355 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum high-density lipoprotein (HDL) levels β: 7.99 — Beta (p-value): 0.00036 age, age^2, sex, GRS_LDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000154 PGS000060
(GRS_HDL)
 PSS000099|
Hispanic or Latin American Ancestry|
1,256 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum high-density lipoprotein (HDL) levels β: 10.97 — Beta (p-value): 6.48e-10 age, age^2, sex, GRS_LDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000155 PGS000061
(GRS_LDL)
 PSS000098|
European Ancestry|
2,063 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum low-density lipoprotein (LDL) levels β: 15.0 — Beta (p-value): 0.0352 age, age^2, sex, GRS_HDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000156 PGS000061
(GRS_LDL)
 PSS000097|
East Asian Ancestry|
666 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum low-density lipoprotein (LDL) levels β: 5.58 — Beta (p-value): 0.697 age, age^2, sex, GRS_HDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000157 PGS000061
(GRS_LDL)
 PSS000096|
African Ancestry|
1,355 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum low-density lipoprotein (LDL) levels β: 30.04 — Beta (p-value): 0.00282 age, age^2, sex, GRS_HDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000158 PGS000061
(GRS_LDL)
 PSS000099|
Hispanic or Latin American Ancestry|
1,256 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum low-density lipoprotein (LDL) levels β: 42.86 — Beta (p-value): 2e-05 age, age^2, sex, GRS_HDL, GRS_TC, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000159 PGS000062
(GRS_TC)
 PSS000098|
European Ancestry|
2,063 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum total cholesterol (TC) levels β: 20.69 — Beta (p-value): 0.0108 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000160 PGS000062
(GRS_TC)
 PSS000097|
East Asian Ancestry|
666 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum total cholesterol (TC) levels β: 8.57 — Beta (p-value): 0.583 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000161 PGS000062
(GRS_TC)
 PSS000096|
African Ancestry|
1,355 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum total cholesterol (TC) levels β: 1.99 — Beta (p-value): 0.852 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000162 PGS000062
(GRS_TC)
 PSS000099|
Hispanic or Latin American Ancestry|
1,256 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum total cholesterol (TC) levels β: -2.62 — Beta (p-value): 0.815 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TG Association (p-value; unadjusted for covariates) < 0.001
PPM000163 PGS000063
(GRS_TG)
 PSS000098|
European Ancestry|
2,063 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum triglyceride (TG) levels β: 0.464 — Beta (p-value): 1.71e-11 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TC Association (p-value; unadjusted for covariates) < 0.001
PPM000164 PGS000063
(GRS_TG)
 PSS000097|
East Asian Ancestry|
666 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum triglyceride (TG) levels β: 0.337 — Beta (p-value): 0.0107 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TC Association (p-value; unadjusted for covariates) < 0.001
PPM000166 PGS000063
(GRS_TG)
 PSS000099|
Hispanic or Latin American Ancestry|
1,256 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum triglyceride (TG) levels β: 0.5 — Beta (p-value): 1.09e-10 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TC Association (p-value; unadjusted for covariates) < 0.001
PPM000165 PGS000063
(GRS_TG)
 PSS000096|
African Ancestry|
1,355 individuals
 PGP000045 |
Johnson L et al. PLoS One (2015)
 Reported Trait: Serum triglyceride (TG) levels β: 0.047 — Beta (p-value): 0.526 age, age^2, sex, GRS_HDL, GRS_LDL, GRS_TC —

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
PSS000097 Lipid levels are represented in mg/dL, individuals on any lipid-lowering medication (n = 1,018) were omitted from all analyses. — 666 individuals,
50.15 % Male samples
 Mean = 61.5 years East Asian — MESA MESA Classic Cohort
PSS000098 Lipid levels are represented in mg/dL, individuals on any lipid-lowering medication (n = 1,018) were omitted from all analyses. — 2,063 individuals,
46.78 % Male samples
 Mean = 62.09 years European — MESA MESA Classic Cohort
PSS000099 Lipid levels are represented in mg/dL, individuals on any lipid-lowering medication (n = 1,018) were omitted from all analyses. — 1,256 individuals,
48.89 % Male samples
 Mean = 60.65 years Hispanic or Latin American — MESA MESA Classic Cohort
PSS000096 Lipid levels are represented in mg/dL, individuals on any lipid-lowering medication (n = 1,018) were omitted from all analyses. — 1,355 individuals,
46.2 % Male samples
 Mean = 61.68 years African American or Afro-Caribbean — MESA MESA Classic Cohort