PGS Publication: PGP000599

Publication Information (EuropePMC)
Title Contemporary Polygenic Scores of Low-Density Lipoprotein Cholesterol and Coronary Artery Disease Predict Coronary Atherosclerosis in Adolescents and Young Adults.
PubMed ID 37409455(Europe PMC)
doi 10.1161/circgen.122.004047
Publication Date July 6, 2023
Journal Circ Genom Precis Med
Author(s) Guarischi-Sousa R, Salfati E, Kho PF, Iyer KR, Hilliard AT, Herrington DM, Tsao PS, Clarke SL, Assimes TL.
Released in PGS Catalog: March 18, 2024

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

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)
PGS001351
(MAGICTA_EUR_PGS_FI)
 PGP000246 |
Chen J et al. Nat Genet (2021)
 Fasting insulin fasting blood insulin measurement 1,025,098
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001351/ScoringFiles/PGS001351.txt.gz
PGS002026
(portability-ldpred2_250.2)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 830,783
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002026/ScoringFiles/PGS002026.txt.gz
PGS002009
(portability-PLR_systolic_BP)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Systolic blood pressure, automated reading systolic blood pressure 68,449
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002009/ScoringFiles/PGS002009.txt.gz
PGS002161
(portability-ldpred2_log_BMI)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Body mass index (BMI) body mass index 990,022
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002161/ScoringFiles/PGS002161.txt.gz
PGS002197
(portability-ldpred2_log_triglycerides)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Triglycerides triglyceride measurement 731,035
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002197/ScoringFiles/PGS002197.txt.gz
PGS002133
(portability-ldpred2_fat_perc)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Body fat percentage body fat percentage 995,419
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002133/ScoringFiles/PGS002133.txt.gz
PGS000889
(GLGC_2021_ALL_LDL_PRS_weights_PT)
 PGP000230 |
Graham SE et al. Nature (2021)
 LDL cholesterol low density lipoprotein cholesterol measurement 9,009
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000889/ScoringFiles/PGS000889.txt.gz
PGS000667
(LPA_GRS43)
 PGP000127 |
Trinder M et al. JAMA Cardiol (2020)
 Lipoprotein A lipoprotein A measurement 43
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000667/ScoringFiles/PGS000667.txt.gz
PGS003356
(1MH_CAD_PRS_2022_Ldpred)
 PGP000409 |
Aragam KG et al. Nat Genet (2022)
 Coronary artery disease coronary artery disease 2,324,683
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003356/ScoringFiles/PGS003356.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
PPM020896 PGS002197
(portability-ldpred2_log_triglycerides)
 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.03 [0.84, 1.26] — — — —
PPM020882 PGS003356
(1MH_CAD_PRS_2022_Ldpred)
 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.44 [1.18, 1.76] — — — —
PPM020883 PGS000889
(GLGC_2021_ALL_LDL_PRS_weights_PT)
 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.42 [1.16, 1.73] — — — —
PPM020884 PGS002133
(portability-ldpred2_fat_perc)
 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.13 [0.94, 1.37] — — — —
PPM020885 PGS002161
(portability-ldpred2_log_BMI)
 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.12 [0.92, 1.35] — — — —
PPM020886 PGS000667
(LPA_GRS43)
 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.11 [0.9, 1.38] — — — —
PPM020887 PGS001351
(MAGICTA_EUR_PGS_FI)
 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.1 [0.91, 1.34] — — — —
PPM020888 PGS002197
(portability-ldpred2_log_triglycerides)
 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.04 [0.86, 1.25] — — — —
PPM020889 PGS002026
(portability-ldpred2_250.2)
 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 0.96 [0.8, 1.16] — — — —
PPM020890 PGS002009
(portability-PLR_systolic_BP)
 PSS011442|
European Ancestry|
564 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 0.92 [0.77, 1.11] — — — —
PPM020891 PGS000889
(GLGC_2021_ALL_LDL_PRS_weights_PT)
 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.18 [0.95, 1.47] — — — —
PPM020892 PGS001351
(MAGICTA_EUR_PGS_FI)
 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.15 [0.92, 1.42] — — — —
PPM020893 PGS002161
(portability-ldpred2_log_BMI)
 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.1 [0.89, 1.36] — — — —
PPM020894 PGS002026
(portability-ldpred2_250.2)
 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.1 [0.9, 1.35] — — — —
PPM020895 PGS002009
(portability-PLR_systolic_BP)
 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.06 [0.86, 1.31] — — — —
PPM020897 PGS003356
(1MH_CAD_PRS_2022_Ldpred)
 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 1.0 [0.81, 1.24] — — — —
PPM020898 PGS000667
(LPA_GRS43)
 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 0.99 [0.8, 1.24] — — — —
PPM020899 PGS002133
(portability-ldpred2_fat_perc)
 PSS011441|
African Ancestry|
504 individuals
 PGP000599 |
Guarischi-Sousa R et al. Circ Genom Precis Med (2023)
|Ext.		 Reported Trait: Raised coronary lesion OR: 0.94 [0.76, 1.15] — — — —

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
PSS011441 — —
[
  • 165 cases
  • , 339 controls
]
,
82.0 % Male samples
 Mean = 27.5 years African unspecified — PDAY —
PSS011442 — —
[
  • 181 cases
  • , 383 controls
]
,
77.0 % Male samples
 Mean = 26.7 years European — PDAY —