PGS Publication: PGP000665

Publication Information (EuropePMC)
Title Polygenic risk score portability for common diseases across genetically diverse populations.
PubMed ID 39218908(Europe PMC)
doi 10.1186/s40246-024-00664-y
Publication Date Sept. 2, 2024
Journal Human Genomics
Author(s) Moreno-Grau S, Vernekar M, Lopez-Pineda A, Mas-Montserrat D, Barrabés M, Quinto-Cortés CD, Moatamed B, Lee MTM, Yu Z, Numakura K, Matsuda Y, Wall JD, Ioannidis AG, Katsanis N, Takano T, Bustamante CD.
Released in PGS Catalog: Sept. 19, 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

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)
PGS004936
(low_density_lipoprotein_cholesterol_measurement_combined)
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 LDL cholesterol low density lipoprotein cholesterol measurement 139,875
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004936/ScoringFiles/PGS004936.txt.gz
PGS004937
(triglyceride_measurement_combined)
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Triglycerides triglyceride measurement 8,337
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004937/ScoringFiles/PGS004937.txt.gz
PGS004930
(celiac_disease_snpnet_combined)
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Celiac disease celiac disease 463
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004930/ScoringFiles/PGS004930.txt.gz
PGS004929
(AF_Ldpred2_combined)
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Atrial fibrillation atrial fibrillation 178,814
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004929/ScoringFiles/PGS004929.txt.gz
PGS004932
(high_density_lipoprotein_cholesterol_measurement_combined)
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 HDL cholesterol high density lipoprotein cholesterol measurement 17,151
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004932/ScoringFiles/PGS004932.txt.gz
PGS004934
(hypertension_snpnet_combined)
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Hypertension hypertension 15,056
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004934/ScoringFiles/PGS004934.txt.gz
PGS004935
(hypothyroidism_snpnet_combined)
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Hypothyroidism hypothyroidism 6,127
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004935/ScoringFiles/PGS004935.txt.gz
PGS004931
(gout_snpnet_combined)
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Gout gout 1,138
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004931/ScoringFiles/PGS004931.txt.gz
PGS004933
(hemorrhoid_LDpred2_combined)
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Hemorrhoid hemorrhoid 184,519
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004933/ScoringFiles/PGS004933.txt.gz

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)
PGS002066
(portability-ldpred2_555.2)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Ulcerative colitis ulcerative colitis 566,637
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002066/ScoringFiles/PGS002066.txt.gz
PGS000882
(25OHD_SBayesR_PGS)
 PGP000228 |
Revez JA et al. Nat Commun (2020)
 25-hydroxyvitamin D vitamin D measurement 1,094,650
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000882/ScoringFiles/PGS000882.txt.gz
PGS003446
(TEM_CAD_PRS)
 PGP000446 |
Tcheandjieu C et al. Nat Med (2022)
 Coronary artery disease coronary artery disease 538,084
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003446/ScoringFiles/PGS003446.txt.gz
PGS000023
(AA_GRS)
 PGP000013 |
Onengut-Gumuscu S et al. Diabetes Care (2019)
 Type 1 diabetes (T1D) type 1 diabetes mellitus 7
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000023/ScoringFiles/PGS000023.txt.gz
PGS003103
(ExPRSweb_T2D_30054458-GCST006867_PRSCS_MGI_20211120)
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 945,820
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003103/ScoringFiles/PGS003103.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
PPM021725 PGS000023
(AA_GRS)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
|Ext.		 Reported Trait: Type 1 diabetes mellitus OR: 2.31 [2.0, 2.68] AUROC: 0.77 — — —
PPM021717 PGS003446
(TEM_CAD_PRS)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
|Ext.		 Reported Trait: Coronary artery disease OR: 1.6 [1.42, 1.82] AUROC: 0.82 — — —
PPM021718 PGS004930
(celiac_disease_snpnet_combined)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Reported Trait: Celiac disease OR: 1.52 [1.35, 1.71] AUROC: 0.67 — — —
PPM021716 PGS004929
(AF_Ldpred2_combined)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Reported Trait: Atrial fibrillation OR: 1.44 [1.28, 1.63] AUROC: 0.71 — — —
PPM021720 PGS004932
(high_density_lipoprotein_cholesterol_measurement_combined)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Reported Trait: High density lipoprotein cholesterol level OR: 1.02 [0.94, 1.11] AUROC: 0.6 — — —
PPM021721 PGS004933
(hemorrhoid_LDpred2_combined)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Reported Trait: Hemorrhoid OR: 1.1 [1.04, 1.15] AUROC: 0.56 — — —
PPM021722 PGS004934
(hypertension_snpnet_combined)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Reported Trait: Hypertension OR: 1.42 [1.35, 1.5] AUROC: 0.72 — — —
PPM021723 PGS004935
(hypothyroidism_snpnet_combined)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Reported Trait: Hypothyroidism OR: 1.5 [1.41, 1.6] AUROC: 0.7 — — —
PPM021724 PGS004936
(low_density_lipoprotein_cholesterol_measurement_combined)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Reported Trait: Low density lipoprotein cholesterol level OR: 1.35 [1.26, 1.46] AUROC: 0.65 — — —
PPM021726 PGS003103
(ExPRSweb_T2D_30054458-GCST006867_PRSCS_MGI_20211120)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
|Ext.		 Reported Trait: Type 2 diabetes mellitus OR: 1.93 [1.8, 2.07] AUROC: 0.75 — — —
PPM021727 PGS004937
(triglyceride_measurement_combined)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Reported Trait: Triglyceride level OR: 1.64 [1.54, 1.75] AUROC: 0.68 — — —
PPM021728 PGS002066
(portability-ldpred2_555.2)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
|Ext.		 Reported Trait: Ulcerative colitis OR: 1.11 [0.97, 1.28] AUROC: 0.57 — — —
PPM021729 PGS000882
(25OHD_SBayesR_PGS)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
|Ext.		 Reported Trait: Vitamin D level OR: 0.82 [0.78, 0.86] AUROC: 0.63 — — —
PPM021719 PGS004931
(gout_snpnet_combined)
 PSS011762|
European Ancestry|
8,417 individuals
 PGP000665 |
Moreno-Grau S et al. Human Genomics (2024)
 Reported Trait: Gout OR: 1.52 [1.35, 1.71] AUROC: 0.73 — — —

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
PSS011762 — — 8,417 individuals — European — BBofA —