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. |
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) |
---|---|---|---|---|---|---|
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 | — | — | — |
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 | — |