PGS Publication: PGP000365

Publication Information (EuropePMC)
Title Polygenic risk scores for cardiovascular diseases and type 2 diabetes.
PubMed ID 36459520(Europe PMC)
doi 10.1371/journal.pone.0278764
Publication Date Dec. 2, 2022
Journal PLoS One
Author(s) Wong CK, Makalic E, Dite GS, Whiting L, Murphy NM, Hopper JL, Allman R.
Released in PGS Catalog: Dec. 20, 2022

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)
PGS002779
(GTG_T2D_maxCT)
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Incident type 2 diabetes type 2 diabetes mellitus 46,353
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002779/ScoringFiles/PGS002779.txt.gz - Check Terms/Licenses
PGS002774
(GTG_AF_SCT)
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Incident atrial fibrillation atrial fibrillation 216,837
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002774/ScoringFiles/PGS002774.txt.gz - Check Terms/Licenses
PGS002778
(GTG_Hypertension_SCT)
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Incident hypertension hypertension 309,759
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002778/ScoringFiles/PGS002778.txt.gz - Check Terms/Licenses
PGS002780
(GTG_T2D_SCT)
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Incident type 2 diabetes type 2 diabetes mellitus 419,209
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002780/ScoringFiles/PGS002780.txt.gz - Check Terms/Licenses
PGS002773
(GTG_AF_maxCT)
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Incident atrial fibrillation atrial fibrillation 265
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002773/ScoringFiles/PGS002773.txt.gz - Check Terms/Licenses
PGS002775
(GTG_CAD_maxCT)
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Incident coronary artery disease coronary artery disease 1,059
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002775/ScoringFiles/PGS002775.txt.gz - Check Terms/Licenses
PGS002776
(GTG_CAD_SCT)
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Incident coronary artery disease coronary artery disease 390,782
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002776/ScoringFiles/PGS002776.txt.gz - Check Terms/Licenses
PGS002777
(GTG_Hypertension_maxCT)
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Incident hypertension hypertension 61,669
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002777/ScoringFiles/PGS002777.txt.gz - Check Terms/Licenses

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
PPM014973 PGS002773
(GTG_AF_maxCT)
 PSS009940|
European Ancestry|
12,306 individuals
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Reported Trait: Incident atrial fibrillation OR: 1.41 [1.35, 1.48] AUROC: 0.599 [0.585, 0.613] — — —
PPM014974 PGS002774
(GTG_AF_SCT)
 PSS009940|
European Ancestry|
12,306 individuals
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Reported Trait: Incident atrial fibrillation OR: 1.49 [1.42, 1.57] AUROC: 0.613 [0.599, 0.626] — — —
PPM014975 PGS002775
(GTG_CAD_maxCT)
 PSS009941|
European Ancestry|
16,374 individuals
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Reported Trait: Incident coronary artery disease OR: 1.29 [1.24, 1.35] AUROC: 0.572 [0.56, 0.584] — — —
PPM014976 PGS002776
(GTG_CAD_SCT)
 PSS009941|
European Ancestry|
16,374 individuals
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Reported Trait: Incident coronary artery disease OR: 1.36 [1.31, 1.42] AUROC: 0.587 [0.576, 0.599] — — —
PPM014977 PGS002777
(GTG_Hypertension_maxCT)
 PSS009942|
European Ancestry|
21,970 individuals
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Reported Trait: Incident hypertension OR: 1.23 [1.18, 1.27] AUROC: 0.559 [0.55, 0.569] — — —
PPM014978 PGS002778
(GTG_Hypertension_SCT)
 PSS009942|
European Ancestry|
21,970 individuals
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Reported Trait: Incident hypertension OR: 1.26 [1.22, 1.3] AUROC: 0.566 [0.556, 0.576] — — —
PPM014979 PGS002779
(GTG_T2D_maxCT)
 PSS009943|
European Ancestry|
5,472 individuals
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Reported Trait: Incident type 2 diabetes OR: 1.35 [1.25, 1.45] AUROC: 0.585 [0.564, 0.605] — — —
PPM014980 PGS002780
(GTG_T2D_SCT)
 PSS009943|
European Ancestry|
5,472 individuals
 PGP000365 |
Wong CK et al. PLoS One (2022)
 Reported Trait: Incident type 2 diabetes OR: 1.41 [1.31, 1.51] AUROC: 0.595 [0.575, 0.615] — — —

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
PSS009941 We used the disease definitions described in the supplement of Said et al (2018). PMID: 29955826 —
[
  • 2,729 cases
  • , 13,645 controls
]
,
46.0 % Male samples
 European — UKB —
PSS009942 We used the disease definitions described in the supplement of Said et al (2018). PMID: 29955826 —
[
  • 4,394 cases
  • , 17,576 controls
]
,
42.0 % Male samples
 European — UKB —
PSS009943 We used the disease definitions described in the supplement of Eastwood et al (2016). PMID: 27631769 —
[
  • 912 cases
  • , 4,560 controls
]
,
45.0 % Male samples
 European — UKB —
PSS009940 We used the disease definitions described in the supplement of Said et al (2018). PMID: 29955826 —
[
  • 2,051 cases
  • , 10,255 controls
]
,
46.0 % Male samples
 European — UKB —