PGS Publication: PGP000104

Publication Information (EuropePMC)
Title Population-specific and trans-ancestry genome-wide analyses identify distinct and shared genetic risk loci for coronary artery disease.
PubMed ID 33020668(Europe PMC)
doi 10.1038/s41588-020-0705-3
Publication Date Oct. 5, 2020
Journal Nat Genet
Author(s) Koyama S, Ito K, Terao C, Akiyama M, Horikoshi M, Momozawa Y, Matsunaga H, Ieki H, Ozaki K, Onouchi Y, Takahashi A, Nomura S, Morita H, Akazawa H, Kim C, Seo JS, Higasa K, Iwasaki M, Yamaji T, Sawada N, Tsugane S, Koyama T, Ikezaki H, Takashima N, Tanaka K, Arisawa K, Kuriki K, Naito M, Wakai K, Suna S, Sakata Y, Sato H, Hori M, Sakata Y, Matsuda K, Murakami Y, Aburatani H, Kubo M, Matsuda F, Kamatani Y, Komuro I.
Released in PGS Catalog: Nov. 5, 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:
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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 PGS Scoring File (FTP Link)
PGS000337
(MetaPRS_CAD)
PGP000104 |
Koyama S et al. Nat Genet (2020)
Coronary artery disease coronary artery disease 75,028
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000337/ScoringFiles/PGS000337.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
PPM000909 PGS000337
(MetaPRS_CAD)
PSS000456|
East Asian Ancestry|
49,230 individuals
PGP000104 |
Koyama S et al. Nat Genet (2020)
Reported Trait: Mortality (diseases of the circulatory system) HR: 1.10351 [1.057, 1.152] Sex, age, age^2, PCs (1-10), disease status
PPM000908 PGS000337
(MetaPRS_CAD)
PSS000454|
East Asian Ancestry|
49,230 individuals
PGP000104 |
Koyama S et al. Nat Genet (2020)
Reported Trait: All-cause Mortality HR: 1.03159 [1.011, 1.052] Sex, age, age^2, PCs (1-10), disease status
PPM000911 PGS000337
(MetaPRS_CAD)
PSS000457|
East Asian Ancestry|
49,230 individuals
PGP000104 |
Koyama S et al. Nat Genet (2020)
Reported Trait: Mortality (ischemic heart disease) HR: 1.2158 [1.109, 1.333] Sex, age, age^2, PCs (1-10), disease status
PPM000912 PGS000337
(MetaPRS_CAD)
PSS000455|
East Asian Ancestry|
49,230 individuals
PGP000104 |
Koyama S et al. Nat Genet (2020)
Reported Trait: Mortality (congestive heart failure) HR: 1.15604 [1.042, 1.2283] Sex, age, age^2, PCs (1-10), disease status
PPM000910 PGS000337
(MetaPRS_CAD)
PSS000458|
East Asian Ancestry|
49,230 individuals
PGP000104 |
Koyama S et al. Nat Genet (2020)
Reported Trait: Mortality (diseases of the respiratory system) HR: 1.07133 [1.012, 1.134] Sex, age, age^2, PCs (1-10), disease status
PPM000907 PGS000337
(MetaPRS_CAD)
PSS000459|
East Asian Ancestry|
10,999 individuals
PGP000104 |
Koyama S et al. Nat Genet (2020)
Reported Trait: Coronary artery disease OR: 1.84 [1.744, 1.943] AUROC: 0.674 [0.661, 0.687] : 0.087 [0.074, 0.101]

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
PSS000454 Cause of death under ICD-10 code Median = 7.7 years
[
  • 9,816 cases
  • , 39,414 controls
]
East Asian
(Japanese)
BBJ
PSS000455 Cause of death under ICD-10.CHF code Median = 7.7 years
[
  • 362 cases
  • , 48,868 controls
]
East Asian
(Japanese)
BBJ
PSS000456 Cause of death under ICD-10.I codes Median = 7.7 years
[
  • 2,122 cases
  • , 47,108 controls
]
East Asian
(Japanese)
BBJ
PSS000457 Cause of death under ICD-10.IHD code Median = 7.7 years
[
  • 464 cases
  • , 48,766 controls
]
East Asian
(Japanese)
BBJ
PSS000458 Cause of death under ICD-10.J codes Median = 7.7 years
[
  • 1,193 cases
  • , 48,037 controls
]
East Asian
(Japanese)
BBJ
PSS000459 CAD was defined as a composite of stable angina, unstable angina and myocardial infarction. The disease definitions are dependent on the physician's diagnosis based on general medical practices following relevant guidelines and according to the clinical symptoms and diagnotic tests.
[
  • 1,827 cases
  • , 9,172 controls
]
,
84.0 % Male samples
East Asian
(Japanese)
BBJ