PGS Publication: PGP000005

Publication Information (EuropePMC)
Title Genomic prediction of coronary heart disease.
PubMed ID 27655226(Europe PMC)
doi 10.1093/eurheartj/ehw450
Publication Date Sept. 21, 2016
Journal Eur Heart J
Author(s) Abraham G, Havulinna AS, Bhalala OG, Byars SG, De Livera AM, Yetukuri L, Tikkanen E, Perola M, Schunkert H, Sijbrands EJ, Palotie A, Samani NJ, Salomaa V, Ripatti S, Inouye M.
Released in PGS Catalog: Oct. 14, 2019

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)
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Additional Asian Ancestries
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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)
PGS000012
(GRS49K)
 PGP000005 |
Abraham G et al. Eur Heart J (2016)
 Coronary artery disease coronary artery disease 49,310
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000012/ScoringFiles/PGS000012.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)
PGS000010
(GRS27)
 PGP000003 |
Mega JL et al. Lancet (2015)
 Coronary heart disease coronary artery disease 27
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000010/ScoringFiles/PGS000010.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
PPM000018 PGS000012
(GRS49K)
 PSS000012|
European Ancestry|
12,676 individuals
 PGP000005 |
Abraham G et al. Eur Heart J (2016)
 Reported Trait: Incident coronary artery disease HR: 1.74 [1.61, 1.86]
OR: 1.74 [1.61, 1.89]		 — — sex, sub-cohort, location (east/west), 5 genetic PCs Used only the 42,364 SNPs that were available in FINRISK
PPM000020 PGS000012
(GRS49K)
 PSS000011|
European Ancestry|
3,406 individuals
 PGP000005 |
Abraham G et al. Eur Heart J (2016)
 Reported Trait: Incident coronary artery disease HR: 1.28 [1.18, 1.38]
OR: 1.28 [1.17, 1.41]		 — — sex, sub-cohort, 5 genetic PCs Used only the 46,773 SNPs that were available in FHS
PPM000019 PGS000010
(GRS27)
 PSS000012|
European Ancestry|
12,676 individuals
 PGP000005 |
Abraham G et al. Eur Heart J (2016)
|Ext.		 Reported Trait: Incident coronary artery disease HR: 1.21 [1.12, 1.3] — — — —
PPM000021 PGS000010
(GRS27)
 PSS000011|
European Ancestry|
3,406 individuals
 PGP000005 |
Abraham G et al. Eur Heart J (2016)
|Ext.		 Reported Trait: Incident coronary artery disease HR: 1.2 [1.07, 1.26] — — — —

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
PSS000011 The main outcome of interest was incident CHD event before age 75y. We used the definition of CHD as employed by the Framingham study, namely, one of • MI recognized, with diagnostic ECG (FHS event code #1) • MI recognized, without diagnostic ECG, with enzymes and history (#2) • MI recognized, without diagnostic ECG, with autopsy evidence (new event) (#3) • MI unrecognized, silent (#4) • MI unrecognized, not silent (#5) • Angina pectoris (AP), first episode only (#6) • Coronary insufficiency (CI), definite by both history and ECG (#7) • Questionable MI at exam 1 (#8) • Acute MI by autopsy, previously coded as 1 or 2 (#9) • Death, CHD sudden, with 1 hour (#21) • Death, CHD 1–23 hours, non sudden (#22) • Death, CHD 24-47 hours, non sudden (#23) • Death, CHD, 48 hours or more, non sudden (#24) —
[
  • 587 cases
  • , 2,819 controls
]
,
45.0 % Male samples
 — European — FHS FHS Original, FHS Offspring
PSS000012 Coronary heart disease (CHD) was defined as falling into any of the following categories: • I21 or I22 (ICD-10) / 410 (ICD-8/9) as the direct or as a contributing cause of death or I20-I25 (ICD-10) /410-414 (ICD-9) as the underlying cause of death • I21 or I22 (ICD-10) / 410 (ICD-8/9) as the main or secondary diagnosis at hospital discharge. • Coronary bypass surgery or coronary angioplasty at hospital discharge or identified from the Finnish registry of invasive cardiac procedures. —
[
  • 757 cases
  • , 11,919 controls
]
,
46.0 % Male samples
 — European
(Finnish)		 — FINRISK FR92, FR97, FR02