Polygenic Score (PGS) ID: PGS002724

Predicted Trait
Reported Trait Ischemic stroke
Mapped Trait(s)
Released in PGS Catalog: Sept. 29, 2022
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GIGASTROKE_iPGS_EUR
Development Method
Name Integrative PGS (also referred to as metaGRS) of 22 component PGSs
Parameters 22 component PGSs are 5 European-specific stroke GWAS, 5 cross-ancestry stroke GWAS, and 12 GWAS of vascular risk traits
Variants
Original Genome Build GRCh37
Number of Variants 1,213,574
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000333
Citation (link to publication) Mishra A et al. Nature (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 63.2%
Multi-ancestry (including European): 32.8%
  • European
  • East Asian
  • African
  • Hispanic or Latin American
  • South Asian
Not Reported: 3.6%
South Asian: 0.2%
East Asian: 0.09%
Hispanic or Latin American: 0.03%
African: 0.02%
Greater Middle Eastern: 0.02%
12,788,906 individuals (100%)
Score Development/Training
European: 100%
10,000 individuals (100%)
PGS Evaluation
European: 44.4%
African: 33.3%
Hispanic or Latin American: 11.1%
East Asian: 11.1%
9 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 108,194 cases
  • , 1,314,496 controls
]
 European, East Asian, African unspecified, Hispanic or Latin American, South Asian NR
—
[
  • 86,271 cases
  • , 1,219,519 controls
]
 European, East Asian, African unspecified, Hispanic or Latin American, South Asian NR
—
[
  • 9,130 cases
  • , 425,336 controls
]
 European, East Asian, African unspecified, Hispanic or Latin American, South Asian NR
—
[
  • 13,066 cases
  • , 480,127 controls
]
 European, East Asian, African unspecified, Hispanic or Latin American, South Asian NR
—
[
  • 12,395 cases
  • , 524,374 controls
]
 European, East Asian, African unspecified, Hispanic or Latin American, South Asian NR
—
[
  • 71,322 cases
  • , 1,046,238 controls
]
 European NR
—
[
  • 60,568 cases
  • , 1,022,072 controls
]
 European NR
—
[
  • 6,310 cases
  • , 253,233 controls
]
 European NR
—
[
  • 6,257 cases
  • , 308,178 controls
]
 European NR
—
[
  • 10,409 cases
  • , 352,425 controls
]
 European NR
GWAS Catalog: GCST006624
Europe PMC: 30224653
 757,601 individuals European NR
GWAS Catalog: GCST006630
Europe PMC: 30224653
 757,601 individuals European NR
GWAS Catalog: GCST002221
Europe PMC: 24097068
 94,595 individuals European NR
GWAS Catalog: GCST002222
Europe PMC: 24097068
 94,595 individuals European NR
GWAS Catalog: GCST002223
Europe PMC: 24097068
 94,595 individuals European NR
GWAS Catalog: GCST002216
Europe PMC: 24097068
 94,595 individuals European NR
GWAS Catalog: GCST006900
Europe PMC: 30124842
 224,849 individuals Not reported NR
GWAS Catalog: GCST006900
Europe PMC: 30124842
 456,426 individuals European NR
GWAS Catalog: GCST006901
Europe PMC: 30124842
 237,103 individuals Not reported NR
GWAS Catalog: GCST006901
Europe PMC: 30124842
 456,426 individuals European NR
GWAS Catalog: GCST000666
Europe PMC: 20418890
 74,035 individuals European NR
GWAS Catalog: GCST006414
Europe PMC: 30061737
 1,030,836 individuals European NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 141,217 individuals European NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 3,139 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 4,095 individuals Hispanic or Latin American NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 25,557 individuals South Asian NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 11,323 individuals East Asian NR
GWAS Catalog: GCST009379
Europe PMC: 30297969
 898,130 individuals European NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 1,003 cases
  • , 8,997 controls
]
 European
(Estonian)		 EB Ischemic stroke — — — EstBB training

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) 		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
PPM014736 PSS009879|
European Ancestry|
403,489 individuals
 PGP000333 |
Mishra A et al. Nature (2022)
 Reported Trait: incident ischemic stroke cases HR: 1.19 [1.16, 1.21] C-index: 0.645 ∆C-index (improvement in C-index over covariates-only model): 0.01 age, sex, 5 PCs —
PPM014738 PSS009876|
European Ancestry|
51,288 individuals
 PGP000333 |
Mishra A et al. Nature (2022)
 Reported Trait: incident ischemic stroke cases HR: 1.19 [1.11, 1.27] C-index: 0.644 ∆C-index (improvement in C-index over covariates-only model): 0.008 age, sex, 5 PCs —
PPM014740 PSS009878|
African Ancestry|
107,343 individuals
 PGP000333 |
Mishra A et al. Nature (2022)
 Reported Trait: incident ischemic stroke cases HR: 1.11 [1.06, 1.17] C-index: 0.653 ∆C-index (improvement in C-index over covariates-only model): 0.003 age, sex, 5 PCs —
PPM014742 PSS009880|
African Ancestry|
3,434 individuals
 PGP000333 |
Mishra A et al. Nature (2022)
 Reported Trait: prevalent ischemic stroke cases OR: 1.09 [1.02, 1.17] AUROC: 0.548 ∆AUROC (improvement in AUROC over covariates-only model): 0.007 age, sex, 5 PCs —
PPM014745 PSS009875|
East Asian Ancestry|
41,929 individuals
 PGP000333 |
Mishra A et al. Nature (2022)
 Reported Trait: prevalent ischemic stroke cases OR: 1.18 [1.12, 1.25] AUROC: 0.643 ∆AUROC (improvement in AUROC over covariates-only model): 0.009 age, sex, 5 PCs —
PPM014734 PSS009877|
European Ancestry|
102,099 individuals
 PGP000333 |
Mishra A et al. Nature (2022)
 Reported Trait: incident ischemic stroke cases HR: 1.26 [1.19, 1.34] C-index: 0.631 ∆C-index (improvement in C-index over covariates-only model): 0.027 age, sex, 5 PCs —
PPM020273 PSS011318|
African Ancestry|
18,505 individuals
 PGP000536 |
Vassy JL et al. JAMA Cardiol (2023)
|Ext.		 Reported Trait: Incident ischemic stroke HR: 1.05 [0.95, 1.17] — — age, sex, and principal components of genetic ancestry —
PPM020274 PSS011319|
Hispanic or Latin American Ancestry|
6,785 individuals
 PGP000536 |
Vassy JL et al. JAMA Cardiol (2023)
|Ext.		 Reported Trait: Incident ischemic stroke HR: 1.08 [0.85, 1.36] — — age, sex, and principal components of genetic ancestry —
PPM020275 PSS011320|
European Ancestry|
53,861 individuals
 PGP000536 |
Vassy JL et al. JAMA Cardiol (2023)
|Ext.		 Reported Trait: Incident ischemic stroke HR: 1.15 [1.08, 1.21] — — age, sex, and principal components of genetic ancestry —

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
PSS009879 Ischemic stroke —
[
  • 8,392 cases
  • , 395,097 controls
]
 — European
(European)		 — MVP —
PSS009880 Ischemic stroke —
[
  • 1,691 cases
  • , 1,743 controls
]
 — Sub-Saharan African
(Nigerian)		 — NR Stroke Investigative Research & Educational Network (SIREN)
PSS011318 — — 18,505 individuals,
81.9 % Male samples
 Mean = 55.4 years
Sd = 11.8 years		 African American or Afro-Caribbean — MVP —
PSS011319 — — 6,785 individuals,
86.5 % Male samples
 Mean = 52.6 years
Sd = 14.8 years		 Hispanic or Latin American — MVP —
PSS011320 — — 53,861 individuals,
88.2 % Male samples
 Mean = 59.3 years
Sd = 13.8 years		 European — MVP —
PSS009875 Ischemic stroke —
[
  • 1,470 cases
  • , 40,459 controls
]
 — East Asian
(Japanese)		 — BBJ % Male: 70.0% for cases and 53.1% for controls. Age information: Mean (cases) = 69.2 years, sd (cases) = 10.8; Mean (controls) = 66.5 years, sd (controls) = 12.5
PSS009876 Ischemic stroke —
[
  • 960 cases
  • , 50,328 controls
]
 — European — NR ClinicalTrials_EUR
PSS009877 Ischemic stroke Mean = 4.6 years
Sd = 4.8 years
[
  • 1,128 cases
  • , 100,971 controls
]
,
37.8 % Male samples
 Mean = 44.0 years
Sd = 15.7 years		 European
(Estonian)		 — EB —
PSS009878 Ischemic stroke —
[
  • 2,227 cases
  • , 105,116 controls
]
 — African American or Afro-Caribbean
(African American)		 — MVP —