Polygenic Score (PGS) ID: PGS002725

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_EAS
Development Method
Name Integrative PGS (also referred to as metaGRS) of 22 component PGSs
Parameters 22 component PGSs are 5 East Asian-specific stroke GWAS, 5 cross-ancestry stroke GWAS, and 12 GWAS of vascular risk traits
Variants
Original Genome Build GRCh37
Number of Variants 6,010,730
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: 60.4%
East Asian: 38%
African: 1%
South Asian: 0.5%
Hispanic or Latin American: 0.2%
10,493,598 individuals (100%)
Score Development/Training
East Asian: 100%
9,809 individuals (100%)
PGS Evaluation
East Asian: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST005979
Europe PMC: 29403010
136,597 individuals East Asian NR
GWAS Catalog: GCST005978
Europe PMC: 29403010
136,615 individuals East Asian NR
GWAS Catalog: GCST006034
Europe PMC: 29403010
128,305 individuals East Asian NR
GWAS Catalog: GCST006004
Europe PMC: 29403010
72,866 individuals East Asian NR
GWAS Catalog: GCST006005
Europe PMC: 29403010
70,657 individuals East Asian NR
GWAS Catalog: GCST006003
Europe PMC: 29403010
105,597 individuals East Asian NR
GWAS Catalog: GCST004904
Europe PMC: 28892062
158,284 individuals East Asian NR
GWAS Catalog: GCST008839
Europe PMC: 31562340
159,095 individuals East Asian NR
GWAS Catalog: GCST009405
Europe PMC: 31089300
72,655 individuals East Asian NR
GWAS Catalog: GCST004373
Europe PMC: 28416822
36,792 individuals East Asian NR
GWAS Catalog: GCST90013687
Europe PMC: 32514122
212,453 individuals East Asian NR
GWAS Catalog: GCST90013693
Europe PMC: 32514122
210,865 individuals East Asian NR
GWAS Catalog: GCST90104534
Europe PMC: 36180795
23,991 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST90104534
Europe PMC: 36180795
264,655 individuals East Asian NR
GWAS Catalog: GCST90104534
Europe PMC: 36180795
1,308,460 individuals European NR
GWAS Catalog: GCST90104534
Europe PMC: 36180795
5,662 individuals Hispanic or Latin American NR
GWAS Catalog: GCST90104534
Europe PMC: 36180795
11,312 individuals South Asian NR
GWAS Catalog: GCST90104535
Europe PMC: 36180795
20,924 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST90104535
Europe PMC: 36180795
256,274 individuals East Asian NR
GWAS Catalog: GCST90104535
Europe PMC: 36180795
1,296,908 individuals European NR
GWAS Catalog: GCST90104535
Europe PMC: 36180795
5,326 individuals Hispanic or Latin American NR
GWAS Catalog: GCST90104535
Europe PMC: 36180795
11,134 individuals South Asian NR
GWAS Catalog: GCST90104537
Europe PMC: 36180795
20,453 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST90104537
Europe PMC: 36180795
242,774 individuals East Asian NR
GWAS Catalog: GCST90104537
Europe PMC: 36180795
1,241,619 individuals European NR
GWAS Catalog: GCST90104537
Europe PMC: 36180795
4,353 individuals Hispanic or Latin American NR
GWAS Catalog: GCST90104537
Europe PMC: 36180795
8,319 individuals South Asian NR
GWAS Catalog: GCST90104536
Europe PMC: 36180795
20,271 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST90104536
Europe PMC: 36180795
238,168 individuals East Asian NR
GWAS Catalog: GCST90104536
Europe PMC: 36180795
1,245,612 individuals European NR
GWAS Catalog: GCST90104536
Europe PMC: 36180795
4,369 individuals Hispanic or Latin American NR
GWAS Catalog: GCST90104536
Europe PMC: 36180795
8,268 individuals South Asian NR
GWAS Catalog: GCST90104544
Europe PMC: 36180795
264,655 individuals East Asian NR
GWAS Catalog: GCST90104545
Europe PMC: 36180795
256,274 individuals East Asian NR
GWAS Catalog: GCST90104548
Europe PMC: 36180795
242,774 individuals East Asian NR
GWAS Catalog: GCST90104547
Europe PMC: 36180795
238,977 individuals East Asian NR
GWAS Catalog: GCST90104546
Europe PMC: 36180795
238,168 individuals East Asian NR
GWAS Catalog: GCST90104538
Europe PMC: 36180795
238,977 individuals East Asian NR
GWAS Catalog: GCST90104538
Europe PMC: 36180795
1,241,207 individuals European NR
GWAS Catalog: GCST90104538
Europe PMC: 36180795
4,313 individuals Hispanic or Latin American NR
GWAS Catalog: GCST90104538
Europe PMC: 36180795
8,377 individuals South Asian NR
GWAS Catalog: GCST90104538
Europe PMC: 36180795
20,243 individuals African American or Afro-Caribbean 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
[
  • 577 cases
  • , 9,232 controls
]
East Asian
(Japanese)
BBJ Ischemic stroke BBJ 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
PPM014747 PSS009881|
East Asian Ancestry|
87,682 individuals
PGP000333 |
Mishra A et al. Nature (2022)
Reported Trait: prevalent ischemic stroke cases OR: 1.18 [1.12, 1.25] AUROC: 0.765 ∆AUROC (improvement in AUROC over covariates-only model): 0.003 age, sex, 5 PCs
PPM014744 PSS009875|
East Asian Ancestry|
41,929 individuals
PGP000333 |
Mishra A et al. Nature (2022)
Reported Trait: prevalent ischemic stroke cases OR: 1.33 [1.26, 1.4] AUROC: 0.653 ∆AUROC (improvement in AUROC over covariates-only model): 0.019 age, sex, 5 PCs

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
PSS009881 Ischemic stroke
[
  • 1,399 cases
  • , 86,283 controls
]
East Asian
(Taiwanese)
TWB
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