PGS Catalog - PGS002725 / Ischemic stroke (Polygenic Score)

Polygenic Score (PGS) ID: PGS002725

Predicted Trait
Reported Trait	Ischemic stroke
Mapped Trait(s)	stroke (EFO_0000712) Ischemic stroke (HP_0002140)

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
—	9,809 individuals [ 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	—	87,682 individuals [ 1,399 cases , 86,283 controls ]	—	East Asian (Taiwanese)	—	TWB	—
PSS009875	Ischemic stroke	—	41,929 individuals [ 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