Polygenic Score (PGS) ID: PGS000039

Predicted Trait
Reported Trait Ischemic stroke
Mapped Trait(s)
Released in PGS Catalog: Dec. 18, 2019
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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 metaGRS_ischaemicstroke
Development Method
Name metaGRS of 19 component PGSs
Parameters LD thinning of 19 component PGSs
Variants
Original Genome Build hg19
Number of Variants 3,225,583
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000027
Citation (link to publication) Abraham G et al. Nat Commun (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 96.8%
East Asian: 1.3%
South Asian: 1%
African: 0.6%
Hispanic or Latin American: 0.2%
Greater Middle Eastern: 0.07%
Additional Asian Ancestries: 0.01%
3,202,307 individuals (100%)
Score Development/Training
European: 100%
11,195 individuals (100%)
PGS Evaluation
European: 61.5%
African: 15.4%
East Asian: 15.4%
Not Reported: 7.7%
13 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST006908
Europe PMC: 29531354
 440,328 individuals European NR
GWAS Catalog: GCST006906
Europe PMC: 29531354
 446,696 individuals European NR
GWAS Catalog: GCST006907
Europe PMC: 29531354
 150,765 individuals European NR
GWAS Catalog: GCST006909
Europe PMC: 29531354
 198,048 individuals European NR
GWAS Catalog: GCST005842
Europe PMC: 29531354
 15,560 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST005842
Europe PMC: 29531354
 211,763 individuals European NR
GWAS Catalog: GCST005842
Europe PMC: 29531354
 791 individuals Hispanic or Latin American NR
GWAS Catalog: GCST005842
Europe PMC: 29531354
 29,042 individuals East Asian NR
GWAS Catalog: GCST005842
Europe PMC: 29531354
 7,129 individuals South Asian NR
GWAS Catalog: GCST005842
Europe PMC: 29531354
 364 individuals Asian unspecified 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: GCST002222
Europe PMC: 24097068
 94,595 individuals European NR
GWAS Catalog: GCST002221
Europe PMC: 24097068
 94,595 individuals European NR
GWAS Catalog: GCST004300
Europe PMC: 28416818
 110,099 individuals European NR
GWAS Catalog: GCST000666
Europe PMC: 2041889
 74,035 individuals European NR
GWAS Catalog: GCST004776
Europe PMC: 28739976
 150,134 individuals European NR
GWAS Catalog: GCST004777
Europe PMC: 28739976
 150,134 individuals European NR
GWAS Catalog: GCST002783
Europe PMC: 25673413
 236,781 individuals European NR
GWAS Catalog: GCST002783
Europe PMC: 25673413
 887 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST002783
Europe PMC: 25673413
 1,276 individuals Hispanic or Latin American NR
GWAS Catalog: GCST002647
Europe PMC: 25282103
 253,288 individuals European NR
GWAS Catalog: GCST004773
Europe PMC: 28566273
 159,208 individuals European NR
GWAS Catalog: GCST003116
Europe PMC: 26343387
 11,323 individuals East Asian 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
 4,095 individuals Hispanic or Latin American 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
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
—
[
  • 888 cases
  • , 10,307 controls
]
 European UKB Prevalent and incident Ischaemic stroke; defined in http://biobank.ndph.ox.ac.uk/showcase/docs/alg_outcome_stroke.pdf — — — Tuning set

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
PPM000091 PSS000058|
European Ancestry|
395,393 individuals
 PGP000027 |
Abraham G et al. Nat Commun (2019)
 Reported Trait: Ischaemic stroke before age 75 HR: 1.26 [1.22, 1.31] C-index: 0.585 [0.574, 0.595] — Sex, genotyping chip, 10 PCs —
PPM002221 PSS001082|
European Ancestry|
12,792 individuals
 PGP000209 |
Neumann JT et al. Stroke (2021)
|Ext.		 Reported Trait: Incident ischemic stroke HR: 1.41 [1.2, 1.65] AUROC: 0.685 [0.64, 0.73] Hazard Ratio (HR, top 33.3% vs bottom 33.3%): 1.74 [1.19, 2.56] Age, sex, smoking status (current or former versus never), systolic blood pressure, non-high-density lipoprotein cholesterol, high-density lipoprotein cholesterol, body mass index, alcohol consumption (current versus former or never consumption), family history of stroke (event occuring before the age of 50 in a first-degree relative), diabetes, randomization to aspirin Only 3,219,276 SNPs from PGS000039 were utilised due to variant identifier mismatch. Only 12,405 individuals (171 cases) were used due to missing values. For AUROC values this was 11,385 individuals (158 cases).
PPM002222 PSS001082|
European Ancestry|
12,792 individuals
 PGP000209 |
Neumann JT et al. Stroke (2021)
|Ext.		 Reported Trait: Incident ischemic stroke — — Net reclassification index (NRI): 0.252 [0.175, 0.434] Age, sex, smoking status (current or former versus never), systolic blood pressure, non-high-density lipoprotein cholesterol, high-density lipoprotein cholesterol, body mass index, alcohol consumption (current versus former or never consumption), family history of stroke (event occuring before the age of 50 in a first-degree relative), diabetes, randomization to aspirin Only 3,219,276 SNPs from PGS000039 were utilised due to variant identifier mismatch. Only 11,385 individuals (158 cases) were used.
PPM002223 PSS001082|
European Ancestry|
12,792 individuals
 PGP000209 |
Neumann JT et al. Stroke (2021)
|Ext.		 Reported Trait: Incident ischemic stroke HR: 1.43 [1.22, 1.68] — — Age, sex, smoking status (current or former versus never), systolic blood pressure, non-high-density lipoprotein cholesterol, high-density lipoprotein cholesterol, body mass index, alcohol consumption (current versus former or never consumption), family history of stroke (event occuring before the age of 50 in a first-degree relative), diabetes, randomization to aspirin, PCs(1-10) Only 3,219,276 SNPs from PGS000039 were utilised due to variant identifier mismatch. Only 12,405 individuals (171 cases) were used due to missing values.
PPM002224 PSS001082|
European Ancestry|
12,792 individuals
 PGP000209 |
Neumann JT et al. Stroke (2021)
|Ext.		 Reported Trait: Incident ischemic stroke HR: 1.43 [1.22, 1.68] — — Age, sex, smoking status (current or former versus never), systolic blood pressure, non-high-density lipoprotein cholesterol, high-density lipoprotein cholesterol, body mass index, alcohol consumption (current versus former or never consumption), family history of stroke (event occuring before the age of 50 in a first-degree relative), diabetes, randomization to aspirin, intake of antihypertensive drugs, intake of statin Only 3,219,276 SNPs from PGS000039 were utilised due to variant identifier mismatch. Only 12,405 individuals (171 cases) were used due to missing values.
PPM002225 PSS001082|
European Ancestry|
12,792 individuals
 PGP000209 |
Neumann JT et al. Stroke (2021)
|Ext.		 Reported Trait: Incident ischemic stroke HR: 1.41 [1.2, 1.66] — — Age, sex, smoking status (current or former versus never), systolic blood pressure, non-high-density lipoprotein cholesterol, high-density lipoprotein cholesterol, body mass index, alcohol consumption (current versus former or never consumption), family history of stroke (event occuring before the age of 50 in a first-degree relative), diabetes, randomization to aspirin, index of relative socio-economic advantage and disadvantage(1-10) Only 3,219,276 SNPs from PGS000039 were utilised due to variant identifier mismatch. Only 12,405 individuals (171 cases) were used due to missing values.
PPM002226 PSS001082|
European Ancestry|
12,792 individuals
 PGP000209 |
Neumann JT et al. Stroke (2021)
|Ext.		 Reported Trait: Incident ischemic stroke HR: 1.4 [1.2, 1.64] — — Age, sex, systolic blood pressure, non-high-density lipoprotein cholesterol, high-density lipoprotein cholesterol, alcohol consumption (current versus former or never consumption) Only 3,219,276 SNPs from PGS000039 were utilised due to variant identifier mismatch. Only 12,405 individuals (171 cases) were used due to missing values.
PPM002227 PSS001082|
European Ancestry|
12,792 individuals
 PGP000209 |
Neumann JT et al. Stroke (2021)
|Ext.		 Reported Trait: Incident ischemic stroke — AUROC: 0.582 [0.537, 0.628] — — Only 3,219,276 SNPs from PGS000039 were utilised due to variant identifier mismatch. For AUROC values only 11,385 individuals (158 cases) were used.
PPM002228 PSS001082|
European Ancestry|
12,792 individuals
 PGP000209 |
Neumann JT et al. Stroke (2021)
|Ext.		 Reported Trait: Incident large vessel ischemic stroke HR: 1.43 [1.05, 1.94] — — Age, sex, smoking status (current or former versus never), systolic blood pressure, non-high-density lipoprotein cholesterol, high-density lipoprotein cholesterol, body mass index, alcohol consumption (current versus former or never consumption), family history of stroke (event occuring before the age of 50 in a first-degree relative), diabetes, randomization to aspirin Only 3,219,276 SNPs from PGS000039 were utilised due to variant identifier mismatch.
PPM002229 PSS001082|
European Ancestry|
12,792 individuals
 PGP000209 |
Neumann JT et al. Stroke (2021)
|Ext.		 Reported Trait: Incident cardiometabolic ischemic stroke HR: 1.74 [1.24, 2.43] — — Age, sex, smoking status (current or former versus never), systolic blood pressure, non-high-density lipoprotein cholesterol, high-density lipoprotein cholesterol, body mass index, alcohol consumption (current versus former or never consumption), family history of stroke (event occuring before the age of 50 in a first-degree relative), diabetes, randomization to aspirin Only 3,219,276 SNPs from PGS000039 were utilised due to variant identifier mismatch.
PPM012987 PSS009641|
European Ancestry|
3,071 individuals
 PGP000315 |
Hämmerle M et al. Stroke (2022)
|Ext.		 Reported Trait: Stroke — — Odds ratio (OR, top 1% vs. rest): 5.82 [2.08, 14.0] Age, sex, BMI, hypertension, cholesterol, diabetes, smoker —
PPM014737 PSS009879|
European Ancestry|
403,489 individuals
 PGP000333 |
Mishra A et al. Nature (2022)
|Ext.		 Reported Trait: incident ischemic stroke cases HR: 1.13 [1.1, 1.15] C-index: 0.64 ∆C-index (improvement in C-index over covariates-only model): 0.006 age, sex, 5 PCs —
PPM014739 PSS009876|
European Ancestry|
51,288 individuals
 PGP000333 |
Mishra A et al. Nature (2022)
|Ext.		 Reported Trait: incident ischemic stroke cases HR: 1.14 [1.06, 1.21] C-index: 0.641 ∆C-index (improvement in C-index over covariates-only model): 0.006 age, sex, 5 PCs —
PPM014741 PSS009878|
African Ancestry|
107,343 individuals
 PGP000333 |
Mishra A et al. Nature (2022)
|Ext.		 Reported Trait: incident ischemic stroke cases HR: 1.09 [1.04, 1.14] C-index: 0.652 ∆C-index (improvement in C-index over covariates-only model): 0.002 age, sex, 5 PCs —
PPM014748 PSS009881|
East Asian Ancestry|
87,682 individuals
 PGP000333 |
Mishra A et al. Nature (2022)
|Ext.		 Reported Trait: prevalent ischemic stroke cases OR: 1.1 [1.04, 1.16] AUROC: 0.763 ∆AUROC (improvement in AUROC over covariates-only model): 0.001 age, sex, 5 PCs —
PPM014735 PSS009877|
European Ancestry|
102,099 individuals
 PGP000333 |
Mishra A et al. Nature (2022)
|Ext.		 Reported Trait: incident ischemic stroke cases HR: 1.19 [1.12, 1.26] C-index: 0.618 ∆C-index (improvement in C-index over covariates-only model): 0.014 age, sex, 5 PCs —
PPM014743 PSS009880|
African Ancestry|
3,434 individuals
 PGP000333 |
Mishra A et al. Nature (2022)
|Ext.		 Reported Trait: prevalent ischemic stroke cases OR: 1.07 [1.0, 1.15] AUROC: 0.547 ∆AUROC (improvement in AUROC over covariates-only model): 0.006 age, sex, 5 PCs —
PPM014746 PSS009875|
East Asian Ancestry|
41,929 individuals
 PGP000333 |
Mishra A et al. Nature (2022)
|Ext.		 Reported Trait: prevalent ischemic stroke cases OR: 1.17 [1.11, 1.23] AUROC: 0.641 ∆AUROC (improvement in AUROC over covariates-only model): 0.007 age, sex, 5 PCs —
PPM016151 PSS010050|
Ancestry Not Reported|
454,756 individuals
 PGP000401 |
Cho BPH et al. JAMA Neurol (2022)
|Ext.		 Reported Trait: Stroke HR: 1.23 [1.2, 1.26] — — age, sex, ethnicity, exome sequencing batch, and the first 10 principal components of genetic ancestry —
PPM021311 PSS011681|
European Ancestry|
306,654 individuals
 PGP000628 |
Sun L et al. PLoS Med (2021)
|Ext.		 Reported Trait: Incident cardiovascular disease outcome HR: 1.18 [1.15, 1.21] — — Age at baseline, smoking status, history of diabetes, systolic blood pressure, total cholesterol, high-density lipoprotein cholesterol levels, stratified by study centre, sex —
PPM021312 PSS011681|
European Ancestry|
306,654 individuals
 PGP000628 |
Sun L et al. PLoS Med (2021)
|Ext.		 Reported Trait: Incident coronary heart disease HR: 1.2 [1.16, 1.24] — — Age at baseline, smoking status, history of diabetes, systolic blood pressure, total cholesterol, high-density lipoprotein cholesterol levels, stratified by study centre, sex —
PPM021313 PSS011681|
European Ancestry|
306,654 individuals
 PGP000628 |
Sun L et al. PLoS Med (2021)
|Ext.		 Reported Trait: Incident stroke HR: 1.19 [1.14, 1.24] — — Age at baseline, stratified by study centre, sex —
PPM021314 PSS011681|
European Ancestry|
306,654 individuals
 PGP000628 |
Sun L et al. PLoS Med (2021)
|Ext.		 Reported Trait: Incident stroke HR: 1.16 [1.11, 1.21] — — Age at baseline, smoking status, history of diabetes, systolic blood pressure, total cholesterol, high-density lipoprotein cholesterol levels, stratified by study centre, sex —
PPM021315 PSS011681|
European Ancestry|
306,654 individuals
 PGP000628 |
Sun L et al. PLoS Med (2021)
|Ext.		 Reported Trait: Combination of incident coronary heart disease, stroke and cardiac revascularisation procedures HR: 1.19 [1.16, 1.22] — — Age at baseline, smoking status, history of diabetes, systolic blood pressure, total cholesterol, high-density lipoprotein cholesterol levels, stratified by study centre, sex —
PPM021765 PSS011789|
European Ancestry|
332 individuals
 PGP000674 |
Lin F et al. Front Stroke (2023)
|Ext.		 Reported Trait: Ischemic stroke OR: 3.0 [0.3, 26.4] — — Age, smoking status —

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)
PSS009881 Ischemic stroke —
[
  • 1,399 cases
  • , 86,283 controls
]
 — East Asian
(Taiwanese)		 — TWB —
PSS011789 — —
[
  • 136 cases
  • , 196 controls
]
,
0.0 % Male samples
 — European — GEOS —
PSS000058 Prevalent and incident Ischaemic stroke; defined in http://biobank.ndph.ox.ac.uk/showcase/docs/alg_outcome_stroke.pdf Mean = 6.3 years
Sd = 1.9 years
[
  • 3,075 cases
  • , 392,318 controls
]
,
45.7 % Male samples
 Mean = 54.3 years European — UKB Validation set
PSS011681 The primary outcome was a first-onset cardiovascular disease event, defined as the composite of CHD (i.e., myocardial infarction or fatal CHD) or any stroke. Secondary outcomes included each of CHD and stroke separately, and a combination of CHD, stroke, and cardiac revascularisation procedures (i.e., percutaneous transluminal cor- onary angioplasty [PTCA] and coronary artery bypass grafting [CABG]). 3333 Cases are CHD events and 2347 are stroke events Median = 8.1 years
[
  • 5,680 cases
  • , 300,974 controls
]
,
43.01 % Male samples
 Mean = 56.0 years
Sd = 8.0 years		 European — UKB —
PSS010050 Participants without history of stroke, coronary heart disease, peripheral vascular disease, or congestive heart failure at recruitment — 454,756 individuals — Not reported — UKB —
PSS001082 Cases were individuals who had experienced an ischemic stroke (IS) event. IS was defined according to the World Health Organization definition and included imaging by computed tomography or magnetic resonance imaging in the majority of cases. All cases of IS were further divided into subtypes of large vessel (n=49), small vessel (n=43), cardioembolic (n=36), and undetermined. Undetermined strokes had undetermined causes, multiple causes identified, or an incomplete evaluation made. All stroke events were assessed by an adjudication committee, blinded to the identity of participants and study treatment group assignment. Median = 4.7 years
IQR = [3.6, 5.7] years
[
  • 173 cases
  • , 12,619 controls
]
,
45.1 % Male samples
 Mean = 75.1 years
Sd = 4.2 years		 European — ASPREE —
PSS009641 A stroke event was defined as hospitalization due to stroke which was self-reported in a structured and standardized inter- view performed by certified and supervised personnel. — 3,071 individuals,
49.0 % Male samples
 Mean = 57.4 years
Sd = 12.9 years		 European — KORA —
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 —