Polygenic Score (PGS) ID: PGS000039

Predicted Trait
Reported Trait Ischaemic stroke
Mapped Trait(s)
Released in PGS Catalog: Dec. 18, 2019
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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: 100%
3 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

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
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
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
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