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
Variants
Original Genome Build hg19
Number of Variants 3,225,583
Development Method
Name metaGRS of 19 component PGSs
Parameters LD thinning of 19 component PGSs
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%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST006908
Europe PMC: 29531354
440,328 individuals European
GWAS Catalog: GCST006906
Europe PMC: 29531354
446,696 individuals European
GWAS Catalog: GCST006907
Europe PMC: 29531354
150,765 individuals European
GWAS Catalog: GCST006909
Europe PMC: 29531354
198,048 individuals European
GWAS Catalog: GCST005842
Europe PMC: 29531354
15,560 individuals African American or Afro-Caribbean
GWAS Catalog: GCST005842
Europe PMC: 29531354
211,763 individuals European
GWAS Catalog: GCST005842
Europe PMC: 29531354
791 individuals Hispanic or Latin American
GWAS Catalog: GCST005842
Europe PMC: 29531354
29,042 individuals East Asian
GWAS Catalog: GCST005842
Europe PMC: 29531354
7,129 individuals South Asian
GWAS Catalog: GCST005842
Europe PMC: 29531354
364 individuals Asian unspecified
GWAS Catalog: GCST002223
Europe PMC: 24097068
94,595 individuals European
GWAS Catalog: GCST002216
Europe PMC: 24097068
94,595 individuals European
GWAS Catalog: GCST002222
Europe PMC: 24097068
94,595 individuals European
GWAS Catalog: GCST002221
Europe PMC: 24097068
94,595 individuals European
GWAS Catalog: GCST004300
Europe PMC: 28416818
110,099 individuals European
GWAS Catalog: GCST000666
Europe PMC: 2041889
74,035 individuals European
GWAS Catalog: GCST004776
Europe PMC: 28739976
150,134 individuals European
GWAS Catalog: GCST004777
Europe PMC: 28739976
150,134 individuals European
GWAS Catalog: GCST002783
Europe PMC: 25673413
236,781 individuals European
GWAS Catalog: GCST002783
Europe PMC: 25673413
887 individuals African American or Afro-Caribbean
GWAS Catalog: GCST002783
Europe PMC: 25673413
1,276 individuals Hispanic or Latin American
GWAS Catalog: GCST002647
Europe PMC: 25282103
253,288 individuals European
GWAS Catalog: GCST004773
Europe PMC: 28566273
159,208 individuals European
GWAS Catalog: GCST003116
Europe PMC: 26343387
11,323 individuals East Asian
GWAS Catalog: GCST003116
Europe PMC: 26343387
25,557 individuals South Asian
GWAS Catalog: GCST003116
Europe PMC: 26343387
2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian)
GWAS Catalog: GCST003116
Europe PMC: 26343387
4,095 individuals Hispanic or Latin American
GWAS Catalog: GCST003116
Europe PMC: 26343387
141,217 individuals European
GWAS Catalog: GCST003116
Europe PMC: 26343387
3,139 individuals African American or Afro-Caribbean
Score Development/Training
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
Prevalent and incident Ischaemic stroke; defined in http://biobank.ndph.ox.ac.uk/showcase/docs/alg_outcome_stroke.pdf
[
  • 888 cases
  • , 10,307 controls
]
European UKB 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

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