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(Variants and weights)

Polygenic Score (PGS) ID: PGS000039

Predicted Trait

Reported Trait: Ischaemic stroke
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): Ischemic stroke

Score Details

Name: metaGRS_ischaemicstroke

Original Genome Build: hg19
Number of Variants: 3,225,583

PGS Development Method: metaGRS of 19 component PGSs
PGS Development Details/Relevant Parameters: LD thinning of 19 component PGSs

Citation: Abraham G et al. bioRxiv (2019) | PGS Catalog Publication ID: PGP000027

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST006908
PubMed: 29531354
440,328 individuals European
GWAS Catalog: GCST006906
PubMed: 29531354
446,696 individuals European
GWAS Catalog: GCST006907
PubMed: 29531354
150,765 individuals European
GWAS Catalog: GCST006909
PubMed: 29531354
198,048 individuals European
GWAS Catalog: GCST005842
PubMed: 29531354
15,560 individuals African American or Afro-Caribbean
GWAS Catalog: GCST005842
PubMed: 29531354
211,763 individuals European
GWAS Catalog: GCST005842
PubMed: 29531354
791 individuals Hispanic or Latin American
GWAS Catalog: GCST005842
PubMed: 29531354
29,042 individuals East Asian
GWAS Catalog: GCST005842
PubMed: 29531354
7,129 individuals South Asian
GWAS Catalog: GCST005842
PubMed: 29531354
364 individuals Asian unspecified
GWAS Catalog: GCST002223
PubMed: 24097068
94,595 individuals European
GWAS Catalog: GCST002216
PubMed: 24097068
94,595 individuals European
GWAS Catalog: GCST002222
PubMed: 24097068
94,595 individuals European
GWAS Catalog: GCST002221
PubMed: 24097068
94,595 individuals European
GWAS Catalog: GCST004300
PubMed: 28416818
110,099 individuals European
GWAS Catalog: GCST000666
PubMed: 20418890
74,035 individuals European
GWAS Catalog: GCST004776
PubMed: 28739976
150,134 individuals European
GWAS Catalog: GCST004777
PubMed: 28739976
150,134 individuals European
GWAS Catalog: GCST002783
PubMed: 25673413
236,781 individuals European
GWAS Catalog: GCST002783
PubMed: 25673413
887 individuals African American or Afro-Caribbean
GWAS Catalog: GCST002783
PubMed: 25673413
1,276 individuals Hispanic or Latin American
GWAS Catalog: GCST002647
PubMed: 25282103
253,288 individuals European
GWAS Catalog: GCST004773
PubMed: 28566273
159,208 individuals European
GWAS Catalog: GCST003116
PubMed: 26343387
11,323 individuals East Asian
GWAS Catalog: GCST003116
PubMed: 26343387
25,557 individuals South Asian
Score Development/Training
Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers 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 11,195 individuals
[ 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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000091 PSS000058 Abraham G et al. (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 Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers 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 395,393 individuals
[ 3,075 cases, 392,318 controls]
45.70 %% Male samples
European UKB Validation set