Polygenic Score (PGS) ID: PGS002053

Predicted Trait
Reported Trait Cerebrovascular disease
Mapped Trait(s) cerebrovascular disorder (EFO_0003763)
Additional Trait Information circulatory system
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_433
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 599,726
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

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
391,124 individuals European UK (+ Ireland) UKB

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
PPM011286 PSS009315|
European Ancestry|
19,915 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cerebrovascular disease Partial Correlation (partial-r): 0.0233 [0.0094, 0.0371] sex, age, birth date, deprivation index, 16 PCs
PPM011287 PSS009089|
European Ancestry|
4,121 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cerebrovascular disease Partial Correlation (partial-r): 0.0114 [-0.0193, 0.042] sex, age, birth date, deprivation index, 16 PCs
PPM011288 PSS008643|
European Ancestry|
6,641 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cerebrovascular disease Partial Correlation (partial-r): 0.0244 sex, age, birth date, deprivation index, 16 PCs
PPM011289 PSS008417|
Greater Middle Eastern Ancestry|
1,198 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cerebrovascular disease Partial Correlation (partial-r): 0.0536 [-0.0036, 0.1103] sex, age, birth date, deprivation index, 16 PCs
PPM011290 PSS008197|
South Asian Ancestry|
6,308 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cerebrovascular disease Partial Correlation (partial-r): 0.0165 [-0.0082, 0.0412] sex, age, birth date, deprivation index, 16 PCs
PPM011291 PSS007979|
East Asian Ancestry|
1,804 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cerebrovascular disease Partial Correlation (partial-r): 0.0131 [-0.0333, 0.0595] sex, age, birth date, deprivation index, 16 PCs
PPM011293 PSS008866|
African Ancestry|
3,912 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cerebrovascular disease Partial Correlation (partial-r): 0.0287 [-0.0027, 0.0601] sex, age, birth date, deprivation index, 16 PCs
PPM011292 PSS007762|
African Ancestry|
2,470 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cerebrovascular disease Partial Correlation (partial-r): 0.0139 [-0.0257, 0.0535] sex, age, birth date, deprivation index, 16 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
PSS009315 19,915 individuals European UK (+ Ireland) UKB
PSS008197 6,308 individuals South Asian India (South Asia) UKB
PSS007979 1,804 individuals East Asian China (East Asia) UKB
PSS007762 2,470 individuals African American or Afro-Caribbean Carribean UKB
PSS009089 4,121 individuals European Poland (NE Europe) UKB
PSS008417 1,198 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008866 3,912 individuals African unspecified Nigeria (West Africa) UKB
PSS008643 6,641 individuals European Italy (South Europe) UKB