Polygenic Score (PGS) ID: PGS002052

Predicted Trait
Reported Trait Occlusion and stenosis of precerebral arteries
Mapped Trait(s) occlusion precerebral artery (EFO_0009677)
Additional Trait Information circulatory system
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_433.1
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 490,459
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
PPM011278 PSS009316|
European Ancestry|
19,445 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Occlusion and stenosis of precerebral arteries Partial Correlation (partial-r): 0.0199 [0.0058, 0.034] sex, age, birth date, deprivation index, 16 PCs
PPM011279 PSS009090|
European Ancestry|
4,046 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Occlusion and stenosis of precerebral arteries Partial Correlation (partial-r): 0.0001 [-0.0308, 0.031] sex, age, birth date, deprivation index, 16 PCs
PPM011280 PSS008644|
European Ancestry|
6,521 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Occlusion and stenosis of precerebral arteries Partial Correlation (partial-r): 0.0191 [-0.0052, 0.0434] sex, age, birth date, deprivation index, 16 PCs
PPM011282 PSS008198|
South Asian Ancestry|
6,173 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Occlusion and stenosis of precerebral arteries Partial Correlation (partial-r): 0.0003 [-0.0247, 0.0253] sex, age, birth date, deprivation index, 16 PCs
PPM011283 PSS007980|
East Asian Ancestry|
1,789 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Occlusion and stenosis of precerebral arteries Partial Correlation (partial-r): -0.0132 [-0.0598, 0.0334] sex, age, birth date, deprivation index, 16 PCs
PPM011284 PSS007763|
African Ancestry|
2,407 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Occlusion and stenosis of precerebral arteries Partial Correlation (partial-r): 0.0003 [-0.0398, 0.0404] sex, age, birth date, deprivation index, 16 PCs
PPM011285 PSS008867|
African Ancestry|
3,806 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Occlusion and stenosis of precerebral arteries Partial Correlation (partial-r): 0.0054 [-0.0265, 0.0372] sex, age, birth date, deprivation index, 16 PCs
PPM011281 PSS008418|
Greater Middle Eastern Ancestry|
1,183 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Occlusion and stenosis of precerebral arteries Partial Correlation (partial-r): -0.0093 [-0.0667, 0.0482] 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
PSS009316 19,445 individuals European UK (+ Ireland) UKB
PSS008644 6,521 individuals European Italy (South Europe) UKB
PSS008198 6,173 individuals South Asian India (South Asia) UKB
PSS007980 1,789 individuals East Asian China (East Asia) UKB
PSS008418 1,183 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS007763 2,407 individuals African American or Afro-Caribbean Carribean UKB
PSS009090 4,046 individuals European Poland (NE Europe) UKB
PSS008867 3,806 individuals African unspecified Nigeria (West Africa) UKB