Polygenic Score (PGS) ID: PGS001847

Predicted Trait
Reported Trait Circulatory disease NEC
Mapped Trait(s) vascular disease (EFO_0004264)
Additional Trait Information circulatory system
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_459.9
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 594
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
PPM009667 PSS009096|
European Ancestry|
4,066 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Circulatory disease NEC Partial Correlation (partial-r): 0.0326 [0.0018, 0.0634] sex, age, birth date, deprivation index, 16 PCs
PPM009668 PSS008650|
European Ancestry|
6,570 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Circulatory disease NEC Partial Correlation (partial-r): 0.0229 [-0.0013, 0.0471] sex, age, birth date, deprivation index, 16 PCs
PPM009669 PSS008424|
Greater Middle Eastern Ancestry|
1,182 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Circulatory disease NEC Partial Correlation (partial-r): -0.0084 [-0.0659, 0.0491] sex, age, birth date, deprivation index, 16 PCs
PPM009670 PSS008204|
South Asian Ancestry|
6,220 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Circulatory disease NEC Partial Correlation (partial-r): 0.0091 [-0.0158, 0.0339] sex, age, birth date, deprivation index, 16 PCs
PPM009671 PSS007986|
East Asian Ancestry|
1,790 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Circulatory disease NEC Partial Correlation (partial-r): 0.0149 [-0.0317, 0.0614] sex, age, birth date, deprivation index, 16 PCs
PPM009672 PSS007769|
African Ancestry|
2,467 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Circulatory disease NEC Partial Correlation (partial-r): -0.0097 [-0.0493, 0.03] sex, age, birth date, deprivation index, 16 PCs
PPM009673 PSS008873|
African Ancestry|
3,882 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Circulatory disease NEC Partial Correlation (partial-r): 0.003 [-0.0285, 0.0345] sex, age, birth date, deprivation index, 16 PCs
PPM009666 PSS009322|
European Ancestry|
19,705 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Circulatory disease NEC Partial Correlation (partial-r): 0.0405 [0.0266, 0.0545] 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
PSS009096 4,066 individuals European Poland (NE Europe) UKB
PSS008424 1,182 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008650 6,570 individuals European Italy (South Europe) UKB
PSS008873 3,882 individuals African unspecified Nigeria (West Africa) UKB
PSS008204 6,220 individuals South Asian India (South Asia) UKB
PSS009322 19,705 individuals European UK (+ Ireland) UKB
PSS007986 1,790 individuals East Asian China (East Asia) UKB
PSS007769 2,467 individuals African American or Afro-Caribbean Carribean UKB