Polygenic Score (PGS) ID: PGS002184

Predicted Trait
Reported Trait Mean carotid IMT (intima-medial thickness) at 120/150/210/240 degrees
Mapped Trait(s) carotid artery intima media thickness (EFO_0007117)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_log_mean_carotid_IMT
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 734,561
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
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM012319 PSS009455|
European Ancestry|
1,841 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean carotid IMT (intima-medial thickness) at 120/150/210/240 degrees — — Partial Correlation (partial-r): 0.2298 [0.1858, 0.2728] sex, age, birth date, deprivation index, 16 PCs —
PPM012320 PSS009229|
European Ancestry|
337 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean carotid IMT (intima-medial thickness) at 120/150/210/240 degrees — — Partial Correlation (partial-r): 0.2112 [0.1034, 0.314] sex, age, birth date, deprivation index, 16 PCs —
PPM012321 PSS008783|
European Ancestry|
516 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean carotid IMT (intima-medial thickness) at 120/150/210/240 degrees — — Partial Correlation (partial-r): 0.1925 [0.1062, 0.2758] sex, age, birth date, deprivation index, 16 PCs —
PPM012323 PSS008335|
South Asian Ancestry|
301 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean carotid IMT (intima-medial thickness) at 120/150/210/240 degrees — — Partial Correlation (partial-r): 0.1712 [0.0553, 0.2826] sex, age, birth date, deprivation index, 16 PCs —
PPM012324 PSS008112|
East Asian Ancestry|
143 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean carotid IMT (intima-medial thickness) at 120/150/210/240 degrees — — Partial Correlation (partial-r): 0.0882 [-0.0903, 0.2611] sex, age, birth date, deprivation index, 16 PCs —
PPM012325 PSS007899|
African Ancestry|
77 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean carotid IMT (intima-medial thickness) at 120/150/210/240 degrees — — Partial Correlation (partial-r): 0.1034 [-0.1615, 0.3544] sex, age, birth date, deprivation index, 16 PCs —
PPM012326 PSS009003|
African Ancestry|
134 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean carotid IMT (intima-medial thickness) at 120/150/210/240 degrees — — Partial Correlation (partial-r): 0.2412 [0.06, 0.4071] sex, age, birth date, deprivation index, 16 PCs —
PPM012322 PSS008557|
Greater Middle Eastern Ancestry|
51 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean carotid IMT (intima-medial thickness) at 120/150/210/240 degrees — — Partial Correlation (partial-r): 0.1746 [-0.1916, 0.4981] 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
PSS009003 — — 134 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009229 — — 337 individuals — European Poland (NE Europe) UKB —
PSS008557 — — 51 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009455 — — 1,841 individuals — European UK (+ Ireland) UKB —
PSS008783 — — 516 individuals — European Italy (South Europe) UKB —
PSS008335 — — 301 individuals — South Asian India (South Asia) UKB —
PSS008112 — — 143 individuals — East Asian China (East Asia) UKB —
PSS007899 — — 77 individuals — African American or Afro-Caribbean Carribean UKB —