Polygenic Score (PGS) ID: PGS001929

Predicted Trait
Reported Trait Standing height
Mapped Trait(s) body height (EFO_0004339)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_height
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 156,514
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
PPM010307 PSS009416|
European Ancestry|
19,953 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Standing height Partial Correlation (partial-r): 0.6344 [0.626, 0.6426] sex, age, birth date, deprivation index, 16 PCs
PPM010308 PSS009190|
European Ancestry|
4,126 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Standing height Partial Correlation (partial-r): 0.6098 [0.5902, 0.6286] sex, age, birth date, deprivation index, 16 PCs
PPM010310 PSS008518|
Greater Middle Eastern Ancestry|
1,180 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Standing height Partial Correlation (partial-r): 0.5167 [0.4732, 0.5576] sex, age, birth date, deprivation index, 16 PCs
PPM010311 PSS008296|
South Asian Ancestry|
6,152 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Standing height Partial Correlation (partial-r): 0.4923 [0.4731, 0.511] sex, age, birth date, deprivation index, 16 PCs
PPM010312 PSS008073|
East Asian Ancestry|
1,801 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Standing height Partial Correlation (partial-r): 0.4504 [0.4125, 0.4866] sex, age, birth date, deprivation index, 16 PCs
PPM010313 PSS007860|
African Ancestry|
2,450 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Standing height Partial Correlation (partial-r): 0.3454 [0.3099, 0.3799] sex, age, birth date, deprivation index, 16 PCs
PPM010314 PSS008964|
African Ancestry|
3,863 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Standing height Partial Correlation (partial-r): 0.2731 [0.2436, 0.3021] sex, age, birth date, deprivation index, 16 PCs
PPM010309 PSS008744|
European Ancestry|
6,633 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Standing height Partial Correlation (partial-r): 0.5938 [0.578, 0.6092] 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
PSS008964 3,863 individuals African unspecified Nigeria (West Africa) UKB
PSS009190 4,126 individuals European Poland (NE Europe) UKB
PSS008518 1,180 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008296 6,152 individuals South Asian India (South Asia) UKB
PSS009416 19,953 individuals European UK (+ Ireland) UKB
PSS008073 1,801 individuals East Asian China (East Asia) UKB
PSS008744 6,633 individuals European Italy (South Europe) UKB
PSS007860 2,450 individuals African American or Afro-Caribbean Carribean UKB