Polygenic Score (PGS) ID: PGS001983

Predicted Trait
Reported Trait Waist circumference
Mapped Trait(s) waist circumference (EFO_0004342)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_log_waist_circ
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 96,496
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
PPM010739 PSS009471|
European Ancestry|
19,966 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Waist circumference Partial Correlation (partial-r): 0.3233 [0.3108, 0.3356] sex, age, birth date, deprivation index, 16 PCs
PPM010740 PSS009245|
European Ancestry|
4,125 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Waist circumference Partial Correlation (partial-r): 0.3113 [0.2834, 0.3387] sex, age, birth date, deprivation index, 16 PCs
PPM010741 PSS008799|
European Ancestry|
6,637 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Waist circumference Partial Correlation (partial-r): 0.303 [0.281, 0.3247] sex, age, birth date, deprivation index, 16 PCs
PPM010742 PSS008573|
Greater Middle Eastern Ancestry|
1,181 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Waist circumference Partial Correlation (partial-r): 0.248 [0.1932, 0.3012] sex, age, birth date, deprivation index, 16 PCs
PPM010743 PSS008351|
South Asian Ancestry|
6,267 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Waist circumference Partial Correlation (partial-r): 0.255 [0.2317, 0.2781] sex, age, birth date, deprivation index, 16 PCs
PPM010744 PSS008128|
East Asian Ancestry|
1,802 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Waist circumference Partial Correlation (partial-r): 0.2068 [0.1619, 0.2508] sex, age, birth date, deprivation index, 16 PCs
PPM010745 PSS007915|
African Ancestry|
2,457 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Waist circumference Partial Correlation (partial-r): 0.1624 [0.1235, 0.2008] sex, age, birth date, deprivation index, 16 PCs
PPM010746 PSS009019|
African Ancestry|
3,868 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Waist circumference Partial Correlation (partial-r): 0.1264 [0.0952, 0.1574] 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
PSS007915 2,457 individuals African American or Afro-Caribbean Carribean UKB
PSS008573 1,181 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008128 1,802 individuals East Asian China (East Asia) UKB
PSS008351 6,267 individuals South Asian India (South Asia) UKB
PSS009019 3,868 individuals African unspecified Nigeria (West Africa) UKB
PSS009245 4,125 individuals European Poland (NE Europe) UKB
PSS009471 19,966 individuals European UK (+ Ireland) UKB
PSS008799 6,637 individuals European Italy (South Europe) UKB