Polygenic Score (PGS) ID: PGS002201

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-ldpred2_log_waist_circ
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 984,035
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
PPM012455 PSS009471|
European Ancestry|
19,966 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Waist circumference — — Partial Correlation (partial-r): 0.3243 [0.3118, 0.3367] sex, age, birth date, deprivation index, 16 PCs —
PPM012456 PSS009245|
European Ancestry|
4,125 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Waist circumference — — Partial Correlation (partial-r): 0.3197 [0.292, 0.3469] sex, age, birth date, deprivation index, 16 PCs —
PPM012457 PSS008799|
European Ancestry|
6,637 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Waist circumference — — Partial Correlation (partial-r): 0.3066 [0.2846, 0.3283] sex, age, birth date, deprivation index, 16 PCs —
PPM012458 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): 0.2581 [0.2036, 0.311] sex, age, birth date, deprivation index, 16 PCs —
PPM012460 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): 0.2159 [0.1712, 0.2597] sex, age, birth date, deprivation index, 16 PCs —
PPM012461 PSS007915|
African Ancestry|
2,457 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Waist circumference — — Partial Correlation (partial-r): 0.1768 [0.138, 0.215] sex, age, birth date, deprivation index, 16 PCs —
PPM012462 PSS009019|
African Ancestry|
3,868 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Waist circumference — — Partial Correlation (partial-r): 0.1284 [0.0972, 0.1593] sex, age, birth date, deprivation index, 16 PCs —
PPM012459 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): 0.2563 [0.2329, 0.2793] 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 —