Polygenic Score (PGS) ID: PGS003555

Predicted Trait
Reported Trait Waist circumference
Mapped Trait(s) waist circumference (EFO_0004342)
Released in PGS Catalog: April 12, 2023
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Terms and Licenses
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Score Details

Score Construction
PGS Name cont-decay-log_waist_circ
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
370,312 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 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
— 370,312 individuals,
0.46 % Male samples
 European UKB — Mean = 56.9 years
Sd = 8.0 years		 — white British —

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
PPM017903 PSS010501|
South Asian Ancestry|
6,215 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Waist circumference — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM017483 PSS010921|
European Ancestry|
19,954 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Waist circumference — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017567 PSS010837|
European Ancestry|
4,114 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Waist circumference — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017651 PSS010669|
European Ancestry|
6,474 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Waist circumference — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017735 PSS010585|
Greater Middle Eastern Ancestry|
1,152 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Waist circumference — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM017819 PSS010249|
European Ancestry|
2,344 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Waist circumference — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017987 PSS010417|
East Asian Ancestry|
1,790 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Waist circumference — — partial-R2: 0.04 sex, age, deprivation index, PC1-16 —
PPM018071 PSS010333|
African Ancestry|
2,444 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Waist circumference — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018155 PSS010753|
African Ancestry|
3,839 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Waist circumference — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —

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
PSS010753 — — 3,839 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010501 — — 6,215 individuals,
54.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010921 — — 19,954 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010249 — — 2,344 individuals,
45.0 % Male samples
 Mean = 58.1 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010669 — — 6,474 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010417 — — 1,790 individuals,
33.0 % Male samples
 Mean = 52.4 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010837 — — 4,114 individuals,
38.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —
PSS010585 — — 1,152 individuals,
60.0 % Male samples
 Mean = 52.0 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010333 — — 2,444 individuals,
36.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —