Polygenic Score (PGS) ID: PGS003556

Predicted Trait
Reported Trait Whole body water mass
Mapped Trait(s) whole body water mass (EFO_0009805)
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_water_mass
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%
364,426 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
— 364,426 individuals,
0.46 % Male samples
 European UKB — Mean = 56.8 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
PPM017484 PSS010922|
European Ancestry|
19,662 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body water mass — — partial-R2: 0.2 sex, age, deprivation index, PC1-16 —
PPM017568 PSS010838|
European Ancestry|
4,063 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body water mass — — partial-R2: 0.2 sex, age, deprivation index, PC1-16 —
PPM017652 PSS010670|
European Ancestry|
6,377 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body water mass — — partial-R2: 0.18 sex, age, deprivation index, PC1-16 —
PPM017736 PSS010586|
Greater Middle Eastern Ancestry|
1,124 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body water mass — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017820 PSS010250|
European Ancestry|
2,318 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body water mass — — partial-R2: 0.19 sex, age, deprivation index, PC1-16 —
PPM018072 PSS010334|
African Ancestry|
2,408 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body water mass — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM018156 PSS010754|
African Ancestry|
3,773 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body water mass — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM017904 PSS010502|
South Asian Ancestry|
6,134 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body water mass — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017988 PSS010418|
East Asian Ancestry|
1,770 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Whole body water mass — — partial-R2: 0.09 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
PSS010334 — — 2,408 individuals,
36.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010754 — — 3,773 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010502 — — 6,134 individuals,
54.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010922 — — 19,662 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010250 — — 2,318 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010670 — — 6,377 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010418 — — 1,770 individuals,
34.0 % Male samples
 Mean = 52.4 years
Sd = 7.7 years		 East Asian Chinese UKB —
PSS010838 — — 4,063 individuals,
38.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —
PSS010586 — — 1,124 individuals,
60.0 % Male samples
 Mean = 52.0 years
Sd = 7.9 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —