Polygenic Score (PGS) ID: PGS003540

Predicted Trait
Reported Trait Impedance of whole body
Mapped Trait(s) whole body water mass (EFO_0009805)
Released in PGS Catalog: April 12, 2023
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Score Details

Score Construction
PGS Name cont-decay-log_impedance
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%
364,252 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
— 364,252 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
PPM017552 PSS010821|
European Ancestry|
4,059 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Impedance of whole body — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017468 PSS010905|
European Ancestry|
19,653 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Impedance of whole body — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017636 PSS010653|
European Ancestry|
6,373 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Impedance of whole body — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017720 PSS010569|
Greater Middle Eastern Ancestry|
1,123 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Impedance of whole body — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017804 PSS010233|
European Ancestry|
2,316 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Impedance of whole body — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017888 PSS010485|
South Asian Ancestry|
6,127 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Impedance of whole body — — partial-R2: 0.13 sex, age, deprivation index, PC1-16 —
PPM017972 PSS010401|
East Asian Ancestry|
1,770 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Impedance of whole body — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM018056 PSS010317|
African Ancestry|
2,405 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Impedance of whole body — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM018140 PSS010737|
African Ancestry|
3,770 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Impedance of whole body — — partial-R2: 0.03 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
PSS010401 — — 1,770 individuals,
34.0 % Male samples
 Mean = 52.4 years
Sd = 7.7 years		 East Asian Chinese UKB —
PSS010821 — — 4,059 individuals,
38.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —
PSS010569 — — 1,123 individuals,
60.0 % Male samples
 Mean = 52.0 years
Sd = 7.9 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010905 — — 19,653 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010317 — — 2,405 individuals,
36.0 % Male samples
 Mean = 52.4 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010737 — — 3,770 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010485 — — 6,127 individuals,
54.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010233 — — 2,316 individuals,
45.0 % Male samples
 Mean = 58.1 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010653 — — 6,373 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —