Polygenic Score (PGS) ID: PGS003525

Predicted Trait
Reported Trait Body mass index (BMI)
Mapped Trait(s) body mass index (EFO_0004340)
Released in PGS Catalog: April 12, 2023
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name cont-decay-log_BMI
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%
369,738 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
369,738 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
PPM017453 PSS010888|
European Ancestry|
19,935 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Body mass index (BMI) partial-R2: 0.13 sex, age, deprivation index, PC1-16
PPM017537 PSS010804|
European Ancestry|
4,114 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Body mass index (BMI) partial-R2: 0.13 sex, age, deprivation index, PC1-16
PPM017621 PSS010636|
European Ancestry|
6,459 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Body mass index (BMI) partial-R2: 0.13 sex, age, deprivation index, PC1-16
PPM017705 PSS010552|
Greater Middle Eastern Ancestry|
1,149 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Body mass index (BMI) partial-R2: 0.08 sex, age, deprivation index, PC1-16
PPM017789 PSS010216|
European Ancestry|
2,344 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Body mass index (BMI) partial-R2: 0.12 sex, age, deprivation index, PC1-16
PPM017873 PSS010468|
South Asian Ancestry|
6,093 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Body mass index (BMI) partial-R2: 0.09 sex, age, deprivation index, PC1-16
PPM017957 PSS010384|
East Asian Ancestry|
1,787 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Body mass index (BMI) partial-R2: 0.06 sex, age, deprivation index, PC1-16
PPM018041 PSS010300|
African Ancestry|
2,431 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Body mass index (BMI) partial-R2: 0.05 sex, age, deprivation index, PC1-16
PPM018125 PSS010720|
African Ancestry|
3,830 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Body mass index (BMI) partial-R2: 0.02 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
PSS010720 3,830 individuals,
46.0 % Male samples
Mean = 51.9 years
Sd = 8.1 years
African unspecified Nigerian UKB
PSS010468 6,093 individuals,
53.0 % Male samples
Mean = 53.3 years
Sd = 8.4 years
South Asian Indian UKB
PSS010888 19,935 individuals,
46.0 % Male samples
Mean = 56.9 years
Sd = 7.9 years
European white British UKB
PSS010216 2,344 individuals,
45.0 % Male samples
Mean = 58.1 years
Sd = 7.1 years
European Ashkenazi UKB
PSS010636 6,459 individuals,
45.0 % Male samples
Mean = 54.5 years
Sd = 8.4 years
European Italian UKB
PSS010384 1,787 individuals,
33.0 % Male samples
Mean = 52.4 years
Sd = 7.7 years
East Asian Chinese UKB
PSS010804 4,114 individuals,
38.0 % Male samples
Mean = 54.3 years
Sd = 7.5 years
European Polish UKB
PSS010552 1,149 individuals,
60.0 % Male samples
Mean = 52.0 years
Sd = 8.0 years
Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB
PSS010300 2,431 individuals,
36.0 % Male samples
Mean = 52.5 years
Sd = 8.1 years
African American or Afro-Caribbean Caribbean UKB