Polygenic Score (PGS) ID: PGS003539

Predicted Trait
Reported Trait IGF-1
Mapped Trait(s) IGF-1 measurement (EFO_0004627)
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_IGF1
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%
351,649 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
— 351,649 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
PPM017551 PSS010820|
European Ancestry|
3,924 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.13 sex, age, deprivation index, PC1-16 —
PPM017467 PSS010904|
European Ancestry|
19,017 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017635 PSS010652|
European Ancestry|
6,139 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.13 sex, age, deprivation index, PC1-16 —
PPM017719 PSS010568|
Greater Middle Eastern Ancestry|
1,089 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017803 PSS010232|
European Ancestry|
2,227 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.17 sex, age, deprivation index, PC1-16 —
PPM017887 PSS010484|
South Asian Ancestry|
5,908 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM017971 PSS010400|
East Asian Ancestry|
1,699 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM018055 PSS010316|
African Ancestry|
2,316 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018139 PSS010736|
African Ancestry|
3,608 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: IGF-1 — — partial-R2: 0.04 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
PSS010400 — — 1,699 individuals,
33.0 % Male samples
 Mean = 52.4 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010232 — — 2,227 individuals,
45.0 % Male samples
 Mean = 58.1 years
Sd = 7.0 years		 European Ashkenazi UKB —
PSS010820 — — 3,924 individuals,
38.0 % Male samples
 Mean = 54.4 years
Sd = 7.5 years		 European Polish UKB —
PSS010568 — — 1,089 individuals,
60.0 % Male samples
 Mean = 51.9 years
Sd = 7.9 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010316 — — 2,316 individuals,
37.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010736 — — 3,608 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010484 — — 5,908 individuals,
54.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010904 — — 19,017 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010652 — — 6,139 individuals,
45.0 % Male samples
 Mean = 54.4 years
Sd = 8.4 years		 European Italian UKB —