Polygenic Score (PGS) ID: PGS003552

Predicted Trait
Reported Trait Sex hormone binding globulin (SHBG)
Mapped Trait(s) sex hormone-binding globulin measurement (EFO_0004696)
Released in PGS Catalog: April 12, 2023
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Score Details

Score Construction
PGS Name cont-decay-log_SHBG
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%
320,421 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
— 320,421 individuals,
0.47 % 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
PPM017480 PSS010918|
European Ancestry|
17,359 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sex hormone binding globulin (SHBG) — — partial-R2: 0.18 sex, age, deprivation index, PC1-16 —
PPM017648 PSS010666|
European Ancestry|
5,599 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sex hormone binding globulin (SHBG) — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017732 PSS010582|
Greater Middle Eastern Ancestry|
996 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sex hormone binding globulin (SHBG) — — partial-R2: 0.13 sex, age, deprivation index, PC1-16 —
PPM017816 PSS010246|
European Ancestry|
2,029 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sex hormone binding globulin (SHBG) — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017900 PSS010498|
South Asian Ancestry|
5,386 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sex hormone binding globulin (SHBG) — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017984 PSS010414|
East Asian Ancestry|
1,538 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sex hormone binding globulin (SHBG) — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM018068 PSS010330|
African Ancestry|
2,129 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sex hormone binding globulin (SHBG) — — partial-R2: 0.04 sex, age, deprivation index, PC1-16 —
PPM018152 PSS010750|
African Ancestry|
3,347 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sex hormone binding globulin (SHBG) — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM017564 PSS010834|
European Ancestry|
3,551 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Sex hormone binding globulin (SHBG) — — partial-R2: 0.14 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
PSS010750 — — 3,347 individuals,
47.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010498 — — 5,386 individuals,
55.0 % Male samples
 Mean = 53.2 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010918 — — 17,359 individuals,
47.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010246 — — 2,029 individuals,
46.0 % Male samples
 Mean = 58.1 years
Sd = 7.0 years		 European Ashkenazi UKB —
PSS010666 — — 5,599 individuals,
46.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010414 — — 1,538 individuals,
33.0 % Male samples
 Mean = 52.5 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010834 — — 3,551 individuals,
39.0 % Male samples
 Mean = 54.4 years
Sd = 7.5 years		 European Polish UKB —
PSS010582 — — 996 individuals,
60.0 % Male samples
 Mean = 51.9 years
Sd = 7.9 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010330 — — 2,129 individuals,
37.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —