Polygenic Score (PGS) ID: PGS003528

Predicted Trait
Reported Trait Cystatin C
Mapped Trait(s) cystatin C measurement (EFO_0004617)
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_cystatinC
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%
353,524 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
— 353,524 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
PPM017456 PSS010891|
European Ancestry|
19,120 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Cystatin C — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017540 PSS010807|
European Ancestry|
3,942 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Cystatin C — — partial-R2: 0.18 sex, age, deprivation index, PC1-16 —
PPM017624 PSS010639|
European Ancestry|
6,167 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Cystatin C — — partial-R2: 0.14 sex, age, deprivation index, PC1-16 —
PPM017708 PSS010555|
Greater Middle Eastern Ancestry|
1,097 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Cystatin C — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017792 PSS010219|
European Ancestry|
2,236 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Cystatin C — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017876 PSS010471|
South Asian Ancestry|
5,948 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Cystatin C — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017960 PSS010387|
East Asian Ancestry|
1,707 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Cystatin C — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM018044 PSS010303|
African Ancestry|
2,330 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Cystatin C — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018128 PSS010723|
African Ancestry|
3,629 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Cystatin C — — 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
PSS010303 — — 2,330 individuals,
37.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010723 — — 3,629 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010471 — — 5,948 individuals,
54.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010219 — — 2,236 individuals,
45.0 % Male samples
 Mean = 58.1 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010891 — — 19,120 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010639 — — 6,167 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010387 — — 1,707 individuals,
33.0 % Male samples
 Mean = 52.4 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010807 — — 3,942 individuals,
38.0 % Male samples
 Mean = 54.4 years
Sd = 7.5 years		 European Polish UKB —
PSS010555 — — 1,097 individuals,
60.0 % Male samples
 Mean = 51.9 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —