Polygenic Score (PGS) ID: PGS002165

Predicted Trait
Reported Trait Cystatin C
Mapped Trait(s) cystatin C measurement (EFO_0004617)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_log_cystatinC
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 781,302
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM012167 PSS009441|
European Ancestry|
18,996 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cystatin C — — Partial Correlation (partial-r): 0.4072 [0.3953, 0.419] sex, age, birth date, deprivation index, 16 PCs —
PPM012168 PSS009215|
European Ancestry|
3,953 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cystatin C — — Partial Correlation (partial-r): 0.4276 [0.4017, 0.4528] sex, age, birth date, deprivation index, 16 PCs —
PPM012169 PSS008769|
European Ancestry|
6,319 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cystatin C — — Partial Correlation (partial-r): 0.371 [0.3495, 0.3921] sex, age, birth date, deprivation index, 16 PCs —
PPM012170 PSS008543|
Greater Middle Eastern Ancestry|
1,126 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cystatin C — — Partial Correlation (partial-r): 0.3446 [0.2916, 0.3956] sex, age, birth date, deprivation index, 16 PCs —
PPM012171 PSS008321|
South Asian Ancestry|
6,001 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cystatin C — — Partial Correlation (partial-r): 0.3009 [0.2777, 0.3238] sex, age, birth date, deprivation index, 16 PCs —
PPM012173 PSS007885|
African Ancestry|
2,342 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cystatin C — — Partial Correlation (partial-r): 0.181 [0.1414, 0.2201] sex, age, birth date, deprivation index, 16 PCs —
PPM012174 PSS008989|
African Ancestry|
3,658 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cystatin C — — Partial Correlation (partial-r): 0.1653 [0.1335, 0.1967] sex, age, birth date, deprivation index, 16 PCs —
PPM012172 PSS008098|
East Asian Ancestry|
1,718 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cystatin C — — Partial Correlation (partial-r): 0.2565 [0.2115, 0.3004] sex, age, birth date, deprivation index, 16 PCs —

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
PSS008769 — — 6,319 individuals — European Italy (South Europe) UKB —
PSS007885 — — 2,342 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008543 — — 1,126 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008989 — — 3,658 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009441 — — 18,996 individuals — European UK (+ Ireland) UKB —
PSS009215 — — 3,953 individuals — European Poland (NE Europe) UKB —
PSS008321 — — 6,001 individuals — South Asian India (South Asia) UKB —
PSS008098 — — 1,718 individuals — East Asian China (East Asia) UKB —