Polygenic Score (PGS) ID: PGS001947

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-PLR_log_cystatinC
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 84,459
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM010455 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): 0.3057 [0.2826, 0.3285] sex, age, birth date, deprivation index, 16 PCs
PPM010451 PSS009441|
European Ancestry|
18,996 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.418 [0.4062, 0.4297] sex, age, birth date, deprivation index, 16 PCs
PPM010452 PSS009215|
European Ancestry|
3,953 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.4317 [0.4059, 0.4568] sex, age, birth date, deprivation index, 16 PCs
PPM010454 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): 0.3385 [0.2852, 0.3897] sex, age, birth date, deprivation index, 16 PCs
PPM010457 PSS007885|
African Ancestry|
2,342 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.1917 [0.1522, 0.2306] sex, age, birth date, deprivation index, 16 PCs
PPM010458 PSS008989|
African Ancestry|
3,658 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.1856 [0.1541, 0.2168] sex, age, birth date, deprivation index, 16 PCs
PPM010453 PSS008769|
European Ancestry|
6,319 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cystatin C Partial Correlation (partial-r): 0.3864 [0.3652, 0.4072] sex, age, birth date, deprivation index, 16 PCs
PPM010456 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): 0.2689 [0.2242, 0.3125] 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
PSS008321 6,001 individuals South Asian India (South Asia) UKB
PSS008989 3,658 individuals African unspecified Nigeria (West Africa) UKB
PSS009215 3,953 individuals European Poland (NE Europe) UKB
PSS009441 18,996 individuals European UK (+ Ireland) UKB
PSS008098 1,718 individuals East Asian China (East Asia) UKB