Polygenic Score (PGS) ID: PGS000675

Predicted Trait
Reported Trait C-reactive protein [mg/L]
Mapped Trait(s) C-reactive protein measurement (EFO_0004458)
Released in PGS Catalog: Feb. 3, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.C_reactive_protein
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
Variants
Original Genome Build hg19
Number of Variants 17,378
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)
Ancestry Distribution
Score Development/Training
European: 100%
255,256 individuals (100%)
PGS Evaluation
European: 45.5%
African: 18.2%
East Asian: 18.2%
South Asian: 18.2%
11 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
223,327 individuals European
(British)		 UKB — — — — Training
31,929 individuals European
(British)		 UKB — — — — Validation

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
PPM001438 PSS000653|
East Asian Ancestry|
1,077 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: C-reactive protein [mg/L] — — R²: 0.10659
Spearman's ρ: 0.274		 Age, sex, PCs(1-40) —
PPM001473 PSS000654|
European Ancestry|
23,534 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: C-reactive protein [mg/L] — — R²: 0.15954
Spearman's ρ: 0.346		 Age, sex, PCs(1-40) —
PPM001508 PSS000655|
South Asian Ancestry|
7,316 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: C-reactive protein [mg/L] — — R²: 0.13562
Spearman's ρ: 0.315		 Age, sex, PCs(1-40) —
PPM001543 PSS000656|
European Ancestry|
63,656 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: C-reactive protein [mg/L] — — R²: 0.14786
Spearman's ρ: 0.353		 Age, sex, PCs(1-40) —
PPM001593 PSS000801|
European Ancestry|
2,128 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: C-reactive protein [mg/L] — — Spearman's ρ: 0.254 Age, sex —
PPM001403 PSS000652|
African Ancestry|
6,006 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: C-reactive protein [mg/L] — — R²: 0.07691
Spearman's ρ: 0.196		 Age, sex, PCs(1-40) —
PPM007302 PSS007138|
European Ancestry|
23,721 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: C-reactive protein — — R²: 0.03906 [0.03434, 0.04378]
Incremental R2 (full-covars): 0.02747
PGS R2 (no covariates): 0.03496 [0.03048, 0.03945]		 age, sex, UKB array type, Genotype PCs —
PPM007303 PSS007139|
South Asian Ancestry|
7,404 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: C-reactive protein — — R²: 0.05308 [0.04342, 0.06274]
Incremental R2 (full-covars): 0.03091
PGS R2 (no covariates): 0.04237 [0.03364, 0.0511]		 age, sex, UKB array type, Genotype PCs —
PPM007304 PSS007140|
European Ancestry|
64,332 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: C-reactive protein — — R²: 0.03346 [0.03079, 0.03613]
Incremental R2 (full-covars): 0.02832
PGS R2 (no covariates): 0.03414 [0.03145, 0.03684]		 age, sex, UKB array type, Genotype PCs —
PPM007300 PSS007136|
African Ancestry|
6,088 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: C-reactive protein — — R²: 0.03482 [0.02607, 0.04358]
Incremental R2 (full-covars): 0.01008
PGS R2 (no covariates): 0.01186 [0.00663, 0.01709]		 age, sex, UKB array type, Genotype PCs —
PPM007301 PSS007137|
East Asian Ancestry|
1,611 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: C-reactive protein — — R²: 0.03926 [0.02122, 0.05729]
Incremental R2 (full-covars): 0.02473
PGS R2 (no covariates): 0.02923 [0.0135, 0.04496]		 age, sex, UKB array type, Genotype 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
PSS007136 — — 6,088 individuals — African unspecified — UKB —
PSS000652 — — 6,006 individuals — African unspecified — UKB —
PSS000653 — — 1,077 individuals — East Asian — UKB —
PSS000654 — — 23,534 individuals — European Non-British White UKB —
PSS000655 — — 7,316 individuals — South Asian — UKB —
PSS000656 — — 63,656 individuals — European
(British)		 — UKB —
PSS007138 — — 23,721 individuals — European non-white British ancestry UKB —
PSS007139 — — 7,404 individuals — South Asian — UKB —
PSS007140 — — 64,332 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS007137 — — 1,611 individuals — East Asian — UKB —
PSS000801 — — 2,128 individuals — European Participants self-identifying as white MESA —