Polygenic Score (PGS) ID: PGS000698

Predicted Trait
Reported Trait Total protein [g/L]
Mapped Trait(s) total blood protein measurement (EFO_0004536)
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.Total_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 16,420
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: 40%
African: 20%
East Asian: 20%
South Asian: 20%
10 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
PPM001426 PSS000767|
African Ancestry|
5,573 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Total protein [g/L] — — R²: 0.04363
Spearman's ρ: 0.144		 Age, sex, PCs(1-40) —
PPM001531 PSS000770|
South Asian Ancestry|
6,687 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Total protein [g/L] — — R²: 0.10522
Spearman's ρ: 0.258		 Age, sex, PCs(1-40) —
PPM001566 PSS000771|
European Ancestry|
58,196 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Total protein [g/L] — — R²: 0.11218
Spearman's ρ: 0.284		 Age, sex, PCs(1-40) —
PPM001461 PSS000768|
East Asian Ancestry|
984 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Total protein [g/L] — — R²: 0.09275
Spearman's ρ: 0.247		 Age, sex, PCs(1-40) —
PPM001496 PSS000769|
European Ancestry|
21,516 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Total protein [g/L] — — R²: 0.11654
Spearman's ρ: 0.282		 Age, sex, PCs(1-40) —
PPM007415 PSS007201|
African Ancestry|
5,659 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Total protein — — R²: 0.01038 [0.00548, 0.01528]
Incremental R2 (full-covars): 0.00061
PGS R2 (no covariates): 0.02117 [0.01425, 0.0281]		 age, sex, UKB array type, Genotype PCs —
PPM007416 PSS007202|
East Asian Ancestry|
1,474 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Total protein — — R²: 0.04549 [0.0262, 0.06478]
Incremental R2 (full-covars): 0.00107
PGS R2 (no covariates): 0.05677 [0.03548, 0.07807]		 age, sex, UKB array type, Genotype PCs —
PPM007417 PSS007203|
European Ancestry|
21,730 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Total protein — — R²: 0.01493 [0.01194, 0.01792]
Incremental R2 (full-covars): 0.00167
PGS R2 (no covariates): 0.07937 [0.07293, 0.08581]		 age, sex, UKB array type, Genotype PCs —
PPM007418 PSS007204|
South Asian Ancestry|
6,788 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Total protein — — R²: 0.01363 [0.00853, 0.01873]
Incremental R2 (full-covars): 0.00134
PGS R2 (no covariates): 0.0679 [0.05715, 0.07866]		 age, sex, UKB array type, Genotype PCs —
PPM007419 PSS007205|
European Ancestry|
59,024 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Total protein — — R²: 0.00668 [0.00545, 0.0079]
Incremental R2 (full-covars): 0.00176
PGS R2 (no covariates): 0.08081 [0.07687, 0.08476]		 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
PSS007201 — — 5,659 individuals — African unspecified — UKB —
PSS007202 — — 1,474 individuals — East Asian — UKB —
PSS007203 — — 21,730 individuals — European non-white British ancestry UKB —
PSS007204 — — 6,788 individuals — South Asian — UKB —
PSS007205 — — 59,024 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS000767 — — 5,573 individuals — African unspecified — UKB —
PSS000768 — — 984 individuals — East Asian — UKB —
PSS000769 — — 21,516 individuals — European Non-British White UKB —
PSS000770 — — 6,687 individuals — South Asian — UKB —
PSS000771 — — 58,196 individuals — European
(British)		 — UKB —