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
Variants
Original Genome Build hg19
Number of Variants 16,420
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
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%
5 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
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
PPM001496 PSS000769|
European Ancestry|
21,516 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Total protein [g/L] : 0.11654
Spearman's ρ: 0.282
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] : 0.09275
Spearman's ρ: 0.247
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] : 0.11218
Spearman's ρ: 0.284
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] : 0.10522
Spearman's ρ: 0.258
Age, sex, PCs(1-40)
PPM001426 PSS000767|
African Ancestry|
5,573 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Total protein [g/L] : 0.04363
Spearman's ρ: 0.144
Age, sex, PCs(1-40)

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
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