Polygenic Score (PGS) ID: PGS000260

Predicted Trait
Reported Trait Lectin-like oxidized LDL receptor 1 (LOX-1) serum levels
Mapped Trait(s) blood protein measurement (EFO_0007937)
Additional Trait Information uniprot:P78380
Released in PGS: Oct. 19, 2020
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name LOX-1
Variants
Original Genome Build GRCh37
Number of Variants 552,046
Development Method
Name LDpred
Parameters HapMap3 SNPs with MAF >0.05, HWE P>1e-05, imputation quality>0.95, fraction of causal markers 0.1.
PGS Source
PGS Catalog Publication (PGP) ID PGP000089
Citation (link to publication) Folkersen L et al. Nat Metab (2020)

Contributing 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
21,758 individuals European 13 cohorts
  • EB
  • ,EpiHealth
  • ,IMPROVE
  • ,INTERVAL
  • ,LifeLines
  • ,MPP
  • ,NSPHS
  • ,ORCADES
  • ,PIVUS
  • ,STABILITY
  • ,STANLEY
  • ,ULSAM
  • ,VIS
Average per-protein sample size was 17,747

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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000681 PSS000364 PGP000089
Folkersen L et al. (2020)
Reported Trait: Lectin-like oxidized LDL receptor 1 (LOX-1) serum levels : 0.01745
R² difference (PGS+covariates vs. covariates only): 0.01045
age + sex + 10 genetic PCs The main manuscript further reports scores divided into genome-wide significant loci (major loci) and remaining polygenic loci, but this performance metric just reports the sum of both.

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000364 4,678 individuals European
(Swedish)
MDC