Polygenic Score (PGS) ID: PGS000283

Predicted Trait
Reported Trait Spondin-1 (SPON1) serum levels
Mapped Trait(s) blood protein measurement (EFO_0007937)
Additional Trait Information uniprot:Q9HCB6
Released in PGS Catalog: Oct. 19, 2020
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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 SPON1
Development Method
Name LDpred
Parameters HapMap3 SNPs with MAF >0.05, HWE P>1e-05, imputation quality>0.95, fraction of causal markers 0.03.
Variants
Original Genome Build GRCh37
Number of Variants 552,703
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000089
Citation (link to publication) Folkersen L et al. Nat Metab (2020)
Ancestry Distribution
Score Development/Training
European: 100%
21,758 individuals (100%)
PGS Evaluation
European: 100%
1 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
— 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) 		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
PPM000706 PSS000364|
European Ancestry|
4,678 individuals
 PGP000089 |
Folkersen L et al. Nat Metab (2020)
 Reported Trait: Spondin-1 (SPON1) serum levels — — R²: 0.06873
R² difference (PGS+covariates vs. covariates only): 0.02773		 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) 		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 —