Polygenic Score (PGS) ID: PGS000228

Predicted Trait
Reported Trait Cathepsin L1 (CTSL1) serum levels
Mapped Trait(s) blood protein measurement (EFO_0007937)
Additional Trait Information uniprot:P07711
Released in PGS Catalog: Oct. 19, 2020
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Score Details

Score Construction
PGS Name CTSL1
Variants
Original Genome Build GRCh37
Number of Variants 552,084
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.
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
PPM000712 PSS000364 PGP000089
Folkersen L et al. (2020) 		Reported Trait: Cathepsin L1 (CTSL1) serum levels — — R²: 0.09752
R² difference (PGS+covariates vs. covariates only): 0.03852		 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 —