Polygenic Score (PGS) ID: PGS012539

Predicted Trait
Reported Trait Pediatric steroid-sensitive nephrotic syndrome
Mapped Trait(s) nephrotic syndrome (MONDO_0005377)
Released in PGS Catalog: April 13, 2026
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Score Details

Score Construction
PGS Name pSSNS
Development Method
Name PRS-CSx (v7-29-2021)
Parameters We generated a PRS using 1974 cases and 20,039 controls from the GWAS of European, East Asian, African, and South Asian populations using PRS-CSx. Gamma-gamma prior a=1, b=1, global shrinkage parameter = 1E-4
Variants
Original Genome Build hg38
Number of Variants 1,081,086
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000789
Citation (link to publication) Barry A et al. Nat Commun (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • European
  • East Asian
  • African
  • South Asian
22,013 individuals (100%)
Score Development/Training
European: 100%
2,256 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 1,974 cases
  • , 20,039 controls
]
 European, East Asian, African unspecified, South Asian NR
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
—
[
  • 250 cases
  • , 2,006 controls
]
 European NR same as above — — — —

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
PPM030645 PSS012215|
European Ancestry|
233 individuals
 PGP000789 |
Barry A et al. Nat Commun (2023)
 Reported Trait: Age of onset of Pediatric Steroid-Sensitive Nephrotic Syndrome β: -2.05 (0.68) — — sex, relapse pattern, 4PCs —
PPM030644 PSS012214|
European Ancestry|
565 individuals
 PGP000789 |
Barry A et al. Nat Commun (2023)
 Reported Trait: Pediatric Steroid-Sensitive Nephrotic Syndrome — AUROC: 0.73 F-measure: 0.35 — While our goal of this analysis was to explore the relationships between the PRS and clinical correlates within case cohorts, not case/control prediction, we used prediction accuracy to optimize the gamma-gamma priors and the global shrinkage parameter used in the PRS-CSx model. We varied the hyper parameters and chose the model with the best prediction accuracy (F-measure; Supp. Table 15). The regression betas from the best model were used to weight the population-specific PRS.

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
PSS012214 same as above —
[
  • 63 cases
  • , 502 controls
]
 — European — NR —
PSS012215 — — 233 individuals — European — NR —