PGS Publication: PGP000789

Publication Information (EuropePMC)
Title Multi-population genome-wide association study implicates immune and non-immune factors in pediatric steroid-sensitive nephrotic syndrome.
PubMed ID 37120605(Europe PMC)
doi 10.1038/s41467-023-37985-w
Publication Date April 29, 2023
Journal Nat Commun
Author(s) Barry A, McNulty MT, Jia X, Gupta Y, Debiec H, Luo Y, Nagano C, Horinouchi T, Jung S, Colucci M, Ahram DF, Mitrotti A, Sinha A, Teeninga N, Jin G, Shril S, Caridi G, Bodria M, Lim TY, Westland R, Zanoni F, Marasa M, Turudic D, Giordano M, Gesualdo L, Magistroni R, Pisani I, Fiaccadori E, Reiterova J, Maringhini S, Morello W, Montini G, Weng PL, Scolari F, Saraga M, Tasic V, Santoro D, van Wijk JAE, Milošević D, Kawai Y, Kiryluk K, Pollak MR, Gharavi A, Lin F, Simœs E Silva AC, Loos RJF, Kenny EE, Schreuder MF, Zurowska A, Dossier C, Ariceta G, Drozynska-Duklas M, Hogan J, Jankauskiene A, Hildebrandt F, Prikhodina L, Song K, Bagga A, Cheong H, Ghiggeri GM, Vachvanichsanong P, Nozu K, Lee D, Vivarelli M, Raychaudhuri S, Tokunaga K, Sanna-Cherchi S, Ronco P, Iijima K, Sampson MG.
Released in PGS Catalog: April 13, 2026

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS012539
(pSSNS)
 PGP000789 |
Barry A et al. Nat Commun (2023)
 Pediatric steroid-sensitive nephrotic syndrome nephrotic syndrome 1,081,086
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS012539/ScoringFiles/PGS012539.txt.gz

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) 		Evaluated Score 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 PGS012539
(pSSNS)
 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 PGS012539
(pSSNS)
 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 —