Polygenic Score (PGS) ID: PGS000341

Predicted Trait
Reported Trait Systemic sclerosis
Mapped Trait(s) systemic scleroderma (EFO_0000717)
Released in PGS Catalog: Nov. 20, 2020
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Score Details

Score Construction
PGS Name GRS33_SSc
Development Method
Name LD Clumping, PRSice-2
Parameters R^2=0.13, p=1.27e-17
Variants
Original Genome Build GRCh37
Number of Variants 33
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000110
Citation (link to publication) Bossini-Castillo L et al. Ann Rheum Dis (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
26,679 individuals (100%)
Score Development/Training
European: 100%
971 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST009131
Europe PMC: 31672989
 26,679 individuals European 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
—
[
  • 400 cases
  • , 571 controls
]
 European PRECISESADS The diagnosttic criteria for each disease was based on gold-standard clinical guidelines. — — — —

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
PPM000970 PSS000489|
European Ancestry|
339 individuals
 PGP000110 |
Bossini-Castillo L et al. Ann Rheum Dis (2020)
 Reported Trait: Systemic sclerosis — AUROC: 0.787 [0.73, 0.84] — Systemic sclerosis status, age and immune cell counts of: memory B cells, resting NK cells, M0 macrophages and activated dendritic cells *Some overlap with score development and testing samples
PPM000969 PSS000489|
European Ancestry|
339 individuals
 PGP000110 |
Bossini-Castillo L et al. Ann Rheum Dis (2020)
 Reported Trait: Systemic sclerosis — AUROC: 0.722 — Systemic sclerosis status and immune cell counts of: memory B cells, resting NK cells, M0 macrophages and activated dendritic cells *Some overlap with score development and testing samples
PPM000968 PSS000489|
European Ancestry|
339 individuals
 PGP000110 |
Bossini-Castillo L et al. Ann Rheum Dis (2020)
 Reported Trait: Systemic sclerosis — AUROC: 0.644 — — *Some overlap with score development and testing samples

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
PSS000489 The diagnosttic criteria for each disease was based on gold-standard clinical guidelines. — 339 individuals — European
(Spanish)		 — PRECISESADS —