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
Variants
Original Genome Build GRCh37
Number of Variants 33
Development Method
Name LD Clumping, PRSice-2
Parameters R^2=0.13, p=1.27e-17
PGS Source
PGS Catalog Publication (PGP) ID PGP000110
Citation (link to publication) Bossini-Castillo L et al. Ann Rheum Dis (2020)

Contributing Samples

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

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
PPM000968 PSS000489 PGP000110
Bossini-Castillo L et al. (2020)
Reported Trait: Systemic sclerosis AUROC: 0.644 *Some overlap with score development and testing samples
PPM000969 PSS000489 PGP000110
Bossini-Castillo L et al. (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
PPM000970 PSS000489 PGP000110
Bossini-Castillo L et al. (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

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