Trait: systemic scleroderma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000717
Description A chronic disorder, possibly autoimmune, marked by excessive production of collagen which results in hardening and thickening of body tissues. The two types of systemic scleroderma, limited cutaneous and diffuse cutaneous are classified with focus on the extent of affected skin. A relationship exists between the extent of skin area affected and degree of internal organ/system involvement. Systemic scleroderma can manifest itself in pulmonary fibrosis, Raynaud's syndrome, digestive system telangiectasias, renal hypertension and/or pulmonary hypertension. [NCIT: C72070]
Trait category
Immune system disorder
Synonyms 24 synonyms
  • PSS (progressive systemic sclerosis)
  • PSS - Progressive systemic sclerosis
  • Progressive systemic sclerosis
  • SS - Systemic sclerosis
  • SSc
  • SSc, diffuse sclerosis
  • Scleroderma
  • Scleroderma
  • Scleroderma (& [systemic sclerosis])
  • Scleroderma syndrome
  • Scleroderma, Systemic
  • Scleroderma, diffuse
  • Scleroderma, systemic
  • Sclerosis, Systemic
  • Systemic Scleroderma
  • Systemic sclerosis
  • Systemic sclerosis (disorder)
  • Thibierge-Weissenbach syndrome
  • diffuse Scleroderma
  • diffuse sclerosis
  • progressive systemic sclerosis
  • systemic Scleroderma
  • systemic scleroderma
  • systemic sclerosis
Mapped terms 22 mapped terms
  • DOID:418
  • GARD:9748
  • ICD10:M34
  • ICD9:710.1
  • MEDGEN:19897
  • MESH:D012595
  • MONDO:0005100
  • MeSH:D012595
  • MedDRA:10036814
  • MedDRA:10042953
  • MedDRA:10078638
  • NANDO:1200277
  • NANDO:2200429
  • NCIT:C72070
  • NCIt:C72070
  • NORD:2007
  • Orphanet:90291
  • SCTID:89155008
  • SNOMEDCT:444133002
  • SNOMEDCT:89155008
  • UMLS:C0036421
  • icd11.foundation:1084365812

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Additional Diverse Ancestries
Not Reported
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)
PGS000341
(GRS33_SSc)
 PGP000110 |
Bossini-Castillo L et al. Ann Rheum Dis (2020)
 Systemic sclerosis systemic scleroderma 33
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000341/ScoringFiles/PGS000341.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
PPM000970 PGS000341
(GRS33_SSc)
 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 PGS000341
(GRS33_SSc)
 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 PGS000341
(GRS33_SSc)
 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 —