Trait: vasculitis

Trait Information
Identifier MONDO_0018882
Description Vasculitis represents a clinically heterogenous group of diseases of multifactorial etiology characterized by inflammation of either large-sized vessels (large-vessel vasculitis, e.g. Giant-cell arteritis and Takayasu arteritis), medium-sized vessels (medium-vessel vasculitis e.g. polyarteritis nodosa and Kawasaki disease), or small-sized vessels (small-vessel vasculitis, e.g. granulomatosis with polyangiitis, microscopic polyangiitis, immunoglobulin A vasculitis, and cutaneous leukocytoclastic angiitis). Vasculitis occurs at any age, may be acute or chronic, and manifests with general symptoms such as fever, weight loss and fatigue, as well as more specific clinical signs depending on the type of vessels and organs affected. The degree of severity is variable, ranging from life or sight threatening disease (e.g. Behcet disease) to relatively minor skin disease. [Orphanet: 52759]
Trait categories
Cardiovascular disease
Other disease
Synonym systemic vasculitis
Child trait(s) phlebitis

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:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Note: This table shows PGS for child terms of "vasculitis" in the EFO hierarchy.
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)
PGS000961
(GBE_HC987)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Phlebitis and thrombophlebitis (time-to-event) Thrombophlebitis,
phlebitis		 1,143
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000961/ScoringFiles/PGS000961.txt.gz
PGS001844
(portability-PLR_451)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Phlebitis and thrombophlebitis Thrombophlebitis,
phlebitis		 431
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001844/ScoringFiles/PGS001844.txt.gz
PGS002056
(portability-ldpred2_451)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Phlebitis and thrombophlebitis Thrombophlebitis,
phlebitis		 114,679
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002056/ScoringFiles/PGS002056.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
PPM007629 PGS000961
(GBE_HC987)
 PSS004756|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE phlebitis and thrombophlebitis — AUROC: 0.63235 [0.59259, 0.67211] R²: 0.02507
Incremental AUROC (full-covars): 0.00771
PGS R2 (no covariates): 0.00171
PGS AUROC (no covariates): 0.53507 [0.4917, 0.57844]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007630 PGS000961
(GBE_HC987)
 PSS004757|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE phlebitis and thrombophlebitis — AUROC: 0.66631 [0.52571, 0.80691] R²: 0.04004
Incremental AUROC (full-covars): -0.006
PGS R2 (no covariates): 4e-05
PGS AUROC (no covariates): 0.50807 [0.37643, 0.63972]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007631 PGS000961
(GBE_HC987)
 PSS004758|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE phlebitis and thrombophlebitis — AUROC: 0.66949 [0.64981, 0.68916] R²: 0.04365
Incremental AUROC (full-covars): 0.03126
PGS R2 (no covariates): 0.01428
PGS AUROC (no covariates): 0.59647 [0.57489, 0.61804]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007632 PGS000961
(GBE_HC987)
 PSS004759|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE phlebitis and thrombophlebitis — AUROC: 0.63064 [0.58623, 0.67504] R²: 0.02362
Incremental AUROC (full-covars): 0.00728
PGS R2 (no covariates): 0.0042
PGS AUROC (no covariates): 0.55251 [0.5057, 0.59933]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007633 PGS000961
(GBE_HC987)
 PSS004760|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE phlebitis and thrombophlebitis — AUROC: 0.64191 [0.63056, 0.65326] R²: 0.03444
Incremental AUROC (full-covars): 0.03745
PGS R2 (no covariates): 0.01698
PGS AUROC (no covariates): 0.58931 [0.57719, 0.60143]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009642 PGS001844
(portability-PLR_451)
 PSS009319|
European Ancestry|
18,164 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): 0.0525 [0.038, 0.067] sex, age, birth date, deprivation index, 16 PCs —
PPM009643 PGS001844
(portability-PLR_451)
 PSS009093|
European Ancestry|
3,734 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): 0.068 [0.036, 0.1] sex, age, birth date, deprivation index, 16 PCs —
PPM009644 PGS001844
(portability-PLR_451)
 PSS008647|
European Ancestry|
6,014 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): 0.0468 [0.0215, 0.072] sex, age, birth date, deprivation index, 16 PCs —
PPM009645 PGS001844
(portability-PLR_451)
 PSS008421|
Greater Middle Eastern Ancestry|
1,102 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): 0.0855 [0.0261, 0.1444] sex, age, birth date, deprivation index, 16 PCs —
PPM009646 PGS001844
(portability-PLR_451)
 PSS008201|
South Asian Ancestry|
5,719 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): 0.0329 [0.0069, 0.0588] sex, age, birth date, deprivation index, 16 PCs —
PPM009647 PGS001844
(portability-PLR_451)
 PSS007983|
East Asian Ancestry|
1,622 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): -0.0182 [-0.0671, 0.0308] sex, age, birth date, deprivation index, 16 PCs —
PPM009648 PGS001844
(portability-PLR_451)
 PSS007766|
African Ancestry|
2,283 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): 0.0073 [-0.0339, 0.0485] sex, age, birth date, deprivation index, 16 PCs —
PPM009649 PGS001844
(portability-PLR_451)
 PSS008870|
African Ancestry|
3,611 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): -0.0032 [-0.0359, 0.0295] sex, age, birth date, deprivation index, 16 PCs —
PPM011310 PGS002056
(portability-ldpred2_451)
 PSS009319|
European Ancestry|
18,164 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): 0.0561 [0.0416, 0.0706] sex, age, birth date, deprivation index, 16 PCs —
PPM011311 PGS002056
(portability-ldpred2_451)
 PSS009093|
European Ancestry|
3,734 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): 0.0729 [0.0408, 0.1048] sex, age, birth date, deprivation index, 16 PCs —
PPM011312 PGS002056
(portability-ldpred2_451)
 PSS008647|
European Ancestry|
6,014 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): 0.0469 [0.0216, 0.0722] sex, age, birth date, deprivation index, 16 PCs —
PPM011313 PGS002056
(portability-ldpred2_451)
 PSS008421|
Greater Middle Eastern Ancestry|
1,102 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): 0.085 [0.0256, 0.1439] sex, age, birth date, deprivation index, 16 PCs —
PPM011314 PGS002056
(portability-ldpred2_451)
 PSS008201|
South Asian Ancestry|
5,719 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): 0.0284 [0.0025, 0.0543] sex, age, birth date, deprivation index, 16 PCs —
PPM011315 PGS002056
(portability-ldpred2_451)
 PSS007983|
East Asian Ancestry|
1,622 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): -0.0188 [-0.0677, 0.0302] sex, age, birth date, deprivation index, 16 PCs —
PPM011316 PGS002056
(portability-ldpred2_451)
 PSS007766|
African Ancestry|
2,283 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): -0.001 [-0.0422, 0.0402] sex, age, birth date, deprivation index, 16 PCs —
PPM011317 PGS002056
(portability-ldpred2_451)
 PSS008870|
African Ancestry|
3,611 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Phlebitis and thrombophlebitis — — Partial Correlation (partial-r): -0.0043 [-0.037, 0.0284] sex, age, birth date, deprivation index, 16 PCs —

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
PSS009093 — — 3,734 individuals — European Poland (NE Europe) UKB —
PSS008421 — — 1,102 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009319 — — 18,164 individuals — European UK (+ Ireland) UKB —
PSS008647 — — 6,014 individuals — European Italy (South Europe) UKB —
PSS008201 — — 5,719 individuals — South Asian India (South Asia) UKB —
PSS008870 — — 3,611 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007983 — — 1,622 individuals — East Asian China (East Asia) UKB —
PSS007766 — — 2,283 individuals — African American or Afro-Caribbean Carribean UKB —
PSS004756 — —
[
  • 173 cases
  • , 6,324 controls
]
 — African unspecified — UKB —
PSS004757 — —
[
  • 15 cases
  • , 1,689 controls
]
 — East Asian — UKB —
PSS004758 — —
[
  • 710 cases
  • , 24,195 controls
]
 — European non-white British ancestry UKB —
PSS004759 — —
[
  • 145 cases
  • , 7,686 controls
]
 — South Asian — UKB —
PSS004760 — —
[
  • 2,312 cases
  • , 65,113 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)