Trait: thrombotic disease

Trait Information
Identifier MONDO_0000831
Description The formation of a blood clot in the lumen of a vessel or heart chamber; causes include coagulation disorders and vascular endothelial injury. [NCIT: C26891]
Trait category
Cardiovascular disease
Synonyms 8 synonyms
  • Clots, blood
  • Thromboses
  • blood Clots
  • blood clot
  • clot, blood
  • thrombosis
  • thrombotic disorder
  • thrombus
Mapped terms 7 mapped terms
  • DOID:0060903
  • ICD9:453.9
  • MEDGEN:21160
  • MESH:D013927
  • NCIT:C26891
  • SCTID:439127006
  • UMLS:C0040053

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
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)
PGS000930
(GBE_BIN_FC3006152)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Blood clot (diagnosed by doctor) thrombotic disease 118
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000930/ScoringFiles/PGS000930.txt.gz
PGS000931
(GBE_BIN_FC11006152)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Blood clot or deep vein thrombosis (diagnosed by doctor) deep vein thrombosis,
thrombotic disease		 534
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000931/ScoringFiles/PGS000931.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
PPM007477 PGS000930
(GBE_BIN_FC3006152)
 PSS003914|
African Ancestry|
4,286 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot diagnosed by doctor — AUROC: 0.64618 [0.56748, 0.72489] R²: 0.02826
Incremental AUROC (full-covars): 0.00845
PGS R2 (no covariates): 0.00198
PGS AUROC (no covariates): 0.53535 [0.45318, 0.61752]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007478 PGS000930
(GBE_BIN_FC3006152)
 PSS003915|
East Asian Ancestry|
945 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot diagnosed by doctor — AUROC: 0.83468 [0.6451, 1.0] R²: 0.18847
Incremental AUROC (full-covars): -0.00149
PGS R2 (no covariates): 0.00357
PGS AUROC (no covariates): 0.56702 [0.36049, 0.77355]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007479 PGS000930
(GBE_BIN_FC3006152)
 PSS003916|
European Ancestry|
17,235 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot diagnosed by doctor — AUROC: 0.62906 [0.59189, 0.66622] R²: 0.02094
Incremental AUROC (full-covars): 0.04321
PGS R2 (no covariates): 0.01048
PGS AUROC (no covariates): 0.59654 [0.5564, 0.63667]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007480 PGS000930
(GBE_BIN_FC3006152)
 PSS003917|
South Asian Ancestry|
5,381 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot diagnosed by doctor — AUROC: 0.71068 [0.63185, 0.78951] R²: 0.04649
Incremental AUROC (full-covars): 0.02778
PGS R2 (no covariates): 0.00789
PGS AUROC (no covariates): 0.59225 [0.49685, 0.68766]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007481 PGS000930
(GBE_BIN_FC3006152)
 PSS003918|
European Ancestry|
46,847 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot diagnosed by doctor — AUROC: 0.6205 [0.59778, 0.64322] R²: 0.01789
Incremental AUROC (full-covars): 0.05259
PGS R2 (no covariates): 0.01324
PGS AUROC (no covariates): 0.60274 [0.57915, 0.62633]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007482 PGS000931
(GBE_BIN_FC11006152)
 PSS003790|
African Ancestry|
4,390 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot or DVT diagnosed by doctor — AUROC: 0.61925 [0.57619, 0.6623] R²: 0.02193
Incremental AUROC (full-covars): -0.00229
PGS R2 (no covariates): 0.00035
PGS AUROC (no covariates): 0.50724 [0.46275, 0.55173]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007483 PGS000931
(GBE_BIN_FC11006152)
 PSS003791|
East Asian Ancestry|
952 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot or DVT diagnosed by doctor — AUROC: 0.68652 [0.54244, 0.83061] R²: 0.05141
Incremental AUROC (full-covars): 0.00532
PGS R2 (no covariates): 0.00103
PGS AUROC (no covariates): 0.5328 [0.37688, 0.68873]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007484 PGS000931
(GBE_BIN_FC11006152)
 PSS003792|
European Ancestry|
17,648 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot or DVT diagnosed by doctor — AUROC: 0.64786 [0.62647, 0.66925] R²: 0.03411
Incremental AUROC (full-covars): 0.03737
PGS R2 (no covariates): 0.01507
PGS AUROC (no covariates): 0.59359 [0.57084, 0.61634]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007485 PGS000931
(GBE_BIN_FC11006152)
 PSS003793|
South Asian Ancestry|
5,480 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot or DVT diagnosed by doctor — AUROC: 0.63964 [0.59263, 0.68666] R²: 0.02677
Incremental AUROC (full-covars): 0.01249
PGS R2 (no covariates): 0.00502
PGS AUROC (no covariates): 0.55473 [0.50496, 0.60449]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007486 PGS000931
(GBE_BIN_FC11006152)
 PSS003794|
European Ancestry|
48,060 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Blood clot or DVT diagnosed by doctor — AUROC: 0.62837 [0.61546, 0.64128] R²: 0.02953
Incremental AUROC (full-covars): 0.0429
PGS R2 (no covariates): 0.01795
PGS AUROC (no covariates): 0.59176 [0.57816, 0.60536]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS003914 — —
[
  • 54 cases
  • , 4,232 controls
]
 — African unspecified — UKB —
PSS003915 — —
[
  • 5 cases
  • , 940 controls
]
 — East Asian — UKB —
PSS003916 — —
[
  • 211 cases
  • , 17,024 controls
]
 — European non-white British ancestry UKB —
PSS003917 — —
[
  • 36 cases
  • , 5,345 controls
]
 — South Asian — UKB —
PSS003918 — —
[
  • 584 cases
  • , 46,263 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003790 — —
[
  • 160 cases
  • , 4,230 controls
]
 — African unspecified — UKB —
PSS003791 — —
[
  • 12 cases
  • , 940 controls
]
 — East Asian — UKB —
PSS003792 — —
[
  • 640 cases
  • , 17,008 controls
]
 — European non-white British ancestry UKB —
PSS003793 — —
[
  • 136 cases
  • , 5,344 controls
]
 — South Asian — UKB —
PSS003794 — —
[
  • 1,859 cases
  • , 46,201 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)