Trait: blood coagulation disease

Trait Information
Identifier MONDO_0001531
Description A condition in which there is a deviation from or interruption of the normal coagulation properties of the blood. [NCIT: C2902]
Trait category
Other disease
Synonyms 8 synonyms
  • blood coagulation disorder
  • coagulation defect
  • coagulation disorder
  • coagulation disorder, blood
  • coagulation disorders, blood
  • coagulopathy
  • disorder, blood coagulation
  • disorders, blood coagulation
Child trait(s) congenital vitamin K-dependent coagulation factors deficiency

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 all PGS for "blood coagulation disease" and any child terms of this trait in the EFO hierarchy by default.
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)
PGS001033
(GBE_HC624)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Other coagulation defects (time-to-event) blood coagulation disease 1
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001033/ScoringFiles/PGS001033.txt.gz
PGS001826
(portability-PLR_286.12)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Congenital deficiency of other clotting factors (including factor VII) congenital vitamin K-dependent coagulation factors deficiency 45
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001826/ScoringFiles/PGS001826.txt.gz
PGS002034
(portability-ldpred2_286.12)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Congenital deficiency of other clotting factors (including factor VII) congenital vitamin K-dependent coagulation factors deficiency 32,552
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002034/ScoringFiles/PGS002034.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
PPM007928 PGS001033
(GBE_HC624)
 PSS004546|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other coagulation defects — AUROC: 0.68816 [0.60114, 0.77518] R²: 0.03983
Incremental AUROC (full-covars): -0.00134
PGS R2 (no covariates): 0.00067
PGS AUROC (no covariates): 0.49799 [0.49722, 0.49876]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007929 PGS001033
(GBE_HC624)
 PSS004547|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other coagulation defects — AUROC: 0.8546 [0.65205, 1.0] R²: 0.119
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 8e-05
PGS AUROC (no covariates): 0.49971 [0.49913, 0.50028]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007930 PGS001033
(GBE_HC624)
 PSS004548|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other coagulation defects — AUROC: 0.64742 [0.59655, 0.69828] R²: 0.03199
Incremental AUROC (full-covars): 0.06677
PGS R2 (no covariates): 0.0303
PGS AUROC (no covariates): 0.58367 [0.54735, 0.61999]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007931 PGS001033
(GBE_HC624)
 PSS004549|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other coagulation defects — AUROC: 0.66881 [0.55798, 0.77963] R²: 0.02584
Incremental AUROC (full-covars): 0.02341
PGS R2 (no covariates): 0.00994
PGS AUROC (no covariates): 0.54143 [0.46669, 0.61618]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007932 PGS001033
(GBE_HC624)
 PSS004550|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other coagulation defects — AUROC: 0.65623 [0.61832, 0.69414] R²: 0.05179
Incremental AUROC (full-covars): 0.12049
PGS R2 (no covariates): 0.05781
PGS AUROC (no covariates): 0.63402 [0.60616, 0.66189]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009505 PGS001826
(portability-PLR_286.12)
 PSS009296|
European Ancestry|
19,864 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Congenital deficiency of other clotting factors (including factor VII) — — Partial Correlation (partial-r): 0.0562 [0.0424, 0.0701] sex, age, birth date, deprivation index, 16 PCs —
PPM009506 PGS001826
(portability-PLR_286.12)
 PSS009070|
European Ancestry|
4,108 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Congenital deficiency of other clotting factors (including factor VII) — — Partial Correlation (partial-r): 0.0487 [0.018, 0.0792] sex, age, birth date, deprivation index, 16 PCs —
PPM009507 PGS001826
(portability-PLR_286.12)
 PSS008624|
European Ancestry|
6,613 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Congenital deficiency of other clotting factors (including factor VII) — — Partial Correlation (partial-r): 0.0377 [0.0136, 0.0618] sex, age, birth date, deprivation index, 16 PCs —
PPM009508 PGS001826
(portability-PLR_286.12)
 PSS008178|
South Asian Ancestry|
6,272 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Congenital deficiency of other clotting factors (including factor VII) — — Partial Correlation (partial-r): 0.0354 [0.0106, 0.0601] sex, age, birth date, deprivation index, 16 PCs —
PPM011143 PGS002034
(portability-ldpred2_286.12)
 PSS009296|
European Ancestry|
19,864 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Congenital deficiency of other clotting factors (including factor VII) — — Partial Correlation (partial-r): 0.0563 [0.0424, 0.0702] sex, age, birth date, deprivation index, 16 PCs —
PPM011144 PGS002034
(portability-ldpred2_286.12)
 PSS009070|
European Ancestry|
4,108 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Congenital deficiency of other clotting factors (including factor VII) — — Partial Correlation (partial-r): 0.0533 [0.0227, 0.0838] sex, age, birth date, deprivation index, 16 PCs —
PPM011145 PGS002034
(portability-ldpred2_286.12)
 PSS008624|
European Ancestry|
6,613 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Congenital deficiency of other clotting factors (including factor VII) — — Partial Correlation (partial-r): 0.046 [0.0219, 0.07] sex, age, birth date, deprivation index, 16 PCs —
PPM011146 PGS002034
(portability-ldpred2_286.12)
 PSS008178|
South Asian Ancestry|
6,272 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Congenital deficiency of other clotting factors (including factor VII) — — Partial Correlation (partial-r): 0.0358 [0.011, 0.0605] 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
PSS004546 — —
[
  • 35 cases
  • , 6,462 controls
]
 — African unspecified — UKB —
PSS004547 — —
[
  • 3 cases
  • , 1,701 controls
]
 — East Asian — UKB —
PSS004548 — —
[
  • 123 cases
  • , 24,782 controls
]
 — European non-white British ancestry UKB —
PSS004549 — —
[
  • 18 cases
  • , 7,813 controls
]
 — South Asian — UKB —
PSS004550 — —
[
  • 268 cases
  • , 67,157 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS009070 — — 4,108 individuals — European Poland (NE Europe) UKB —
PSS009296 — — 19,864 individuals — European UK (+ Ireland) UKB —
PSS008624 — — 6,613 individuals — European Italy (South Europe) UKB —
PSS008178 — — 6,272 individuals — South Asian India (South Asia) UKB —