Polygenic Score (PGS) ID: PGS000931

Predicted Trait
Reported Trait Blood clot or deep vein thrombosis (diagnosed by doctor)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC11006152
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_BIN_FC11006152
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 534
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
192,089 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
Phenotype Definitions & Methods
Age of Study Participants
Participant Follow-up Time
Additional Ancestry Description
Additional Sample/Cohort Information
—
[
  • 7,351 cases
  • , 184,738 controls
]
EuropeanUKB———white British ancestry—
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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.

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PGS Performance
Metric ID (PPM)
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
PPM007482PSS003790|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007483PSS003791|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007484PSS003792|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007485PSS003793|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007486PSS003794|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
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Evaluated Samples

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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
PSS003790——
[
  • 160 cases
  • , 4,230 controls
]
—African unspecified—UKB—
PSS003791——
[
  • 12 cases
  • , 940 controls
]
—East Asian—UKB—
PSS003792——
[
  • 640 cases
  • , 17,008 controls
]
—Europeannon-white British ancestryUKB—
PSS003793——
[
  • 136 cases
  • , 5,344 controls
]
—South Asian—UKB—
PSS003794——
[
  • 1,859 cases
  • , 46,201 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
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