Polygenic Score (PGS) ID: PGS001136

Predicted Trait
Reported Trait Hematologic disease, genetic
Mapped Trait(s) hematologic disease (EFO_0005803)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC413
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_HC413
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 30
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%
269,704 individuals (100%)
PGS Evaluation
European: 50%
African: 25%
South Asian: 25%
4 Sample Sets

Development Samples

Score Development/Training
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
—
[
  • 245 cases
  • , 269,459 controls
]
 European UKB — — — white British ancestry —

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) 		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
PPM008408 PSS004481|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Genetic haematological disorder — AUROC: 0.70006 [0.42128, 0.97885] R²: 0.03928
Incremental AUROC (full-covars): -0.02126
PGS R2 (no covariates): 0.01794
PGS AUROC (no covariates): 0.33706 [0.08609, 0.58803]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008409 PSS004483|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Genetic haematological disorder — AUROC: 0.74771 [0.64556, 0.84987] R²: 0.04759
Incremental AUROC (full-covars): 0.0501
PGS R2 (no covariates): 0.01517
PGS AUROC (no covariates): 0.6101 [0.48056, 0.73964]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008410 PSS004484|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Genetic haematological disorder — AUROC: 0.86122 [0.58992, 1.0] R²: 0.17517
Incremental AUROC (full-covars): -0.03046
PGS R2 (no covariates): 0.0343
PGS AUROC (no covariates): 0.45357 [0.0, 1.0]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008411 PSS004485|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Genetic haematological disorder — AUROC: 0.67815 [0.59919, 0.75712] R²: 0.04564
Incremental AUROC (full-covars): 0.21126
PGS R2 (no covariates): 0.0569
PGS AUROC (no covariates): 0.69867 [0.61574, 0.78161]		 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
PSS004484 — —
[
  • 2 cases
  • , 7,829 controls
]
 — South Asian — UKB —
PSS004485 — —
[
  • 59 cases
  • , 67,366 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004481 — —
[
  • 5 cases
  • , 6,492 controls
]
 — African unspecified — UKB —
PSS004483 — —
[
  • 20 cases
  • , 24,885 controls
]
 — European non-white British ancestry UKB —