Polygenic Score (PGS) ID: PGS000932

Predicted Trait
Reported Trait Other intervertebral disk disorders (time-to-event)
Mapped Trait(s) vertebral column disorder (MONDO_0000812)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1248
Released in PGS Catalog: Oct. 21, 2021
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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_HC1248
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 111
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: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
—
[
  • 12,433 cases
  • , 257,271 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
PPM007487 PSS004233|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other intervertebral disk disorders — AUROC: 0.61914 [0.58359, 0.6547] R²: 0.02448
Incremental AUROC (full-covars): 0.00264
PGS R2 (no covariates): 0.00207
PGS AUROC (no covariates): 0.53493 [0.49884, 0.57101]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007488 PSS004234|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other intervertebral disk disorders — AUROC: 0.67311 [0.59003, 0.7562] R²: 0.04246
Incremental AUROC (full-covars): 0.00165
PGS R2 (no covariates): 0.00022
PGS AUROC (no covariates): 0.51372 [0.42189, 0.60556]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007489 PSS004235|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other intervertebral disk disorders — AUROC: 0.55895 [0.54143, 0.57647] R²: 0.00607
Incremental AUROC (full-covars): 0.01294
PGS R2 (no covariates): 0.00286
PGS AUROC (no covariates): 0.54031 [0.52281, 0.55781]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007490 PSS004236|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other intervertebral disk disorders — AUROC: 0.59693 [0.5672, 0.62666] R²: 0.01653
Incremental AUROC (full-covars): 0.00562
PGS R2 (no covariates): 0.00176
PGS AUROC (no covariates): 0.52887 [0.49726, 0.56049]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007491 PSS004237|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other intervertebral disk disorders — AUROC: 0.54155 [0.53124, 0.55187] R²: 0.00313
Incremental AUROC (full-covars): 0.01449
PGS R2 (no covariates): 0.00232
PGS AUROC (no covariates): 0.5375 [0.52711, 0.54788]		 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
PSS004233 — —
[
  • 234 cases
  • , 6,263 controls
]
 — African unspecified — UKB —
PSS004234 — —
[
  • 37 cases
  • , 1,667 controls
]
 — East Asian — UKB —
PSS004235 — —
[
  • 1,073 cases
  • , 23,832 controls
]
 — European non-white British ancestry UKB —
PSS004236 — —
[
  • 344 cases
  • , 7,487 controls
]
 — South Asian — UKB —
PSS004237 — —
[
  • 3,084 cases
  • , 64,341 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)