Polygenic Score (PGS) ID: PGS000964

Predicted Trait
Reported Trait Slipped disc
Mapped Trait(s) Epiphyses, Slipped (EFO_1001317)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC176
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_HC176
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 47
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
—
[
  • 4,921 cases
  • , 264,783 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
PPM007644 PSS004326|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prolapsed disc/slipped disc — AUROC: 0.63682 [0.56928, 0.70437] R²: 0.02156
Incremental AUROC (full-covars): 0.00372
PGS R2 (no covariates): 0.00327
PGS AUROC (no covariates): 0.55166 [0.47346, 0.62985]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007645 PSS004327|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prolapsed disc/slipped disc — AUROC: 0.81007 [0.70133, 0.91881] R²: 0.11316
Incremental AUROC (full-covars): -0.00081
PGS R2 (no covariates): 0.00529
PGS AUROC (no covariates): 0.44295 [0.26666, 0.61923]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007646 PSS004328|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prolapsed disc/slipped disc — AUROC: 0.56388 [0.53738, 0.59039] R²: 0.00535
Incremental AUROC (full-covars): 0.00616
PGS R2 (no covariates): 0.00079
PGS AUROC (no covariates): 0.5207 [0.49331, 0.54808]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007647 PSS004329|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prolapsed disc/slipped disc — AUROC: 0.61724 [0.56387, 0.67062] R²: 0.01708
Incremental AUROC (full-covars): 0.00757
PGS R2 (no covariates): 0.00213
PGS AUROC (no covariates): 0.54913 [0.49663, 0.60163]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007648 PSS004330|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prolapsed disc/slipped disc — AUROC: 0.5452 [0.52946, 0.56094] R²: 0.0026
Incremental AUROC (full-covars): 0.01313
PGS R2 (no covariates): 0.00226
PGS AUROC (no covariates): 0.54225 [0.5262, 0.5583]		 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
PSS004326 — —
[
  • 69 cases
  • , 6,428 controls
]
 — African unspecified — UKB —
PSS004327 — —
[
  • 11 cases
  • , 1,693 controls
]
 — East Asian — UKB —
PSS004328 — —
[
  • 434 cases
  • , 24,471 controls
]
 — European non-white British ancestry UKB —
PSS004329 — —
[
  • 110 cases
  • , 7,721 controls
]
 — South Asian — UKB —
PSS004330 — —
[
  • 1,236 cases
  • , 66,189 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)