Trait: vertebral column disease

Trait Information
Identifier MONDO_0000812
Description A disease involving the vertebral column. [MONDO: patterns/location_top]
Trait category
Other disease
Synonyms 6 synonyms
  • disease of spine
  • disease of vertebral column
  • disease or disorder of vertebral column
  • disorder of vertebral column
  • vertebral column disease
  • vertebral column disease or disorder
Mapped terms 5 mapped terms
  • DOID:0060564
  • ICD9:724.9
  • MESH:D013122
  • SCTID:699699005
  • UMLS:C0037933
Child trait(s) ankylosing spondylitis

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 "vertebral column 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 Scoring File (FTP Link)
PGS000932
(GBE_HC1248)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Other intervertebral disk disorders (time-to-event) vertebral column disease 111
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000932/ScoringFiles/PGS000932.txt.gz
PGS001267
(GBE_HC422)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Ankylosing spondylitis ankylosing spondylitis 10
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001267/ScoringFiles/PGS001267.txt.gz
PGS001268
(GBE_HC1242)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Ankylosing spondylitis (time-to-event) ankylosing spondylitis 10
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001268/ScoringFiles/PGS001268.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
PPM007487 PGS000932
(GBE_HC1248)
PSS004233|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other intervertebral disk disorders AUROC: 0.61914 [0.58359, 0.6547] : 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 PGS000932
(GBE_HC1248)
PSS004234|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other intervertebral disk disorders AUROC: 0.67311 [0.59003, 0.7562] : 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 PGS000932
(GBE_HC1248)
PSS004235|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other intervertebral disk disorders AUROC: 0.55895 [0.54143, 0.57647] : 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 PGS000932
(GBE_HC1248)
PSS004236|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other intervertebral disk disorders AUROC: 0.59693 [0.5672, 0.62666] : 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 PGS000932
(GBE_HC1248)
PSS004237|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other intervertebral disk disorders AUROC: 0.54155 [0.53124, 0.55187] : 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
PPM008840 PGS001267
(GBE_HC422)
PSS004486|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ankylosing spondylitis AUROC: 0.86744 [0.75569, 0.97918] : 0.1463
Incremental AUROC (full-covars): -0.00062
PGS R2 (no covariates): 0.00216
PGS AUROC (no covariates): 0.4722 [0.12421, 0.82018]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008841 PGS001267
(GBE_HC422)
PSS004487|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ankylosing spondylitis AUROC: 0.98913 [0.972, 1.0] : 0.44316
Incremental AUROC (full-covars): 0.0423
PGS R2 (no covariates): 0.24382
PGS AUROC (no covariates): 0.81698 [0.46329, 1.0]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008842 PGS001267
(GBE_HC422)
PSS004488|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ankylosing spondylitis AUROC: 0.73638 [0.67151, 0.80124] : 0.10414
Incremental AUROC (full-covars): 0.06004
PGS R2 (no covariates): 0.07222
PGS AUROC (no covariates): 0.67545 [0.60736, 0.74353]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008843 PGS001267
(GBE_HC422)
PSS004489|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ankylosing spondylitis AUROC: 0.73535 [0.61203, 0.85867] : 0.03713
Incremental AUROC (full-covars): -0.01782
PGS R2 (no covariates): 0.00902
PGS AUROC (no covariates): 0.42181 [0.29024, 0.55338]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008844 PGS001267
(GBE_HC422)
PSS004490|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Ankylosing spondylitis AUROC: 0.74328 [0.70673, 0.77983] : 0.10925
Incremental AUROC (full-covars): 0.12994
PGS R2 (no covariates): 0.09877
PGS AUROC (no covariates): 0.72651 [0.68965, 0.76337]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008845 PGS001268
(GBE_HC1242)
PSS004228|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE ankylosing spondylitis AUROC: 0.86811 [0.75774, 0.97849] : 0.14598
Incremental AUROC (full-covars): 6e-05
PGS R2 (no covariates): 0.00104
PGS AUROC (no covariates): 0.48424 [0.12443, 0.84406]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008846 PGS001268
(GBE_HC1242)
PSS004229|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE ankylosing spondylitis AUROC: 0.99148 [0.9789, 1.0] : 0.44858
Incremental AUROC (full-covars): 0.04465
PGS R2 (no covariates): 0.23755
PGS AUROC (no covariates): 0.81257 [0.45025, 1.0]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008847 PGS001268
(GBE_HC1242)
PSS004230|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE ankylosing spondylitis AUROC: 0.73336 [0.66901, 0.79772] : 0.10217
Incremental AUROC (full-covars): 0.0575
PGS R2 (no covariates): 0.06991
PGS AUROC (no covariates): 0.67405 [0.607, 0.74111]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008848 PGS001268
(GBE_HC1242)
PSS004231|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE ankylosing spondylitis AUROC: 0.73282 [0.61573, 0.84991] : 0.03979
Incremental AUROC (full-covars): -0.01963
PGS R2 (no covariates): 0.00774
PGS AUROC (no covariates): 0.4297 [0.29438, 0.56502]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008849 PGS001268
(GBE_HC1242)
PSS004232|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE ankylosing spondylitis AUROC: 0.74878 [0.71314, 0.78442] : 0.115
Incremental AUROC (full-covars): 0.12686
PGS R2 (no covariates): 0.10232
PGS AUROC (no covariates): 0.7346 [0.69884, 0.77037]
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
PSS004228
[
  • 5 cases
  • , 6,492 controls
]
African unspecified UKB
PSS004229
[
  • 2 cases
  • , 1,702 controls
]
East Asian UKB
PSS004486
[
  • 5 cases
  • , 6,492 controls
]
African unspecified UKB
PSS004487
[
  • 2 cases
  • , 1,702 controls
]
East Asian UKB
PSS004488
[
  • 79 cases
  • , 24,826 controls
]
European non-white British ancestry UKB
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)
PSS004489
[
  • 14 cases
  • , 7,817 controls
]
South Asian UKB
PSS004490
[
  • 268 cases
  • , 67,157 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004231
[
  • 15 cases
  • , 7,816 controls
]
South Asian UKB
PSS004230
[
  • 80 cases
  • , 24,825 controls
]
European non-white British ancestry UKB
PSS004232
[
  • 278 cases
  • , 67,147 controls
]
European white British ancestry UKB Testing cohort (heldout set)