Trait: osteoarthritis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0002506
Description A noninflammatory degenerative joint disease occurring chiefly in older persons, characterised by degeneration of the articular cartilage, hypertrophy of bone at the margins and changes in the synovial membrane. It is accompanied by pain and stiffness, particularly after prolonged activity. [NCIT: C3293]
Trait category
Other disease
Synonyms 16 synonyms
  • Arthritides, Degenerative
  • Arthritis, Degenerative
  • Degenerative Arthritides
  • Degenerative Arthritis
  • OA
  • Osteoarthritides
  • Osteoarthroses
  • Osteoarthrosis
  • Osteoarthrosis Deformans
  • arthrosis
  • degenerative arthritis
  • degenerative joint disease
  • hypertrophic arthritis
  • osteoarthritis
  • osteoarthrosis
  • osteoarthrosis and allied disorder
Mapped terms 18 mapped terms
  • DOID:8398
  • EV:0400132
  • GARD:0011929
  • HP:0002758
  • ICD10:M15
  • ICD10:M19
  • ICD9:715.3
  • MESH:D010003
  • MONDO:0005178
  • MeSH:D010003
  • MedDRA:10031161
  • NCIT:C3293
  • NCIt:C3293
  • OMIM:140600
  • OMIM:165720
  • OMIM:607850
  • OMIM:612400
  • SNOMEDCT:396275006
Child trait(s) 2 child traits

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 "osteoarthritis" 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)
PGS000967
(GBE_HC1221)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Coxarthrosis [arthrosis of hip] (time-to-event) osteoarthritis, hip 634
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000967/ScoringFiles/PGS000967.txt.gz
PGS001192
(GBE_HC1222)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Gonarthrosis [arthrosis of knee] (time-to-event) osteoarthritis, knee 4,525
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001192/ScoringFiles/PGS001192.txt.gz
PGS001290
(GBE_HC376)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Osteoarthritis osteoarthritis 579
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001290/ScoringFiles/PGS001290.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
PPM007658 PGS000967
(GBE_HC1221)
PSS004208|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE coxarthrosis [arthrosis of hip] AUROC: 0.63448 [0.57611, 0.69284] : 0.02258
Incremental AUROC (full-covars): 0.01789
PGS R2 (no covariates): 0.0065
PGS AUROC (no covariates): 0.57452 [0.51022, 0.63883]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007659 PGS000967
(GBE_HC1221)
PSS004209|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE coxarthrosis [arthrosis of hip] AUROC: 0.67991 [0.52221, 0.83761] : 0.03974
Incremental AUROC (full-covars): 0.00141
PGS R2 (no covariates): 0.00044
PGS AUROC (no covariates): 0.52299 [0.39821, 0.64778]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007660 PGS000967
(GBE_HC1221)
PSS004210|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE coxarthrosis [arthrosis of hip] AUROC: 0.71352 [0.69682, 0.73022] : 0.07227
Incremental AUROC (full-covars): 0.00368
PGS R2 (no covariates): 0.00258
PGS AUROC (no covariates): 0.54164 [0.52116, 0.56213]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007661 PGS000967
(GBE_HC1221)
PSS004211|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE coxarthrosis [arthrosis of hip] AUROC: 0.72467 [0.66733, 0.78201] : 0.06598
Incremental AUROC (full-covars): -0.00237
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.50363 [0.44232, 0.56493]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007662 PGS000967
(GBE_HC1221)
PSS004212|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE coxarthrosis [arthrosis of hip] AUROC: 0.69051 [0.68108, 0.69995] : 0.06247
Incremental AUROC (full-covars): 0.00918
PGS R2 (no covariates): 0.00628
PGS AUROC (no covariates): 0.5611 [0.55051, 0.57168]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008609 PGS001192
(GBE_HC1222)
PSS004213|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE gonarthrosis [arthrosis of knee] AUROC: 0.68497 [0.65949, 0.71044] : 0.07256
Incremental AUROC (full-covars): -0.01106
PGS R2 (no covariates): 0.00014
PGS AUROC (no covariates): 0.48548 [0.45782, 0.51313]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008610 PGS001192
(GBE_HC1222)
PSS004214|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE gonarthrosis [arthrosis of knee] AUROC: 0.6973 [0.62907, 0.76552] : 0.05404
Incremental AUROC (full-covars): -0.01876
PGS R2 (no covariates): 0.00104
PGS AUROC (no covariates): 0.48101 [0.40847, 0.55354]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008611 PGS001192
(GBE_HC1222)
PSS004215|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE gonarthrosis [arthrosis of knee] AUROC: 0.66024 [0.6461, 0.67438] PGS R2 (no covariates): 0.00516
: 0.04745
Incremental AUROC (full-covars): 0.00488
PGS AUROC (no covariates): 0.54777 [0.53172, 0.56382]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008612 PGS001192
(GBE_HC1222)
PSS004216|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE gonarthrosis [arthrosis of knee] AUROC: 0.72749 [0.70853, 0.74646] : 0.11678
Incremental AUROC (full-covars): 0.00024
PGS R2 (no covariates): 0.00229
PGS AUROC (no covariates): 0.53307 [0.5103, 0.55585]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008613 PGS001192
(GBE_HC1222)
PSS004217|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE gonarthrosis [arthrosis of knee] AUROC: 0.64504 [0.63733, 0.65274] : 0.04312
Incremental AUROC (full-covars): 0.0104
PGS R2 (no covariates): 0.0068
PGS AUROC (no covariates): 0.55655 [0.54824, 0.56485]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008948 PGS001290
(GBE_HC376)
PSS004461|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Osteoarthritis AUROC: 0.75416 [0.72668, 0.78163] : 0.12216
Incremental AUROC (full-covars): -3e-05
PGS R2 (no covariates): 0.00052
PGS AUROC (no covariates): 0.51951 [0.48655, 0.55248]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008949 PGS001290
(GBE_HC376)
PSS004462|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Osteoarthritis AUROC: 0.74181 [0.68024, 0.80338] : 0.09715
Incremental AUROC (full-covars): -0.00139
PGS R2 (no covariates): 0.00189
PGS AUROC (no covariates): 0.54245 [0.47153, 0.61338]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008950 PGS001290
(GBE_HC376)
PSS004463|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Osteoarthritis AUROC: 0.70244 [0.69044, 0.71444] : 0.08191
Incremental AUROC (full-covars): 0.0007
PGS R2 (no covariates): 0.0006
PGS AUROC (no covariates): 0.51661 [0.5024, 0.53082]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008951 PGS001290
(GBE_HC376)
PSS004464|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Osteoarthritis AUROC: 0.72534 [0.70181, 0.74887] : 0.09768
Incremental AUROC (full-covars): -0.00173
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.49787 [0.47035, 0.52539]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008952 PGS001290
(GBE_HC376)
PSS004465|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Osteoarthritis AUROC: 0.67419 [0.66753, 0.68085] : 0.0674
Incremental AUROC (full-covars): 0.00134
PGS R2 (no covariates): 0.00109
PGS AUROC (no covariates): 0.52166 [0.51404, 0.52927]
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
PSS004464
[
  • 425 cases
  • , 7,406 controls
]
South Asian UKB
PSS004461
[
  • 305 cases
  • , 6,192 controls
]
African unspecified UKB
PSS004462
[
  • 56 cases
  • , 1,648 controls
]
East Asian UKB
PSS004463
[
  • 1,688 cases
  • , 23,217 controls
]
European non-white British ancestry UKB
PSS004208
[
  • 85 cases
  • , 6,412 controls
]
African unspecified UKB
PSS004209
[
  • 16 cases
  • , 1,688 controls
]
East Asian UKB
PSS004210
[
  • 779 cases
  • , 24,126 controls
]
European non-white British ancestry UKB
PSS004211
[
  • 74 cases
  • , 7,757 controls
]
South Asian UKB
PSS004212
[
  • 2,783 cases
  • , 64,642 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004213
[
  • 443 cases
  • , 6,054 controls
]
African unspecified UKB
PSS004214
[
  • 56 cases
  • , 1,648 controls
]
East Asian UKB
PSS004215
[
  • 1,333 cases
  • , 23,572 controls
]
European non-white British ancestry UKB
PSS004216
[
  • 684 cases
  • , 7,147 controls
]
South Asian UKB
PSS004217
[
  • 4,861 cases
  • , 62,564 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004465
[
  • 6,097 cases
  • , 61,328 controls
]
European white British ancestry UKB Testing cohort (heldout set)