Trait: spondyloarthropathy

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000706
Description A group of inflammatory rheumatic diseases associated with arthritis and enthesitis, and often involving the axial skeleton. The most common form of spondyloarthritis is ankylosing spondylitis. Other forms include axial spondyloarthritis, peripheral spondyloarthritis, reactive arthritis, psoriatic arthritis/spondylitis and enteropathic arthritis/spondylitis. [NCIT: C116778]
Trait category
Immune system disorder
Synonyms 24 synonyms
  • Disorder of joint of spine
  • Disorder of joint of spine (disorder)
  • JOINT DIS NOS-OTH JT
  • OA - Osteoarthritis of spine
  • OA - Osteoarthritis of the spine
  • Osteoarthritis of spine
  • SPONDYLOS NOS W/O MYELOP
  • Spondarthropathy
  • Spondylarthropathies
  • Spondylarthropathy
  • Spondylarthrosis
  • Spondylarthrosis NOS
  • Spondylarthrosis, NOS
  • Spondyloarthropathy (disorder)
  • Spondylosis
  • Spondylosis (disorder)
  • Spondylosis of unspecified site without mention of myelopathy
  • Spondylosis, NOS
  • Unspecified joint disorder of other specified sites
  • seronegative spondyloarthropathy
  • spondarthropathy
  • spondylarthrosis
  • spondyloarthritis
  • spondyloarthropathy
Mapped terms 12 mapped terms
  • DOID:1123
  • GARD:0004971
  • ICD10:M47
  • MONDO:0005095
  • MeSH:D025242
  • MeSH:D055009
  • MedDRA:10051265
  • NCIT:C116778
  • OMIM:106300
  • SCTID:372109003
  • SNOMEDCT:372109003
  • SNOMEDCT:8847002
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 "spondyloarthropathy" 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)
PGS000197
(G-PROB_SpA)
PGP000081 |
Knevel R et al. Sci Transl Med (2020)
Spondyloarthroparthy spondyloarthropathy 250
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000197/ScoringFiles/PGS000197.txt.gz
PGS001267
(GBE_HC422)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
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. PLoS Genet (2022)
Ankylosing spondylitis (time-to-event) ankylosing spondylitis 10
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001268/ScoringFiles/PGS001268.txt.gz
PGS001876
(portability-PLR_715.2)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Ankylosing spondylitis ankylosing spondylitis 85
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001876/ScoringFiles/PGS001876.txt.gz
PGS002089
(portability-ldpred2_715.2)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Ankylosing spondylitis ankylosing spondylitis 22,026
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002089/ScoringFiles/PGS002089.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
PPM000580 PGS000197
(G-PROB_SpA)
PSS000317|
European Ancestry|
243 individuals
PGP000081 |
Knevel R et al. Sci Transl Med (2020)
Reported Trait: Spondyloarthropathy diagnosis in patient with arthritis AUROC: 0.56 [0.33, 0.84] (Setting III: Selecting patients presenting with inflammatory arthritis at their first visit)
PPM000574 PGS000197
(G-PROB_SpA)
PSS000316|
European Ancestry|
245 individuals
PGP000081 |
Knevel R et al. Sci Transl Med (2020)
Reported Trait: Spondyloarthropathy diagnosis in patient with arthritis AUROC: 0.87 [0.76, 0.96] (Setting II: Assigning patient diagnoses based on medical records)
PPM000568 PGS000197
(G-PROB_SpA)
PSS000323|
Multi-ancestry (including European)|
1,211 individuals
PGP000081 |
Knevel R et al. Sci Transl Med (2020)
Reported Trait: Spondyloarthropathy diagnosis in patient with arthritis AUROC: 0.58 [0.5, 0.67] (Setting I: Assigning patient diagnoses based on billing codes)
PPM008840 PGS001267
(GBE_HC422)
PSS004486|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
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. PLoS Genet (2022)
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. PLoS Genet (2022)
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. PLoS Genet (2022)
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. PLoS Genet (2022)
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. PLoS Genet (2022)
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. PLoS Genet (2022)
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. PLoS Genet (2022)
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. PLoS Genet (2022)
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. PLoS Genet (2022)
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
PPM009896 PGS001876
(portability-PLR_715.2)
PSS009353|
European Ancestry|
18,262 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ankylosing spondylitis Partial Correlation (partial-r): 0.0797 [0.0653, 0.0941] sex, age, birth date, deprivation index, 16 PCs
PPM009897 PGS001876
(portability-PLR_715.2)
PSS009127|
European Ancestry|
3,854 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ankylosing spondylitis Partial Correlation (partial-r): 0.0453 [0.0137, 0.0769] sex, age, birth date, deprivation index, 16 PCs
PPM009898 PGS001876
(portability-PLR_715.2)
PSS008681|
European Ancestry|
6,216 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ankylosing spondylitis Partial Correlation (partial-r): 0.0521 [0.0272, 0.0769] sex, age, birth date, deprivation index, 16 PCs
PPM009899 PGS001876
(portability-PLR_715.2)
PSS008455|
Greater Middle Eastern Ancestry|
1,124 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ankylosing spondylitis Partial Correlation (partial-r): 0.1472 [0.0889, 0.2044] sex, age, birth date, deprivation index, 16 PCs
PPM009900 PGS001876
(portability-PLR_715.2)
PSS008235|
South Asian Ancestry|
5,671 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ankylosing spondylitis Partial Correlation (partial-r): 0.0279 [0.0019, 0.054] sex, age, birth date, deprivation index, 16 PCs
PPM011572 PGS002089
(portability-ldpred2_715.2)
PSS009353|
European Ancestry|
18,262 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ankylosing spondylitis Partial Correlation (partial-r): 0.0919 [0.0775, 0.1063] sex, age, birth date, deprivation index, 16 PCs
PPM011573 PGS002089
(portability-ldpred2_715.2)
PSS009127|
European Ancestry|
3,854 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ankylosing spondylitis Partial Correlation (partial-r): 0.0476 [0.016, 0.0791] sex, age, birth date, deprivation index, 16 PCs
PPM011574 PGS002089
(portability-ldpred2_715.2)
PSS008681|
European Ancestry|
6,216 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ankylosing spondylitis Partial Correlation (partial-r): 0.0596 [0.0348, 0.0844] sex, age, birth date, deprivation index, 16 PCs
PPM011576 PGS002089
(portability-ldpred2_715.2)
PSS008235|
South Asian Ancestry|
5,671 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ankylosing spondylitis Partial Correlation (partial-r): 0.0424 [0.0163, 0.0684] sex, age, birth date, deprivation index, 16 PCs
PPM011575 PGS002089
(portability-ldpred2_715.2)
PSS008455|
Greater Middle Eastern Ancestry|
1,124 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ankylosing spondylitis Partial Correlation (partial-r): 0.1631 [0.1051, 0.22] sex, age, birth date, deprivation index, 16 PCs

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
PSS009127 3,854 individuals European Poland (NE Europe) UKB
PSS008455 1,124 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009353 18,262 individuals European UK (+ Ireland) UKB
PSS008681 6,216 individuals European Italy (South Europe) UKB
PSS008235 5,671 individuals South Asian India (South Asia) UKB
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
PSS000316 Setting II: Based on ICD codes and review of medical records from Partners HealthCare Biobank; controls = other non-matching arthritis diseases Median = 8.0 years
[
  • 31 cases
  • , 214 controls
]
,
32.0 % Male samples
European PHB
PSS000317 Setting III: Based on ICD codes and final diagnosis in medical records from Partners HealthCare Biobank; controls = other non-matching arthritis diseases Median = 7.0 years
[
  • 8 cases
  • , 235 controls
]
,
32.0 % Male samples
European PHB
PSS004489
[
  • 14 cases
  • , 7,817 controls
]
South Asian UKB
PSS004490
[
  • 268 cases
  • , 67,157 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004230
[
  • 80 cases
  • , 24,825 controls
]
European non-white British ancestry UKB
PSS004231
[
  • 15 cases
  • , 7,816 controls
]
South Asian UKB
PSS004232
[
  • 278 cases
  • , 67,147 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS000323 Setting I: Based on ICD codes and expert opinion (ACR2010 criteria), in eMERGE network EMR database from Stanaway 2018; controls = other non-matching arthritis diseases Median = 16.0 years
[
  • 65 cases
  • , 1,146 controls
]
,
43.0 % Male samples
European, African unspecified, Asian unspecified, NR Primarily European, African and Asian ancestry eMERGE