Trait: osteoporosis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0003882
Description A condition of reduced bone mass, with decreased cortical thickness and a decrease in the number and size of the trabeculae of cancellous bone (but normal chemical composition), resulting in increased fracture incidence. Osteoporosis is classified as primary (Type 1, postmenopausal osteoporosis; Type 2, age-associated osteoporosis; and idiopathic, which can affect juveniles, premenopausal women, and middle-aged men) and secondary osteoporosis (which results from an identifiable cause of bone mass loss). [NCIT: C3298]
Trait category
Other disease
Synonyms 24 synonyms
  • AGE RELAT OSTEOPOROSIS
  • Age Related Osteoporosis
  • Age-Related Bone Loss
  • Age-Related Bone Losses
  • Age-Related Osteoporoses
  • Age-Related Osteoporosis
  • BONE LOSS AGE RELAT
  • Bone Loss, Age Related
  • Bone Loss, Age-Related
  • Bone Losses, Age-Related
  • OSTEOPOROSIS AGE RELAT
  • Osteoporoses
  • Osteoporoses, Age-Related
  • Osteoporoses, Senile
  • Osteoporosis, Age Related
  • Osteoporosis, Age-Related
  • Osteoporosis, Post Traumatic
  • Osteoporosis, Post-Traumatic
  • Osteoporosis, Senile
  • Post-Traumatic Osteoporoses
  • Post-Traumatic Osteoporosis
  • Senile Osteoporoses
  • Senile Osteoporosis
  • osteoporosis
Mapped terms 19 mapped terms
  • DOID:11476
  • GARD:0011932
  • ICD10:M80
  • ICD10:M81
  • ICD10:M81.0
  • ICD10:M82
  • ICD9:733.0
  • ICD9:733.00
  • ICD9:733.09
  • MESH:D010024
  • MONDO:0005298
  • MeSH:D010024
  • MedDRA:10031282
  • MedDRA:10031289
  • NCIT:C3298
  • NCIt:C3298
  • OMIM:166710
  • SCTID:64859006
  • SNOMEDCT:64859006

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
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS001273
(GBE_HC22)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Osteoporosis osteoporosis 316
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001273/ScoringFiles/PGS001273.txt.gz
PGS001274
(GBE_HC1268)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Osteoporosis without pathological fracture (time-to-event) osteoporosis 1,270
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001274/ScoringFiles/PGS001274.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
PPM008872 PGS001274
(GBE_HC1268)
PSS004247|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE osteoporosis without pathological fracture AUROC: 0.77492 [0.76604, 0.7838] : 0.12779
Incremental AUROC (full-covars): 0.00797
PGS R2 (no covariates): 0.0089
PGS AUROC (no covariates): 0.57419 [0.56237, 0.586]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008871 PGS001274
(GBE_HC1268)
PSS004246|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE osteoporosis without pathological fracture AUROC: 0.81463 [0.78571, 0.84355] : 0.16403
Incremental AUROC (full-covars): -0.00198
PGS R2 (no covariates): 0.00037
PGS AUROC (no covariates): 0.51416 [0.47459, 0.55374]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008870 PGS001274
(GBE_HC1268)
PSS004245|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE osteoporosis without pathological fracture AUROC: 0.79652 [0.78363, 0.8094] : 0.15697
Incremental AUROC (full-covars): 0.00777
PGS R2 (no covariates): 0.00945
PGS AUROC (no covariates): 0.57595 [0.55816, 0.59374]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008869 PGS001274
(GBE_HC1268)
PSS004244|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE osteoporosis without pathological fracture AUROC: 0.81083 [0.73828, 0.88338] : 0.14813
Incremental AUROC (full-covars): -0.0044
PGS R2 (no covariates): 9e-05
PGS AUROC (no covariates): 0.50546 [0.40063, 0.61028]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008868 PGS001274
(GBE_HC1268)
PSS004243|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE osteoporosis without pathological fracture AUROC: 0.74925 [0.69511, 0.80339] : 0.08288
Incremental AUROC (full-covars): -0.00137
PGS R2 (no covariates): 0.00122
PGS AUROC (no covariates): 0.51972 [0.45381, 0.58563]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008867 PGS001273
(GBE_HC22)
PSS004373|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Osteoporosis AUROC: 0.7643 [0.75478, 0.77381] : 0.1146
Incremental AUROC (full-covars): 0.00589
PGS R2 (no covariates): 0.00698
PGS AUROC (no covariates): 0.5684 [0.55603, 0.58076]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008866 PGS001273
(GBE_HC22)
PSS004372|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Osteoporosis AUROC: 0.82202 [0.79395, 0.85009] : 0.17031
Incremental AUROC (full-covars): 0.00037
PGS R2 (no covariates): 5e-05
PGS AUROC (no covariates): 0.50461 [0.4652, 0.54402]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008865 PGS001273
(GBE_HC22)
PSS004371|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Osteoporosis AUROC: 0.78972 [0.77584, 0.8036] : 0.14567
Incremental AUROC (full-covars): 0.00477
PGS R2 (no covariates): 0.00688
PGS AUROC (no covariates): 0.5685 [0.55009, 0.58691]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008864 PGS001273
(GBE_HC22)
PSS004370|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Osteoporosis AUROC: 0.85769 [0.79768, 0.9177] : 0.20187
Incremental AUROC (full-covars): -0.00208
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.50947 [0.39122, 0.62773]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008863 PGS001273
(GBE_HC22)
PSS004369|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Osteoporosis AUROC: 0.75545 [0.70356, 0.80735] : 0.08703
Incremental AUROC (full-covars): -0.00106
PGS R2 (no covariates): 0.00045
PGS AUROC (no covariates): 0.51891 [0.45926, 0.57855]
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
PSS004373
[
  • 2,151 cases
  • , 65,274 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004371
[
  • 932 cases
  • , 23,973 controls
]
European non-white British ancestry UKB
PSS004369
[
  • 92 cases
  • , 6,405 controls
]
African unspecified UKB
PSS004370
[
  • 24 cases
  • , 1,680 controls
]
East Asian UKB
PSS004243
[
  • 85 cases
  • , 6,412 controls
]
African unspecified UKB
PSS004244
[
  • 30 cases
  • , 1,674 controls
]
East Asian UKB
PSS004245
[
  • 1,020 cases
  • , 23,885 controls
]
European non-white British ancestry UKB
PSS004246
[
  • 205 cases
  • , 7,626 controls
]
South Asian UKB
PSS004247
[
  • 2,326 cases
  • , 65,099 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004372
[
  • 195 cases
  • , 7,636 controls
]
South Asian UKB