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 30 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
  • bone mineral density variation QTL, osteoporosis
  • fracture, hip, susceptibility to
  • osteoporosis
  • osteoporosis, involutional
  • osteoporosis, postmenopausal
  • osteoporosis, postmenopausal, susceptibility
  • osteoporosis, susceptibility to
Mapped terms 22 mapped terms
  • DOID:11476
  • GARD:11932
  • ICD10:M80
  • ICD10:M81
  • ICD10:M82
  • ICD10CM:M81
  • ICD9:733.0
  • ICD9:733.00
  • ICD9:733.09
  • MEDGEN:14535
  • MESH:D010024
  • MONDO:0005298
  • MeSH:D010024
  • MedDRA:10031282
  • MedDRA:10031289
  • NCIT:C3298
  • NCIt:C3298
  • OMIM:166710
  • SCTID:64859006
  • SNOMEDCT:64859006
  • UMLS:C0029456
  • icd11.foundation:2113001430

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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001273
(GBE_HC22)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 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. PLoS Genet (2022)
 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
PGS001883
(portability-PLR_743.1)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Osteoporosis osteoporosis 365
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001883/ScoringFiles/PGS001883.txt.gz
PGS002095
(portability-ldpred2_743.1)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Osteoporosis osteoporosis 658,775
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002095/ScoringFiles/PGS002095.txt.gz
PGS002768
(BMD_prscs)
 PGP000364 |
Mars N et al. Am J Hum Genet (2022)
 Osteoporosis osteoporosis,
heel bone mineral density		 1,091,549
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002768/ScoringFiles/PGS002768.txt.gz
PGS004490
(disease.M81.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 M81 (Osteoporosis without pathological fracture) osteoporosis 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004490/ScoringFiles/PGS004490.txt.gz
PGS004495
(disease.osteoporosis.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Osteoporosis osteoporosis 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004495/ScoringFiles/PGS004495.txt.gz
PGS004560
(meta.M81.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 M81 (Osteoporosis without pathological fracture) osteoporosis 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004560/ScoringFiles/PGS004560.txt.gz
PGS004565
(meta.osteoporosis.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Osteoporosis osteoporosis 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004565/ScoringFiles/PGS004565.txt.gz
PGS004809
(osteoporosis_PRSmix_eur)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Osteoporosis osteoporosis 863,731
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004809/ScoringFiles/PGS004809.txt.gz
PGS004810
(osteoporosis_PRSmixPlus_eur)
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Osteoporosis osteoporosis 1,876,917
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004810/ScoringFiles/PGS004810.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
PPM008863 PGS001273
(GBE_HC22)
 PSS004369|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoporosis — AUROC: 0.75545 [0.70356, 0.80735] R²: 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
PPM008864 PGS001273
(GBE_HC22)
 PSS004370|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoporosis — AUROC: 0.85769 [0.79768, 0.9177] R²: 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
PPM008865 PGS001273
(GBE_HC22)
 PSS004371|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoporosis — AUROC: 0.78972 [0.77584, 0.8036] R²: 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
PPM008866 PGS001273
(GBE_HC22)
 PSS004372|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoporosis — AUROC: 0.82202 [0.79395, 0.85009] R²: 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
PPM008867 PGS001273
(GBE_HC22)
 PSS004373|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Osteoporosis — AUROC: 0.7643 [0.75478, 0.77381] R²: 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
PPM008868 PGS001274
(GBE_HC1268)
 PSS004243|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE osteoporosis without pathological fracture — AUROC: 0.74925 [0.69511, 0.80339] R²: 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
PPM008869 PGS001274
(GBE_HC1268)
 PSS004244|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE osteoporosis without pathological fracture — AUROC: 0.81083 [0.73828, 0.88338] R²: 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
PPM008870 PGS001274
(GBE_HC1268)
 PSS004245|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE osteoporosis without pathological fracture — AUROC: 0.79652 [0.78363, 0.8094] R²: 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
PPM008871 PGS001274
(GBE_HC1268)
 PSS004246|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE osteoporosis without pathological fracture — AUROC: 0.81463 [0.78571, 0.84355] R²: 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
PPM008872 PGS001274
(GBE_HC1268)
 PSS004247|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE osteoporosis without pathological fracture — AUROC: 0.77492 [0.76604, 0.7838] R²: 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
PPM009948 PGS001883
(portability-PLR_743.1)
 PSS009360|
European Ancestry|
19,982 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0308 [0.017, 0.0447] sex, age, birth date, deprivation index, 16 PCs —
PPM009949 PGS001883
(portability-PLR_743.1)
 PSS009134|
European Ancestry|
4,130 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): -0.0002 [-0.0308, 0.0303] sex, age, birth date, deprivation index, 16 PCs —
PPM009950 PGS001883
(portability-PLR_743.1)
 PSS008688|
European Ancestry|
6,657 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0348 [0.0108, 0.0588] sex, age, birth date, deprivation index, 16 PCs —
PPM009952 PGS001883
(portability-PLR_743.1)
 PSS008242|
South Asian Ancestry|
6,327 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): -0.0028 [-0.0274, 0.0219] sex, age, birth date, deprivation index, 16 PCs —
PPM009953 PGS001883
(portability-PLR_743.1)
 PSS008020|
East Asian Ancestry|
1,808 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0046 [-0.0418, 0.0509] sex, age, birth date, deprivation index, 16 PCs —
PPM009954 PGS001883
(portability-PLR_743.1)
 PSS007806|
African Ancestry|
2,483 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): -0.0024 [-0.0419, 0.0371] sex, age, birth date, deprivation index, 16 PCs —
PPM009955 PGS001883
(portability-PLR_743.1)
 PSS008910|
African Ancestry|
3,923 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0028 [-0.0286, 0.0342] sex, age, birth date, deprivation index, 16 PCs —
PPM009951 PGS001883
(portability-PLR_743.1)
 PSS008462|
Greater Middle Eastern Ancestry|
1,199 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0115 [-0.0456, 0.0686] sex, age, birth date, deprivation index, 16 PCs —
PPM011616 PGS002095
(portability-ldpred2_743.1)
 PSS009360|
European Ancestry|
19,982 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0268 [0.013, 0.0407] sex, age, birth date, deprivation index, 16 PCs —
PPM011617 PGS002095
(portability-ldpred2_743.1)
 PSS009134|
European Ancestry|
4,130 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0131 [-0.0174, 0.0437] sex, age, birth date, deprivation index, 16 PCs —
PPM011618 PGS002095
(portability-ldpred2_743.1)
 PSS008688|
European Ancestry|
6,657 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0248 sex, age, birth date, deprivation index, 16 PCs —
PPM011619 PGS002095
(portability-ldpred2_743.1)
 PSS008462|
Greater Middle Eastern Ancestry|
1,199 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0116 [-0.0455, 0.0687] sex, age, birth date, deprivation index, 16 PCs —
PPM011620 PGS002095
(portability-ldpred2_743.1)
 PSS008242|
South Asian Ancestry|
6,327 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): -0.0013 [-0.026, 0.0233] sex, age, birth date, deprivation index, 16 PCs —
PPM011621 PGS002095
(portability-ldpred2_743.1)
 PSS008020|
East Asian Ancestry|
1,808 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0077 [-0.0387, 0.054] sex, age, birth date, deprivation index, 16 PCs —
PPM011622 PGS002095
(portability-ldpred2_743.1)
 PSS007806|
African Ancestry|
2,483 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0261 [-0.0135, 0.0655] sex, age, birth date, deprivation index, 16 PCs —
PPM011623 PGS002095
(portability-ldpred2_743.1)
 PSS008910|
African Ancestry|
3,923 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis — — Partial Correlation (partial-r): 0.0012 [-0.0301, 0.0326] sex, age, birth date, deprivation index, 16 PCs —
PPM014968 PGS002768
(BMD_prscs)
 PSS009939|
European Ancestry|
39,444 individuals
 PGP000364 |
Mars N et al. Am J Hum Genet (2022)
 Reported Trait: Osteoporosis OR: 1.31 [1.25, 1.38] — — age, sex, 10 PCs, technical covariates —
PPM020605 PGS004490
(disease.M81.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: M81 (Osteoporosis without pathological fracture) OR: 1.17552 — — — —
PPM020610 PGS004495
(disease.osteoporosis.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: Osteoporosis OR: 1.19793 — — — —
PPM020675 PGS004560
(meta.M81.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: M81 (Osteoporosis without pathological fracture) OR: 1.32082 — — — —
PPM020680 PGS004565
(meta.osteoporosis.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: Osteoporosis OR: 1.32822 — — — —
PPM021034 PGS004809
(osteoporosis_PRSmix_eur)
 PSS011465|
European Ancestry|
9,462 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Osteoporosis — — Incremental R2 (Full model versus model with only covariates): 0.011 [0.007, 0.015] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)
PPM021035 PGS004810
(osteoporosis_PRSmixPlus_eur)
 PSS011465|
European Ancestry|
9,462 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Osteoporosis — — Incremental R2 (Full model versus model with only covariates): 0.022 [0.016, 0.028] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)

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
PSS008910 — — 3,923 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008020 — — 1,808 individuals — East Asian China (East Asia) UKB —
PSS011465 — — 9,462 individuals — European — AllofUs —
PSS008688 — — 6,657 individuals — European Italy (South Europe) UKB —
PSS007806 — — 2,483 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008462 — — 1,199 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009360 — — 19,982 individuals — European UK (+ Ireland) UKB —
PSS004369 — —
[
  • 92 cases
  • , 6,405 controls
]
 — African unspecified — UKB —
PSS004370 — —
[
  • 24 cases
  • , 1,680 controls
]
 — East Asian — UKB —
PSS004371 — —
[
  • 932 cases
  • , 23,973 controls
]
 — European non-white British ancestry UKB —
PSS004372 — —
[
  • 195 cases
  • , 7,636 controls
]
 — South 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)
PSS004373 — —
[
  • 2,151 cases
  • , 65,274 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004243 — —
[
  • 85 cases
  • , 6,412 controls
]
 — African unspecified — UKB —
PSS004244 — —
[
  • 30 cases
  • , 1,674 controls
]
 — East Asian — UKB —
PSS009939 — — 39,444 individuals — European
(Finnish)		 — FinnGen —
PSS011364 — — 56,192 individuals — European — UKB —
PSS009134 — — 4,130 individuals — European Poland (NE Europe) UKB —
PSS008242 — — 6,327 individuals — South Asian India (South Asia) UKB —