Trait: bone cancer

Trait Information
Identifier MONDO_0002129
Description A primary or metastatic malignant neoplasm affecting the bone or articular cartilage. [NCIT: C4016]
Trait category
Other trait
Synonyms 24 synonyms
  • bone cancer
  • bone neoplasm
  • bone tumor
  • bone tumour
  • cancer of bone
  • cancer of skeletal element
  • cancer of the bone
  • malignant bone neoplasm
  • malignant bone tumor
  • malignant neoplasm of bone
  • malignant neoplasm of skeletal element
  • malignant neoplasm of the bone
  • malignant osseous neoplasm
  • malignant osseous tumor
  • malignant osseous tumour
  • malignant skeletal element neoplasm
  • malignant tumor of bone
  • malignant tumor of the bone
  • malignant tumour of bone
  • malignant tumour of the bone
  • osseous cancer
  • osseous tumor
  • osseous tumour
  • skeletal element cancer
Child trait(s) acquired polycythemia vera

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 PGS for child terms of "bone cancer" in the EFO hierarchy.
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)
PGS001810
(portability-PLR_200.1)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Polycythemia vera acquired polycythemia vera 67
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001810/ScoringFiles/PGS001810.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
PPM009382 PGS001810
(portability-PLR_200.1)
 PSS009280|
European Ancestry|
19,539 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Polycythemia vera — — Partial Correlation (partial-r): 0.017 [0.003, 0.031] sex, age, birth date, deprivation index, 16 PCs —
PPM009383 PGS001810
(portability-PLR_200.1)
 PSS009054|
European Ancestry|
4,052 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Polycythemia vera — — Partial Correlation (partial-r): 0.0195 [-0.0114, 0.0503] sex, age, birth date, deprivation index, 16 PCs —
PPM009384 PGS001810
(portability-PLR_200.1)
 PSS008608|
European Ancestry|
6,489 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Polycythemia vera — — Partial Correlation (partial-r): 0.026 [0.0016, 0.0503] sex, age, birth date, deprivation index, 16 PCs —
PPM009385 PGS001810
(portability-PLR_200.1)
 PSS008384|
Greater Middle Eastern Ancestry|
1,178 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Polycythemia vera — — Partial Correlation (partial-r): -0.0173 [-0.0748, 0.0404] sex, age, birth date, deprivation index, 16 PCs —
PPM009386 PGS001810
(portability-PLR_200.1)
 PSS008162|
South Asian Ancestry|
6,171 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Polycythemia vera — — Partial Correlation (partial-r): -0.0038 [-0.0288, 0.0212] sex, age, birth date, deprivation index, 16 PCs —
PPM009387 PGS001810
(portability-PLR_200.1)
 PSS007949|
East Asian Ancestry|
1,787 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Polycythemia vera — — Partial Correlation (partial-r): -0.0072 [-0.0538, 0.0395] 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
PSS007949 — — 1,787 individuals — East Asian China (East Asia) UKB —
PSS009280 — — 19,539 individuals — European UK (+ Ireland) UKB —
PSS009054 — — 4,052 individuals — European Poland (NE Europe) UKB —
PSS008608 — — 6,489 individuals — European Italy (South Europe) UKB —
PSS008384 — — 1,178 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008162 — — 6,171 individuals — South Asian India (South Asia) UKB —