Trait: polycythemia vera

Experimental Factor Ontology (EFO) Information
Identifier EFO_0002429
Description Polycythemia vera (PV) is an acquired myeloproliferative disorder characterized by an elevated absolute red blood cell mass caused by uncontrolled red blood cell production, frequently associated with uncontrolled white blood cell and platelet production. [Orphanet: 729]
Trait categories
Cancer
Immune system disorder
Synonyms 13 synonyms
  • Osler-Vaquez disease
  • Osler-Vaquez syndrome
  • PRV
  • PV
  • Vaquez disease
  • acquired polycythemia vera
  • acquired primary erythrocytosis
  • polycythaemia rubra vera
  • polycythemia rubra vera
  • polycythemia vera
  • polycythemia vera, somatic
  • primary polycythemia
  • proliferative polycythaemia
Mapped terms 18 mapped terms
  • COHD:135214
  • DOID:8997
  • EFO:0002429
  • GARD:0007422
  • GARD:7422
  • ICD10:D45
  • ICD10CM:D45
  • ICD9:238.4
  • ICDO:9950/3
  • MESH:D011087
  • MONDO:0009891
  • MedDRA:10036057
  • NCIT:C3336
  • OMIM:263300
  • ONCOTREE:PV
  • Orphanet:729
  • UMLS:C0032463
  • http://www.nlm.nih.gov/medlineplus/ency/article/000589.htm

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)
PGS001810
(portability-PLR_200.1)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Polycythemia vera 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 —