Polygenic Score (PGS) ID: PGS001810

Predicted Trait
Reported Trait Polycythemia vera
Mapped Trait(s) polycythemia vera (EFO_0002429)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name portability-PLR_200.1
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 67
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 50%
East Asian: 16.7%
Greater Middle Eastern: 16.7%
South Asian: 16.7%
6 Sample Sets

Development Samples

Score Development/Training
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
391,124 individuals European UK (+ Ireland) UKB

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)
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 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 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 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 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 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 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