Polygenic Score (PGS) ID: PGS002021

Predicted Trait
Reported Trait Benign neoplasm of uterus
Mapped Trait(s) uterine benign neoplasm (MONDO_0000632)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_218
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 547,617
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: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
PPM011042 PSS009283|
European Ancestry|
10,254 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of uterus Partial Correlation (partial-r): 0.0479 [0.0286, 0.0672] sex, age, birth date, deprivation index, 16 PCs
PPM011043 PSS009057|
European Ancestry|
2,468 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of uterus Partial Correlation (partial-r): 0.1046 [0.0653, 0.1436] sex, age, birth date, deprivation index, 16 PCs
PPM011044 PSS008611|
European Ancestry|
3,518 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of uterus Partial Correlation (partial-r): 0.0454 [0.0123, 0.0785] sex, age, birth date, deprivation index, 16 PCs
PPM011046 PSS008165|
South Asian Ancestry|
2,817 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of uterus Partial Correlation (partial-r): 0.0966 [0.0597, 0.1332] sex, age, birth date, deprivation index, 16 PCs
PPM011048 PSS007733|
African Ancestry|
1,520 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of uterus Partial Correlation (partial-r): 0.0301 [-0.0205, 0.0806] sex, age, birth date, deprivation index, 16 PCs
PPM011045 PSS008387|
Greater Middle Eastern Ancestry|
467 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of uterus Partial Correlation (partial-r): 0.152 [0.0602, 0.2413] sex, age, birth date, deprivation index, 16 PCs
PPM011047 PSS007952|
East Asian Ancestry|
1,164 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of uterus Partial Correlation (partial-r): 0.0232 [-0.0347, 0.0811] sex, age, birth date, deprivation index, 16 PCs
PPM011049 PSS008836|
African Ancestry|
2,067 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of uterus Partial Correlation (partial-r): 0.0238 [-0.0195, 0.067] 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
PSS008836 2,067 individuals African unspecified Nigeria (West Africa) UKB
PSS008165 2,817 individuals South Asian India (South Asia) UKB
PSS008387 467 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009283 10,254 individuals European UK (+ Ireland) UKB
PSS007952 1,164 individuals East Asian China (East Asia) UKB
PSS007733 1,520 individuals African American or Afro-Caribbean Carribean UKB
PSS009057 2,468 individuals European Poland (NE Europe) UKB
PSS008611 3,518 individuals European Italy (South Europe) UKB