Trait: uterine benign neoplasm

Trait Information
Identifier MONDO_0000632
Description A non-metastasizing neoplasm that arises from the uterine corpus or the cervix. Representative examples include leiomyoma, adenomyoma, and endocervical polyp. [NCIT: P378]
Trait category
Cancer
Synonyms 17 synonyms
  • Uterous neoplasms, benign
  • Uterous tumors, benign
  • benign neoplasm of the uterus
  • benign neoplasm of uterus
  • benign tumor of the uterus
  • benign tumor of uterus
  • benign uterine neoplasm
  • benign uterine neoplasms
  • benign uterine tumor
  • benign uterine tumors
  • benign uterus neoplasm
  • benign uterus neoplasms
  • benign uterus tumor
  • benign uterus tumors
  • uterine neoplasms, benign
  • uterine tumors, benign
  • uterus benign neoplasm
Mapped terms 6 mapped terms
  • DOID:0060095
  • ICD9:219.8
  • ICD9:219.9
  • NCIT:C3609
  • SCTID:92470003
  • UMLS:C0153999
Child trait(s) uterine fibroid

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 all PGS for "uterine benign neoplasm" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS001032
(GBE_HC31)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Uterine fibroids uterine fibroid 161
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001032/ScoringFiles/PGS001032.txt.gz
PGS001813
(portability-PLR_218)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Benign neoplasm of uterus uterine benign neoplasm 1,308
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001813/ScoringFiles/PGS001813.txt.gz
PGS002021
(portability-ldpred2_218)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Benign neoplasm of uterus uterine benign neoplasm 547,617
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002021/ScoringFiles/PGS002021.txt.gz
PGS002263
(PRS_UF)
PGP000291 |
Piekos JA et al. Hum Genet (2022)
Uterine fibroids uterine fibroid 4,457
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002263/ScoringFiles/PGS002263.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
PPM007923 PGS001032
(GBE_HC31)
PSS004432|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Uterine fibroids AUROC: 0.76646 [0.74986, 0.78306] : 0.19353
Incremental AUROC (full-covars): 0.00769
PGS R2 (no covariates): 0.00167
PGS AUROC (no covariates): 0.52708 [0.49761, 0.55655]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007924 PGS001032
(GBE_HC31)
PSS004433|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Uterine fibroids AUROC: 0.78861 [0.72118, 0.85605] : 0.15287
Incremental AUROC (full-covars): -0.00776
PGS R2 (no covariates): 2e-05
PGS AUROC (no covariates): 0.48768 [0.36905, 0.60631]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007925 PGS001032
(GBE_HC31)
PSS004434|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Uterine fibroids AUROC: 0.76622 [0.75066, 0.78178] : 0.12754
Incremental AUROC (full-covars): 0.00896
PGS R2 (no covariates): 0.00275
PGS AUROC (no covariates): 0.54817 [0.52052, 0.57581]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007926 PGS001032
(GBE_HC31)
PSS004435|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Uterine fibroids AUROC: 0.84627 [0.82086, 0.87168] : 0.18068
Incremental AUROC (full-covars): 0.00364
PGS R2 (no covariates): 0.00384
PGS AUROC (no covariates): 0.55148 [0.49383, 0.60912]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007927 PGS001032
(GBE_HC31)
PSS004436|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Uterine fibroids AUROC: 0.78165 [0.77294, 0.79036] : 0.14246
Incremental AUROC (full-covars): 0.00535
PGS R2 (no covariates): 0.00214
PGS AUROC (no covariates): 0.54273 [0.52605, 0.55942]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009404 PGS001813
(portability-PLR_218)
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): 0.0392 [0.0199, 0.0586] sex, age, birth date, deprivation index, 16 PCs
PPM009405 PGS001813
(portability-PLR_218)
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): 0.0775 [0.038, 0.1168] sex, age, birth date, deprivation index, 16 PCs
PPM009406 PGS001813
(portability-PLR_218)
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): 0.0381 [0.005, 0.0712] sex, age, birth date, deprivation index, 16 PCs
PPM009407 PGS001813
(portability-PLR_218)
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): 0.1251 [0.0328, 0.2152] sex, age, birth date, deprivation index, 16 PCs
PPM009408 PGS001813
(portability-PLR_218)
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): 0.0862 [0.0493, 0.1228] sex, age, birth date, deprivation index, 16 PCs
PPM009409 PGS001813
(portability-PLR_218)
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): 0.0245 [-0.0335, 0.0823] sex, age, birth date, deprivation index, 16 PCs
PPM009410 PGS001813
(portability-PLR_218)
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): 0.0263 [-0.0244, 0.0768] sex, age, birth date, deprivation index, 16 PCs
PPM009411 PGS001813
(portability-PLR_218)
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): 0.0186 [-0.0248, 0.0618] sex, age, birth date, deprivation index, 16 PCs
PPM011042 PGS002021
(portability-ldpred2_218)
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 PGS002021
(portability-ldpred2_218)
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 PGS002021
(portability-ldpred2_218)
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 PGS002021
(portability-ldpred2_218)
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 PGS002021
(portability-ldpred2_218)
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 PGS002021
(portability-ldpred2_218)
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 PGS002021
(portability-ldpred2_218)
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 PGS002021
(portability-ldpred2_218)
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
PPM012882 PGS002263
(PRS_UF)
PSS009591|
European Ancestry|
26,637 individuals
PGP000291 |
Piekos JA et al. Hum Genet (2022)
Reported Trait: Uterine fibroid OR: 1.35 [1.34, 1.37] AUROC: 0.6 [0.58, 0.62] BMI, age, 10 principal components
PPM012883 PGS002263
(PRS_UF)
PSS009591|
European Ancestry|
26,637 individuals
PGP000291 |
Piekos JA et al. Hum Genet (2022)
Reported Trait: Benign neoplasm of uterus OR: 1.31 [1.26, 1.37] BMI, age, 10 principal components
PPM012884 PGS002263
(PRS_UF)
PSS009591|
European Ancestry|
26,637 individuals
PGP000291 |
Piekos JA et al. Hum Genet (2022)
Reported Trait: Uterine leiomyoma OR: 1.32 [1.26, 1.37] BMI, age, 10 principal components

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
PSS008611 3,518 individuals European Italy (South Europe) UKB
PSS009591 26,637 individuals,
0.0 % Male samples
Mean = 67.04 years
Sd = 19.14 years
European
(White)
eMERGE
PSS007952 1,164 individuals East Asian China (East Asia) UKB
PSS007733 1,520 individuals African American or Afro-Caribbean Carribean UKB
PSS004432
[
  • 389 cases
  • , 6,108 controls
]
African unspecified UKB
PSS004433
[
  • 28 cases
  • , 1,676 controls
]
East Asian UKB
PSS004434
[
  • 406 cases
  • , 24,499 controls
]
European non-white British ancestry UKB
PSS004435
[
  • 88 cases
  • , 7,743 controls
]
South Asian UKB
PSS004436
[
  • 1,148 cases
  • , 66,277 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS009057 2,468 individuals European Poland (NE Europe) UKB
PSS009283 10,254 individuals European UK (+ Ireland) UKB