Trait: uterine benign neoplasm

Trait Information
Identifier MONDO_0000632
Description A non-metastasizing neoplasm that arises from the uterine corpus or the cervix. Representative examp... les include leiomyoma, adenomyoma, and endocervical polyp. [NCIT: P378]Show more
Trait category
Cancer
Synonyms 23 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 tumour of the uterus
  • benign tumour of uterus
  • benign uterine neoplasm
  • benign uterine neoplasms
  • benign uterine tumor
  • benign uterine tumors
  • benign uterine tumour
  • benign uterine tumours
  • benign uterus neoplasm
  • benign uterus neoplasms
  • benign uterus tumor
  • benign uterus tumors
  • benign uterus tumour
  • benign uterus tumours
  • uterine neoplasms, benign
  • uterine tumors, benign
  • uterus benign neoplasm
Mapped terms 7 mapped terms
  • DOID:0060095
  • ICD9:219.8
  • ICD9:219.9
  • MEDGEN:57809
  • 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.
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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)
PGS001032
(GBE_HC31)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Uterine fibroidsuterine fibroid161
-
D
E
 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 uterusuterine benign neoplasm1,308
-
D
E
 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 uterusuterine benign neoplasm547,617
-
D
E
 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 fibroidsuterine fibroid4,457
G
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002263/ScoringFiles/PGS002263.txt.gz
Showing 1 to 4 of 4 rows

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.

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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
PPM007923PGS001032
(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]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007924PGS001032
(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]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007925PGS001032
(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]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007926PGS001032
(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]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007927PGS001032
(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]R²: 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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM009404PGS001813
(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—
PPM009405PGS001813
(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—
PPM009406PGS001813
(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—
PPM009407PGS001813
(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—
PPM009408PGS001813
(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—
PPM009409PGS001813
(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—
PPM009410PGS001813
(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—
PPM009411PGS001813
(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—
PPM011042PGS002021
(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—
PPM011043PGS002021
(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—
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Evaluated Samples

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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
PSS004432——
[
  • 389 cases
  • , 6,108 controls
]
—African unspecified—UKB—
PSS004433——
[
  • 28 cases
  • , 1,676 controls
]
—East Asian—UKB—
PSS004434——
[
  • 406 cases
  • , 24,499 controls
]
—Europeannon-white British ancestryUKB—
PSS004435——
[
  • 88 cases
  • , 7,743 controls
]
—South Asian—UKB—
PSS004436——
[
  • 1,148 cases
  • , 66,277 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
PSS007733——1,520 individuals—African American or Afro-CaribbeanCarribeanUKB—
PSS007952——1,164 individuals—East AsianChina (East Asia)UKB—
PSS008165——2,817 individuals—South AsianIndia (South Asia)UKB—
PSS008387——467 individuals—Greater Middle Eastern (Middle Eastern, North African or Persian)Iran (Middle East)UKB—
PSS008611——3,518 individuals—EuropeanItaly (South Europe)UKB—
PSS008836——2,067 individuals—African unspecifiedNigeria (West Africa)UKB—
PSS009057——2,468 individuals—EuropeanPoland (NE Europe)UKB—
PSS009283——10,254 individuals—EuropeanUK (+ Ireland)UKB—
PSS009591——26,637 individuals,
0.0 % Male samples
Mean = 67.04 years
Sd = 19.14 years		European
(White)		—eMERGE—
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