Trait Information | |
Identifier | MONDO_0002715 |
Description | Primary or metastatic malignant neoplasm involving the uterine corpus and/or the cervix. [NCIT: C3552] | Trait category |
Cancer
|
Synonyms |
12 synonyms
|
Mapped terms |
8 mapped terms
|
Child trait(s) | 2 child traits |
Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | Ancestry distribution | Scoring File (FTP Link) |
---|---|---|---|---|---|---|
PGS000073 (CC_Cervix) |
PGP000050 | Graff RE et al. Nat Commun (2021) |
Cervical cancer | cervical carcinoma | 10 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000073/ScoringFiles/PGS000073.txt.gz |
PGS000075 (CC_Endo) |
PGP000050 | Graff RE et al. Nat Commun (2021) |
Endometrial cancer | endometrial carcinoma | 9 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000075/ScoringFiles/PGS000075.txt.gz |
PGS000541 (PRSWEB_PHECODE182_GWAS-Catalog-r2019-05-03-X182_P_5e-08_UKB_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Malignant neoplasm of uterus | uterine cancer | 18 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000541/ScoringFiles/PGS000541.txt.gz | |
PGS000542 (PRSWEB_PHECODE182_GWAS-Catalog-r2019-05-03-X182_PT_UKB_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Malignant neoplasm of uterus | uterine cancer | 20 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000542/ScoringFiles/PGS000542.txt.gz | |
PGS000784 (CC_Cervix_IV) |
PGP000186 | Kachuri L et al. Nat Commun (2020) |
Cervical cancer | cervical carcinoma | 10 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000784/ScoringFiles/PGS000784.txt.gz |
PGS000786 (CC_Endo_IV) |
PGP000186 | Kachuri L et al. Nat Commun (2020) |
Endometrial cancer | endometrial carcinoma | 9 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000786/ScoringFiles/PGS000786.txt.gz |
PGS001299 (GBE_cancer1041) |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Cervical cancer | cervical carcinoma | 24 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001299/ScoringFiles/PGS001299.txt.gz |
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 |
---|---|---|---|---|---|---|---|---|---|
PPM000193 | PGS000073 (CC_Cervix) |
PSS000112| European Ancestry| 226,216 individuals |
PGP000050 | Graff RE et al. Nat Commun (2021) |
Reported Trait: Cervical cancer | OR: 1.22 [1.19, 1.25] | — | — | Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, 10 PCs. | Results from meta-analysis of GERA and UKB |
PPM002039 | PGS000073 (CC_Cervix) |
PSS001012| European Ancestry| 211,795 individuals |
PGP000186 | Kachuri L et al. Nat Commun (2020) |Ext. |
Reported Trait: Incident cervical cancer | HR: 1.22 [1.09, 1.37] | AUROC: 0.745 C-index: 0.75 (0.017) |
— | Age at assessment, genotyping array, PCs(1-15), parity ( ≥1 live birth vs. none), oral contraceptive use (never used (0) vs. <20 years vs. ≥20 years), cigarette pack-years | C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years. |
PPM000195 | PGS000075 (CC_Endo) |
PSS000114| European Ancestry| 221,699 individuals |
PGP000050 | Graff RE et al. Nat Commun (2021) |
Reported Trait: Endometrial cancer | OR: 1.19 [1.14, 1.24] | — | — | Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, 10 PCs. | Results from meta-analysis of GERA and UKB |
PPM002041 | PGS000075 (CC_Endo) |
PSS001014| European Ancestry| 212,156 individuals |
PGP000186 | Kachuri L et al. Nat Commun (2020) |Ext. |
Reported Trait: Incident endometrial cancer | HR: 1.19 [1.1, 1.29] | AUROC: 0.755 C-index: 0.749 (0.011) |
— | Age at assessment, family history of cancer, genotyping array, PCs(1-15), parity ( ≥1 live birth vs. none), age at menarche, body mass index, Menopausal status (pre-menopausal vs. post-menopausal vs. unknown or hysterectomy), ever used hormone replacement therapy, oral contraceptive use (never used (0) vs. <20 years vs. ≥20 years), | C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years. |
PPM001226 | PGS000541 (PRSWEB_PHECODE182_GWAS-Catalog-r2019-05-03-X182_P_5e-08_UKB_20200608) |
PSS000571| European Ancestry| 6,987 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Malignant neoplasm of uterus | OR: 1.311 [1.209, 1.422] β: 0.271 (0.0415) |
AUROC: 0.576 [0.553, 0.6] | Nagelkerke's Pseudo-R²: 0.0133 Brier score: 0.082 Odds Ratio (OR, top 1% vs. Rest): 2.12 [1.17, 3.84] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE182_GWAS-Catalog-r2019-05-03-X182_P_5e-08_UKB_20200608 |
PPM001227 | PGS000542 (PRSWEB_PHECODE182_GWAS-Catalog-r2019-05-03-X182_PT_UKB_20200608) |
PSS000571| European Ancestry| 6,987 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Malignant neoplasm of uterus | OR: 1.302 [1.2, 1.413] β: 0.264 (0.0416) |
AUROC: 0.572 [0.549, 0.596] | Nagelkerke's Pseudo-R²: 0.0126 Brier score: 0.082 Odds Ratio (OR, top 1% vs. Rest): 2.6 [1.5, 4.51] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE182_GWAS-Catalog-r2019-05-03-X182_PT_UKB_20200608 |
PPM002055 | PGS000784 (CC_Cervix_IV) |
PSS001012| European Ancestry| 211,795 individuals |
PGP000186 | Kachuri L et al. Nat Commun (2020) |
Reported Trait: Incident cervical cancer | HR: 1.21 [1.07, 1.35] | AUROC: 0.745 C-index: 0.749 (0.017) |
R²: 0.437 | Age at assessment, genotyping array, PCs(1-15), parity ( ≥1 live birth vs. none), oral contraceptive use (never used (0) vs. <20 years vs. ≥20 years), cigarette pack-years | C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years. |
PPM002057 | PGS000786 (CC_Endo_IV) |
PSS001014| European Ancestry| 212,156 individuals |
PGP000186 | Kachuri L et al. Nat Commun (2020) |
Reported Trait: Incident endometrial cancer | HR: 1.18 [1.09, 1.27] | AUROC: 0.754 C-index: 0.749 (0.011) |
R²: 0.486 | Age at assessment, family history of cancer, genotyping array, PCs(1-15), parity ( ≥1 live birth vs. none), age at menarche, body mass index, Menopausal status (pre-menopausal vs. post-menopausal vs. unknown or hysterectomy), ever used hormone replacement therapy, oral contraceptive use (never used (0) vs. <20 years vs. ≥20 years), | C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years. |
PPM008992 | PGS001299 (GBE_cancer1041) |
PSS007631| African Ancestry| 6,497 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cervical cancer | — | AUROC: 0.81923 [0.77827, 0.86018] | R²: 0.1174 Incremental AUROC (full-covars): -0.00507 PGS R2 (no covariates): 0.00206 PGS AUROC (no covariates): 0.46736 [0.35923, 0.57549] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008993 | PGS001299 (GBE_cancer1041) |
PSS007632| East Asian Ancestry| 1,704 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cervical cancer | — | AUROC: 0.91431 [0.84118, 0.98744] | R²: 0.22017 Incremental AUROC (full-covars): 0.00128 PGS R2 (no covariates): 0.0 PGS AUROC (no covariates): 0.52896 [0.28465, 0.77326] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008994 | PGS001299 (GBE_cancer1041) |
PSS007633| European Ancestry| 24,905 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cervical cancer | — | AUROC: 0.76761 [0.74661, 0.7886] | R²: 0.11284 Incremental AUROC (full-covars): 0.00676 PGS R2 (no covariates): 0.00263 PGS AUROC (no covariates): 0.55215 [0.51478, 0.58952] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008995 | PGS001299 (GBE_cancer1041) |
PSS007634| South Asian Ancestry| 7,831 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cervical cancer | — | AUROC: 0.83945 [0.77567, 0.90324] | R²: 0.13265 Incremental AUROC (full-covars): -0.00075 PGS R2 (no covariates): 0.00058 PGS AUROC (no covariates): 0.46169 [0.30956, 0.61382] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM008996 | PGS001299 (GBE_cancer1041) |
PSS007635| European Ancestry| 67,425 individuals |
PGP000244 | Tanigawa Y et al. PLoS Genet (2022) |
Reported Trait: Cervical cancer | — | AUROC: 0.7705 [0.75816, 0.78284] | R²: 0.11652 Incremental AUROC (full-covars): 0.00962 PGS R2 (no covariates): 0.00294 PGS AUROC (no covariates): 0.54769 [0.52291, 0.57247] |
age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
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 |
---|---|---|---|---|---|---|---|---|
PSS007635 | — | — | [
|
— | European | white British ancestry | UKB | Testing cohort (heldout set) |
PSS001012 | Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. | — | [ ,
0.0 % Male samples |
— | European | — | UKB | — |
PSS000571 | PheCode:182; ICD9:179, 182, 182.0, 182.1, 182.8, 233.2; ICD10:C54.0, C54.1, C54.2, C54.3, C54.8, C54.9, C55, D07.0 | — | [
|
— | European | — | UKB | — |
PSS001014 | Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. | — | [ ,
0.0 % Male samples |
— | European | — | UKB | — |
PSS007631 | — | — | [
|
— | African unspecified | — | UKB | — |
PSS007632 | — | — | [
|
— | East Asian | — | UKB | — |
PSS007633 | — | — | [
|
— | European | non-white British ancestry | UKB | — |
PSS007634 | — | — | [
|
— | South Asian | — | UKB | — |
PSS000112 | Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 27010 | — | [ ,
0.0 % Male samples |
— | European | — | GERA, UKB | — |
PSS000114 | Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 27020 | — | [ ,
0.0 % Male samples |
— | European | — | GERA, UKB | — |