Trait: cervical carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0001061
Description A carcinoma arising from either the exocervical squamous epithelium or the endocervical glandular epithelium. The major histologic types of cervical carcinoma are: squamous carcinoma, adenocarcinoma, adenosquamous carcinoma, adenoid cystic carcinoma and undifferentiated carcinoma. [NCIT: C9039]
Trait category
Cancer
Synonyms 14 synonyms
  • cancer of the cervix
  • cancer of the uterine cervix
  • cancer of uterine cervix
  • carcinoma cervix uteri
  • carcinoma of cervix
  • carcinoma of cervix uteri
  • carcinoma of the cervix
  • carcinoma of the cervix uteri
  • carcinoma of the uterine cervix
  • carcinoma of uterine cervix
  • cervical carcinoma
  • cervix carcinoma
  • cervix uteri carcinoma
  • uterine cervix carcinoma
Mapped terms 8 mapped terms
  • DOID:2893
  • DOID:4362
  • EFO:0001061
  • MONDO:0005131
  • NCIT:C9039
  • OMIM:603956
  • SCTID:285432005
  • UMLS:C0302592

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
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
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
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

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
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.
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)
: 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.
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] : 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] : 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] : 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] : 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] : 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

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
PSS001012 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases.
[
  • 282 cases
  • , 211,513 controls
]
,
0.0 % Male samples
European UKB
PSS007631
[
  • 28 cases
  • , 6,469 controls
]
African unspecified UKB
PSS007632
[
  • 6 cases
  • , 1,698 controls
]
East Asian UKB
PSS007633
[
  • 231 cases
  • , 24,674 controls
]
European non-white British ancestry UKB
PSS007634
[
  • 13 cases
  • , 7,818 controls
]
South Asian UKB
PSS007635
[
  • 561 cases
  • , 66,864 controls
]
European white British ancestry UKB Testing cohort (heldout set)
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
[
  • 6,568 cases
  • , 219,648 controls
]
,
0.0 % Male samples
European GERA, UKB