Trait: rectum cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_1000657
Description A primary or metastatic malignant neoplasm that affects the rectum. Representative examples include carcinoma, lymphoma, and sarcoma. [NCIT: C7418]
Trait categories
Cancer
Digestive system disorder
Synonyms 19 synonyms
  • cancer of rectum
  • carcinoma of rectum
  • carcinoma of rectum
  • carcinoma of the rectum
  • carcinoma of the rectum
  • malignant neoplasm of rectum
  • malignant neoplasm of the rectum
  • malignant rectal neoplasm
  • malignant rectal tumor
  • malignant rectal tumour
  • malignant rectum neoplasm
  • malignant rectum tumor
  • malignant rectum tumour
  • malignant tumor of rectum
  • malignant tumor of the rectum
  • malignant tumour of rectum
  • malignant tumour of the rectum
  • rectal cancer
  • rectum cancer
Mapped terms 10 mapped terms
  • DOID:1993
  • EFO:1000657
  • ICD10:C20
  • ICD9:154.1
  • MEDGEN:181763
  • MONDO:0006519
  • MedDRA:10038038
  • NCIT:C7418
  • SCTID:363351006
  • UMLS:C0949022

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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000383
(PRSWEB_PHECODE153.3_C19_PRS-CS_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Malignant neoplasm of rectum, rectosigmoid junction, and anus rectum cancer,
rectosigmoid junction neoplasm		 1,078,799
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000383/ScoringFiles/PGS000383.txt.gz
PGS000384
(PRSWEB_PHECODE153.3_C3-RECTUM_PRS-CS_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Malignant neoplasm of rectum, rectosigmoid junction, and anus rectum cancer,
rectosigmoid junction neoplasm		 1,104,018
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000384/ScoringFiles/PGS000384.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
PPM001068 PGS000383
(PRSWEB_PHECODE153.3_C19_PRS-CS_MGI_20200608)
 PSS000539|
European Ancestry|
3,557 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of rectum, rectosigmoid junction, and anus OR: 1.126 [1.005, 1.262]
β: 0.119 (0.0579)		 AUROC: 0.533 [0.5, 0.567] Nagelkerke's Pseudo-R²: 0.00257
Brier score: 0.0829
Odds Ratio (OR, top 1% vs. Rest): 1.34 [0.491, 3.65]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.3_C19_PRS-CS_MGI_20200608
PPM001069 PGS000384
(PRSWEB_PHECODE153.3_C3-RECTUM_PRS-CS_MGI_20200608)
 PSS000539|
European Ancestry|
3,557 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of rectum, rectosigmoid junction, and anus OR: 1.122 [1.001, 1.257]
β: 0.115 (0.058)		 AUROC: 0.531 [0.495, 0.563] Nagelkerke's Pseudo-R²: 0.00251
Brier score: 0.0829
Odds Ratio (OR, top 1% vs. Rest): 1.02 [0.334, 3.14]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.3_C3-RECTUM_PRS-CS_MGI_20200608

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
PSS000539 PheCode:153.3; ICD9CM:154.0, 154.1, 154.2, 154.3, 209.17, 230.4, 230.5, 230.6, 796.70, 796.71, 796.72, 796.73, 796.74, 796.76, V10.06; ICD10CM:C19, C20, C21.0, C21.1, C7A.026, D01.1, D01.2, D01.3, R85.610, R85.611, R85.612, R85.613, R85.614, R85.619 —
[
  • 325 cases
  • , 3,232 controls
]
 — European — MGI —