Trait: rectum cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_1000657
Description A colorectal cancer that is located_in the rectum.
Trait category
Cancer
Digestive system disorder
Synonyms 15 synonyms
  • cancer of rectum
  • carcinoma of rectum
  • carcinoma of the rectum
  • malignant Rectal tumor
  • malignant neoplasm of rectum
  • malignant neoplasm of the rectum
  • malignant rectal neoplasm
  • malignant rectal tumor
  • malignant rectum neoplasm
  • malignant rectum tumor
  • malignant tumor of rectum
  • malignant tumor of rectum (disorder)
  • malignant tumor of the rectum
  • rectal cancer
  • rectum cancer
Mapped term(s) 8 mapped terms
  • DOID:1993
  • ICD10:C19
  • ICD10:C20
  • ICD9:154.1
  • MONDO:0006519
  • MSH:D012004
  • NCIT:C7418
  • SCTID:363351006

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS 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 rectosigmoid junction neoplasm
rectum cancer		 1,078,799 http://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 rectosigmoid junction neoplasm
rectum cancer		 1,104,018 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000384/ScoringFiles/PGS000384.txt.gz

PGS 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 ID) 		Evaluated Score PGS Sample Set ID
(PSS ID) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM001069 PGS000384 (PRSWEB_PHECODE153.3_C3-RECTUM_PRS-CS_MGI_20200608) PSS000539 PGP000118
Fritsche LG et al. (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
PPM001068 PGS000383 (PRSWEB_PHECODE153.3_C19_PRS-CS_MGI_20200608) PSS000539 PGP000118
Fritsche LG et al. (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

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		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 —