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]Show more
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
JSONXMLCSVTXTMS-Excel
Loading, please wait
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 anusrectum cancer,
rectosigmoid junction neoplasm		1,078,799
G
D
E
 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 anusrectum cancer,
rectosigmoid junction neoplasm		1,104,018
G
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000384/ScoringFiles/PGS000384.txt.gz
Showing 1 to 2 of 2 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.

JSONXMLCSVTXTMS-Excel
Loading, please wait
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
PPM001068PGS000383
(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 anusOR: 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 1-4Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.3_C19_PRS-CS_MGI_20200608
PPM001069PGS000384
(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 anusOR: 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 1-4Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.3_C3-RECTUM_PRS-CS_MGI_20200608
Showing 1 to 2 of 2 rows

Evaluated Samples

JSONXMLCSVTXTMS-Excel
Loading, please wait
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
PSS000539PheCode:153.3; ICD9CM:154.0, 154.1, 154.2, 154.3, 209.17, 230.4, 230.5, 230.6, 796.70, 796.71, 796.7... 2, 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, R85.619Show more—
[
  • 325 cases
  • , 3,232 controls
]
—European—MGI—
Showing 1 to 1 of 1 rows