Experimental Factor Ontology (EFO) Information | |
Identifier | EFO_1000657 |
Description | A colorectal cancer that is located_in the rectum. | Trait category |
Cancer
Digestive system disorder
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Synonyms |
15 synonyms
|
Mapped term(s) |
8 mapped terms
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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 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 |
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 | — | [
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— | European | — | MGI | — |