Trait: colon carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_1001950
Description A malignant epithelial neoplasm that arises from the colon and invades through the muscularis mucosa into the submucosa. The vast majority are adenocarcinomas.
Trait category
Cancer
Digestive system disorder
Synonyms 8 synonyms
  • Carcinoma of Colon
  • Colon Cancer
  • Colonic Carcinoma
  • carcinoma of colon
  • carcinoma of the colon
  • colon cancer
  • colon carcinoma
  • colonic carcinoma
Mapped term(s) 7 mapped terms
  • DOID:1520
  • ICD10:C18
  • MONDO:0002032
  • NCIT:C4910
  • NCIt:C4910
  • SCTID:269533000
  • UMLS:C0699790

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)
PGS000376 PRSWEB_PHECODE153.2_C18_PRS-CS_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Colon cancer colon carcinoma 1,111,490 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000376/ScoringFiles/PGS000376.txt.gz
PGS000377 PRSWEB_PHECODE153.2_C18_LASSOSUM_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Colon cancer colon carcinoma 5,740,814 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000377/ScoringFiles/PGS000377.txt.gz
PGS000378 PRSWEB_PHECODE153.2_C3-COLON_PRS-CS_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Colon cancer colon carcinoma 1,111,399 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000378/ScoringFiles/PGS000378.txt.gz
PGS000379 PRSWEB_PHECODE153.2_C3-COLON_LASSOSUM_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Colon cancer colon carcinoma 5,715,093 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000379/ScoringFiles/PGS000379.txt.gz
PGS000380 PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_PRS-CS_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Colon cancer colon carcinoma 1,119,238 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000380/ScoringFiles/PGS000380.txt.gz
PGS000381 PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_PT_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Colon cancer colon carcinoma 12 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000381/ScoringFiles/PGS000381.txt.gz
PGS000382 PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_LASSOSUM_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Colon cancer colon carcinoma 150 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000382/ScoringFiles/PGS000382.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
PPM001061 PGS000376 (PRSWEB_PHECODE153.2_C18_PRS-CS_MGI_20200608) PSS000538 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Colon cancer OR: 1.177 [1.069, 1.297]
β: 0.163 (0.0491)
AUROC: 0.547 [0.518, 0.576] Nagelkerke's Pseudo-R²: 0.0046
Brier score: 0.0832
Odds Ratio (OR, top 1% vs. Rest): 1.65 [0.753, 3.61]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_C18_PRS-CS_MGI_20200608
PPM001062 PGS000377 (PRSWEB_PHECODE153.2_C18_LASSOSUM_MGI_20200608) PSS000538 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Colon cancer OR: 1.174 [1.066, 1.292]
β: 0.16 (0.049)
AUROC: 0.545 [0.518, 0.574] Nagelkerke's Pseudo-R²: 0.00441
Brier score: 0.0831
Odds Ratio (OR, top 1% vs. Rest): 1.4 [0.607, 3.22]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_C18_LASSOSUM_MGI_20200608
PPM001063 PGS000378 (PRSWEB_PHECODE153.2_C3-COLON_PRS-CS_MGI_20200608) PSS000538 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Colon cancer OR: 1.141 [1.038, 1.254]
β: 0.132 (0.0484)
AUROC: 0.536 [0.509, 0.565] Nagelkerke's Pseudo-R²: 0.00301
Brier score: 0.0832
Odds Ratio (OR, top 1% vs. Rest): 1.82 [0.867, 3.84]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_C3-COLON_PRS-CS_MGI_20200608
PPM001064 PGS000379 (PRSWEB_PHECODE153.2_C3-COLON_LASSOSUM_MGI_20200608) PSS000538 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Colon cancer OR: 1.143 [1.038, 1.258]
β: 0.134 (0.049)
AUROC: 0.536 [0.51, 0.567] Nagelkerke's Pseudo-R²: 0.00302
Brier score: 0.0832
Odds Ratio (OR, top 1% vs. Rest): 0.757 [0.252, 2.28]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_C3-COLON_LASSOSUM_MGI_20200608
PPM001065 PGS000380 (PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_PRS-CS_MGI_20200608) PSS000538 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Colon cancer OR: 1.324 [1.203, 1.457]
β: 0.281 (0.0489)
AUROC: 0.569 [0.539, 0.599] Nagelkerke's Pseudo-R²: 0.0138
Brier score: 0.0827
Odds Ratio (OR, top 1% vs. Rest): 3.85 [2.19, 6.77]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_PRS-CS_MGI_20200608
PPM001066 PGS000381 (PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_PT_MGI_20200608) PSS000538 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Colon cancer OR: 1.212 [1.105, 1.33]
β: 0.193 (0.0472)
AUROC: 0.55 [0.522, 0.577] Nagelkerke's Pseudo-R²: 0.00703
Brier score: 0.0831
Odds Ratio (OR, top 1% vs. Rest): 1.6 [0.733, 3.51]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_PT_MGI_20200608
PPM001067 PGS000382 (PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_LASSOSUM_MGI_20200608) PSS000538 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Colon cancer OR: 1.247 [1.134, 1.371]
β: 0.221 (0.0483)
AUROC: 0.567 [0.54, 0.594] Nagelkerke's Pseudo-R²: 0.00899
Brier score: 0.083
Odds Ratio (OR, top 1% vs. Rest): 1.17 [0.477, 2.87]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.2_UKBB-SAIGE-HRC-X153.2_LASSOSUM_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
PSS000538 PheCode:153.2; ICD9CM:153.0, 153.1, 153.2, 153.3, 153.4, 153.5, 153.6, 153.7, 153.8, 153.9, 159.0, 209.10, 209.11, 209.12, 209.13, 209.14, 209.15, 209.16, 230.3, V10.05; ICD10CM:C18, C18.0, C18.1, C18.2, C18.3, C18.4, C18.5, C18.6, C18.7, C18.8, C18.9, C26.0, C7A.020, C7A.021, C7A.022, C7A.023, C7A.024, C7A.025, C7A.029, D01.0
[
  • 462 cases
  • , 4,569 controls
]
European MGI