Trait: colon carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_1001950
Description A carcinoma that arises from epithelial cells of the colon [MONDO: DesignPattern]
Trait categories
Cancer
Digestive system disorder
Synonyms 6 synonyms
  • carcinoma of colon
  • carcinoma of the colon
  • colon cancer
  • colon cancer
  • colon carcinoma
  • colonic carcinoma
Mapped terms 8 mapped terms
  • DOID:1520
  • EFO:1001950
  • MEDGEN:147065
  • MONDO:0002032
  • NCIT:C4910
  • SCTID:269533000
  • UMLS:C0699790
  • icd11.foundation:865099988

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)
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
https://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
https://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
https://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
https://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
https://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
https://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
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000382/ScoringFiles/PGS000382.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
PPM001061 PGS000376
(PRSWEB_PHECODE153.2_C18_PRS-CS_MGI_20200608)
 PSS000538|
European Ancestry|
5,031 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
5,031 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
5,031 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
5,031 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
5,031 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
5,031 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
5,031 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (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) 		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 —