Trait: malignant colon neoplasm

Trait Information
Identifier MONDO_0021063
Description A primary or metastatic malignant neoplasm that affects the colon. Representative examples include carcinoma, lymphoma, and sarcoma. [NCIT: C9242]
Trait category
Other trait
Synonyms 16 synonyms
  • cancer of colon
  • colon cancer
  • colon neoplasm, malignant
  • colon tumor, malignant
  • malignant colon neoplasm
  • malignant colon tumor
  • malignant colon tumour
  • malignant colonic neoplasm
  • malignant colonic tumor
  • malignant colonic tumour
  • malignant neoplasm of colon
  • malignant neoplasm of the colon
  • malignant tumor of colon
  • malignant tumor of the colon
  • malignant tumour of colon
  • malignant tumour of the colon
Child trait(s) colon carcinoma

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
Note: This table shows all PGS for "malignant colon neoplasm" and any child terms of this trait in the EFO hierarchy by default.
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
PGS018490
(TPMI_153.2_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Colon cancer malignant colon neoplasm 13,140
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018490/ScoringFiles/PGS018490.txt.gz
PGS018491
(TPMI_153.2_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Colon cancer malignant colon neoplasm 939,847
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018491/ScoringFiles/PGS018491.txt.gz
PGS018492
(TPMI_153.2_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Colon cancer malignant colon neoplasm 32,744
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018492/ScoringFiles/PGS018492.txt.gz
PGS018493
(TPMI_153.2_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Colon cancer malignant colon neoplasm 983,802
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018493/ScoringFiles/PGS018493.txt.gz
PGS018494
(TPMI_153.2_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Colon cancer malignant colon neoplasm 996,354
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018494/ScoringFiles/PGS018494.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
PPM036672 PGS018490
(TPMI_153.2_Lassosum2)
 PSS012388|
East Asian Ancestry|
17,023 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Colon cancer — AUROC: 0.62822 R²: 0.0152 sex, age, array, PCs 1-10 —
PPM036673 PGS018491
(TPMI_153.2_LDpred2)
 PSS012387|
East Asian Ancestry|
17,023 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Colon cancer — AUROC: 0.63975 R²: 0.01799 sex, age, array, PCs 1-10 —
PPM036674 PGS018492
(TPMI_153.2_MegaPRS)
 PSS012389|
East Asian Ancestry|
17,023 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Colon cancer — AUROC: 0.62461 R²: 0.01543 sex, age, array, PCs 1-10 —
PPM036675 PGS018493
(TPMI_153.2_PRS-CS)
 PSS012390|
East Asian Ancestry|
17,023 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Colon cancer — AUROC: 0.63049 R²: 0.01696 sex, age, array, PCs 1-10 —
PPM036676 PGS018494
(TPMI_153.2_SBayesR)
 PSS012391|
East Asian Ancestry|
17,023 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Colon cancer — AUROC: 0.6282 R²: 0.0159 sex, age, array, PCs 1-10 —

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
PSS012387 153, 159.0, 209.1, 230.3, V10.05,C18, C26.0, C7A.020, C7A.021, C7A.022, C7A.023, C7A.024, C7A.025, C7A.029, D01.0, Z85.03 —
[
  • 442 cases
  • , 16,581 controls
]
,
44.12 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012388 153, 159.0, 209.1, 230.3, V10.05,C18, C26.0, C7A.020, C7A.021, C7A.022, C7A.023, C7A.024, C7A.025, C7A.029, D01.0, Z85.03 —
[
  • 442 cases
  • , 16,581 controls
]
,
44.12 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012389 153, 159.0, 209.1, 230.3, V10.05,C18, C26.0, C7A.020, C7A.021, C7A.022, C7A.023, C7A.024, C7A.025, C7A.029, D01.0, Z85.03 —
[
  • 442 cases
  • , 16,581 controls
]
,
44.12 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012390 153, 159.0, 209.1, 230.3, V10.05,C18, C26.0, C7A.020, C7A.021, C7A.022, C7A.023, C7A.024, C7A.025, C7A.029, D01.0, Z85.03 —
[
  • 442 cases
  • , 16,581 controls
]
,
44.12 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012391 153, 159.0, 209.1, 230.3, V10.05,C18, C26.0, C7A.020, C7A.021, C7A.022, C7A.023, C7A.024, C7A.025, C7A.029, D01.0, Z85.03 —
[
  • 442 cases
  • , 16,581 controls
]
,
44.12 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
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 —