Trait: colorectal cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005842
Description A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma. [NCIT: C4978]
Trait category
Cancer
Digestive system disorder
Synonyms 27 synonyms
  • malignant tumor of the large bowel
  • malignant tumor of large intestine
  • malignant tumor of large bowel
  • malignant large bowel tumor
  • Colorectal Cancer
  • malignant colorectal tumor
  • malignant colorectum neoplasm
  • malignant neoplasm of large bowel
  • malignant large bowel neoplasm
  • malignant large intestine neoplasm
  • cancer of large bowel
  • malignant neoplasm of the large bowel
  • colorectal cancer
  • malignant neoplasm of large intestine
  • malignant colorectal neoplasm
  • malignant large intestine tumor
  • malignant neoplasm of colorectum
  • colorectum cancer
  • cancer of colorectum
  • cancer of the large bowel
  • malignant tumor of the large intestine
  • Cancers, Colorectal
  • cancer of large intestine
  • Colorectal Cancers
  • malignant neoplasm of the large intestine
  • Malignant Colorectal Neoplasm
  • Cancer, Colorectal
Mapped term(s) 14 mapped terms
  • NCIT:C4978
  • OMIM:114500
  • OMIM:608812
  • ICD10:C18.9
  • SCTID:363510005
  • DOID:9256
  • OMIM:615083
  • OMIM:612591
  • DOID:5672
  • MONDO:0005575
  • KEGG:05210
  • UMLS:C1527249
  • OMIM:612229
  • NCIt:C4978

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)
PGS000055 PRS_CRC PGP000040
Schmit SL et al. J Natl Cancer Inst (2019)
Colorectal cancer colorectal cancer 76 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000055/ScoringFiles/PGS000055.txt.gz
PGS000074 CC_Colorectal PGP000050
Graff RE et al. bioRxiv (2020)
Pre
Colorectal cancer colorectal cancer 103 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000074/ScoringFiles/PGS000074.txt.gz
PGS000146 CRC_GRS_27 PGP000069
Hsu L et al. Gastroenterology (2015)
Colorectal cancer risk colorectal cancer 27 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000146/ScoringFiles/PGS000146.txt.gz
PGS000147 CRC21 PGP000070
Ibáñez-Sanz G et al. Sci Rep (2017)
Colorectal cancer colorectal cancer 21 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000147/ScoringFiles/PGS000147.txt.gz
PGS000148 CRC63 PGP000071
Jeon J et al. Gastroenterology (2018)
Colorectal cancer colorectal cancer 63 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000148/ScoringFiles/PGS000148.txt.gz
PGS000149 CRC41 PGP000072
Smith T et al. Br J Cancer (2018)
Colorectal cancer colorectal cancer 41 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000149/ScoringFiles/PGS000149.txt.gz
PGS000150 GRS48 PGP000073
Weigl K et al. Gastroenterology (2018)
Colorectal cancer colorectal cancer 48 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000150/ScoringFiles/PGS000150.txt.gz
PGS000151 SC_GRS PGP000074
Xin J et al. Gene (2018)
Colorectal cancer colorectal cancer 14 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000151/ScoringFiles/PGS000151.txt.gz
PGS000154 cGRS_Colorectal PGP000075
Shi Z et al. Cancer Med (2019)
Colorectal cancer colorectal cancer 30 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000154/ScoringFiles/PGS000154.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
PPM000194 PGS000074 (CC_Colorectal) PSS000113 PGP000050
Graff RE et al. (2020)
Pre
Reported Trait: Colorectal cancer OR: 1.37[1.33, 1.4] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000438 PGS000146 (CRC_GRS_27) PSS000254 PGP000069
Hsu L et al. (2015)
Reported Trait: Proximal colon cancer OR: 1.07[1.04, 1.1] Study, age, endoscopy, family history
PPM000439 PGS000146 (CRC_GRS_27) PSS000252 PGP000069
Hsu L et al. (2015)
Reported Trait: Distal colon cancer OR: 1.08[1.06, 1.11] Study, age, endoscopy, family history
PPM000464 PGS000149 (CRC41) PSS000263 PGP000072
Smith T et al. (2018)
Reported Trait: Incident colorectal cancer in individuals with a family history C-index: 0.68[0.67, 0.7] Wells et al. model (age, diabetes, multi-vitamin usage, family history of colon cancer, years of education, body mass index, alcohol intake, physical activity, non-steroidal anti-inflammatory drug usage, red meat intake, smoking and oestrogen use [women only]) Fully recalibrated model
PPM000463 PGS000149 (CRC41) PSS000263 PGP000072
Smith T et al. (2018)
Reported Trait: Incident colorectal cancer C-index: 0.68[0.67, 0.7] Wells et al. model (age, diabetes, multi-vitamin usage, family history of colon cancer, years of education, body mass index, alcohol intake, physical activity, non-steroidal anti-inflammatory drug usage, red meat intake, smoking and oestrogen use [women only]) Fully recalibrated model
PPM000459 PGS000149 (CRC41) PSS000262 PGP000072
Smith T et al. (2018)
Reported Trait: Incident colorectal cancer in individuals without a family history C-index: 0.66[0.62, 0.69] Taylor et al. model (age-specific rates of CRC with estimated relative risks for different degrees of CRC family history) Fully recalibrated model
PPM000458 PGS000149 (CRC41) PSS000262 PGP000072
Smith T et al. (2018)
Reported Trait: Incident colorectal cancer in individuals with a family history C-index: 0.69[0.67, 0.7] Taylor et al. model (age-specific rates of CRC with estimated relative risks for different degrees of CRC family history) Fully recalibrated model
PPM000457 PGS000149 (CRC41) PSS000262 PGP000072
Smith T et al. (2018)
Reported Trait: Incident colorectal cancer C-index: 0.68[0.67, 0.7] Taylor et al. model (age-specific rates of CRC with estimated relative risks for different degrees of CRC family history) Fully recalibrated model
PPM000452 PGS000148 (CRC63) PSS000260 PGP000071
Jeon J et al. (2018)
Reported Trait: Colorectal cancer AUROC: 0.59[0.58, 0.6] age, family history, study, endoscopy history Risk prediction using Model III (Family History & G-score)
PPM000451 PGS000148 (CRC63) PSS000261 PGP000071
Jeon J et al. (2018)
Reported Trait: Colorectal cancer AUROC: 0.63[0.62, 0.64] age, family history, study, endoscopy history, E-score (height, body mass index, education, history of type 2 diabetes mellitus, smoking status, alcohol consumption, regular aspirin use, regular NSAIDs use, smoking pack-years, dietary factors, total-energy, physical activity) Risk prediction using Model IV (Family history & E-score & G-score)
PPM000450 PGS000148 (CRC63) PSS000261 PGP000071
Jeon J et al. (2018)
Reported Trait: Colorectal cancer AUROC: 0.59[0.58, 0.6] age, family history, study, endoscopy history Risk prediction using Model III (Family History & G-score)
PPM000465 PGS000149 (CRC41) PSS000263 PGP000072
Smith T et al. (2018)
Reported Trait: Incident colorectal cancer in individuals without a family history C-index: 0.67[0.63, 0.71] Wells et al. model (age, diabetes, multi-vitamin usage, family history of colon cancer, years of education, body mass index, alcohol intake, physical activity, non-steroidal anti-inflammatory drug usage, red meat intake, smoking and oestrogen use [women only]) Fully recalibrated model
PPM000453 PGS000148 (CRC63) PSS000260 PGP000071
Jeon J et al. (2018)
Reported Trait: Colorectal cancer AUROC: 0.62[0.61, 0.63] age, family history, study, endoscopy history, E-score (height, body mass index, education, history of type 2 diabetes mellitus, smoking status, alcohol consumption, regular aspirin use, regular NSAIDs use, regular use of post-menopausal hormones, smoking pack-years, dietary factors, total-energy, physical activity) Risk prediction using Model IV (Family history & E-score & G-score)
PPM000139 PGS000055 (PRS_CRC) PSS000087 PGP000040
Schmit SL et al. (2019)
Reported Trait: Colorectal cancer Familial relative risk explained (%): 11.9[9.2, 15.5]
PRS percentile threshold for Odds Ratio > 2: 95.7
age, sex, PCs, PC*study
PPM000140 PGS000055 (PRS_CRC) PSS000086 PGP000040
Schmit SL et al. (2019)
Reported Trait: Colorectal cancer PRS percentile threshold for Odds Ratio > 2: 99.1 age, sex, PCs, PC*study
PPM000445 PGS000146 (CRC_GRS_27) PSS000257 PGP000069
Hsu L et al. (2015)
Reported Trait: Colorectal cancer AUROC: 0.56[0.51, 0.61] Age, endoscopy, family history
PPM000444 PGS000146 (CRC_GRS_27) PSS000258 PGP000069
Hsu L et al. (2015)
Reported Trait: Colorectal cancer AUROC: 0.59[0.54, 0.64] Age, endoscopy, family history
PPM000443 PGS000146 (CRC_GRS_27) PSS000255 PGP000069
Hsu L et al. (2015)
Reported Trait: Rectal cancer OR: 1.12[1.08, 1.15] Study, age, endoscopy, family history
PPM000442 PGS000146 (CRC_GRS_27) PSS000251 PGP000069
Hsu L et al. (2015)
Reported Trait: Distal colon cancer OR: 1.08[1.05, 1.1] Study, age, endoscopy, family history
PPM000441 PGS000146 (CRC_GRS_27) PSS000253 PGP000069
Hsu L et al. (2015)
Reported Trait: Proximal colon cancer OR: 1.06[1.03, 1.08] Study, age, endoscopy, family history
PPM000440 PGS000146 (CRC_GRS_27) PSS000256 PGP000069
Hsu L et al. (2015)
Reported Trait: Rectal cancer OR: 1.06[1.03, 1.09] Study, age, endoscopy, family history
PPM000448 PGS000147 (CRC21) PSS000259 PGP000070
Ibáñez-Sanz G et al. (2017)
Reported Trait: Colorectal cancer AUROC: 0.63[0.6, 0.66] Odds Ratio (OR; per allele): 1.07[1.04, 1.1] environmental risk factors ( alcohol consumption, obesity, physical activity, red meat and vegetable consumption, nonsteroidal anti-inflammatory drug use), family history
PPM000447 PGS000147 (CRC21) PSS000259 PGP000070
Ibáñez-Sanz G et al. (2017)
Reported Trait: Rectal cancer Odds Ratio (OR; per allele): 1.1[1.06, 1.15] environmental risk factors ( alcohol consumption, obesity, physical activity, red meat and vegetable consumption, nonsteroidal anti-inflammatory drug use), family history
PPM000446 PGS000147 (CRC21) PSS000259 PGP000070
Ibáñez-Sanz G et al. (2017)
Reported Trait: Colon cancer Odds Ratio (OR; per allele): 1.06[1.03, 1.09] environmental risk factors ( alcohol consumption, obesity, physical activity, red meat and vegetable consumption, nonsteroidal anti-inflammatory drug use), family history
PPM000469 PGS000150 (GRS48) PSS000269 PGP000073
Weigl K et al. (2018)
Reported Trait: advanced neoplasm (colorectal cancer) C-index: 0.615 Odds Ratio (OR; highest vs. lowest tertile of GRS): 2.74[1.84, 4.09] sex, age, previous colonoscopy, physical activity
PPM000468 PGS000150 (GRS48) PSS000269 PGP000073
Weigl K et al. (2018)
Reported Trait: advanced neoplasm (colorectal cancer) C-index: 0.599 Odds Ratio (OR; highest vs. lowest tertile of GRS): 2.64[1.77, 3.92] sex, age
PPM000467 PGS000150 (GRS48) PSS000268 PGP000073
Weigl K et al. (2018)
Reported Trait: non-advanced adenoma (colorectal) C-index: 0.596 Odds Ratio (OR; highest vs. lowest tertile of GRS): 1.05[0.7, 1.55] sex, age, previous colonoscopy, physical activity
PPM000466 PGS000150 (GRS48) PSS000268 PGP000073
Weigl K et al. (2018)
Reported Trait: non-advanced adenoma (colorectal) C-index: 0.584 Odds Ratio (OR; highest vs. lowest tertile of GRS): 1.04[0.7, 1.55] sex, age
PPM000471 PGS000151 (SC_GRS) PSS000271 PGP000074
Xin J et al. (2018)
Reported Trait: Colorectal cancer AUROC: 0.607[0.581, 0.633] smoking status
PPM000462 PGS000149 (CRC41) PSS000263 PGP000072
Smith T et al. (2018)
Reported Trait: Incident colorectal cancer in individuals without a family history C-index: 0.57[0.53, 0.6]
PPM000461 PGS000149 (CRC41) PSS000263 PGP000072
Smith T et al. (2018)
Reported Trait: Incident colorectal cancer in individuals with a family history C-index: 0.56[0.55, 0.58]
PPM000460 PGS000149 (CRC41) PSS000263 PGP000072
Smith T et al. (2018)
Reported Trait: Incident colorectal cancer C-index: 0.57[0.55, 0.58]
PPM000456 PGS000149 (CRC41) PSS000262 PGP000072
Smith T et al. (2018)
Reported Trait: Incident colorectal cancer in individuals without a family history C-index: 0.55[0.52, 0.59]
PPM000455 PGS000149 (CRC41) PSS000262 PGP000072
Smith T et al. (2018)
Reported Trait: Incident colorectal cancer in individuals with a family history C-index: 0.57[0.55, 0.58]
PPM000454 PGS000149 (CRC41) PSS000262 PGP000072
Smith T et al. (2018)
Reported Trait: Incident colorectal cancer C-index: 0.56[0.55, 0.58]
PPM000449 PGS000147 (CRC21) PSS000259 PGP000070
Ibáñez-Sanz G et al. (2017)
Reported Trait: Colorectal cancer AUROC: 0.56[0.54, 0.58]
PPM000470 PGS000151 (SC_GRS) PSS000271 PGP000074
Xin J et al. (2018)
Reported Trait: Colorectal cancer AUROC: 0.6[0.579, 0.622]
PPM000485 PGS000154 (cGRS_Colorectal) PSS000274 PGP000075
Shi Z et al. (2019)
Reported Trait: Colorectal cancer Odds Ratio (OR; high vs. average risk groups): 1.18[0.87, 1.61]
PPM000474 PGS000154 (cGRS_Colorectal) PSS000274 PGP000075
Shi Z et al. (2019)
Reported Trait: Colorectal cancer Mean realative risk: 1.08[1.04, 1.12]
Wilcoxon test (case vs. control) p-value: 8.29e-06

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
PSS000268 Unselected participants of the German screening colonoscopy program are recruited by gastroenterology practices in southern Germany in this multicenter study.Colonoscopy and histology reports are collected and information from these reports is extracted independently in a standardized way by two trained investigators, who are blinded with respect to questionnaire and genotype data and who resolve discrepancies by consensus after further review and discussion. Based on colonoscopy reports, participants are categorized with respect to the most advanced lesion: CRC, advanced adenoma (AA), non-advanced adenoma (NAA), hyperplastic polyp, or undefined polyp. Advanced adenomas are defined as adenomas ≥1 cm or adenomas with cellular or structural atypia.
[
  • 294 cases
  • , 749 controls
]
,
61.74 % Male samples
Range = [50.0, 79.0] years European BLITZ
PSS000269 Unselected participants of the German screening colonoscopy program are recruited by gastroenterology practices in southern Germany in this multicenter study.Colonoscopy and histology reports are collected and information from these reports is extracted independently in a standardized way by two trained investigators, who are blinded with respect to questionnaire and genotype data and who resolve discrepancies by consensus after further review and discussion. Based on colonoscopy reports, participants are categorized with respect to the most advanced lesion: CRC, advanced adenoma (AA), non-advanced adenoma (NAA), hyperplastic polyp, or undefined polyp. Advanced adenomas are defined as adenomas ≥1 cm or adenomas with cellular or structural atypia.
[
  • 249 cases
  • , 500 controls
]
,
60.48 % Male samples
Range = [50.0, 79.0] years European BLITZ
PSS000251 Colorectal adenocarcinoma located in the distal colon confirmed by medical records, pathology reports, or death certificate
[
  • 1,026 cases
  • , 3,860 controls
]
,
0.0 % Male samples
European 6 cohorts
  • DACHS
  • ,DALS
  • ,HPFS
  • ,NHS
  • ,VITAL
  • ,WHI
Training and test split not relevant to PGS
PSS000252 Colorectal adenocarcinoma located in the distal colon confirmed by medical records, pathology reports, or death certificate
[
  • 827 cases
  • , 2,442 controls
]
,
100.0 % Male samples
European 6 cohorts
  • DACHS
  • ,DALS
  • ,HPFS
  • ,NHS
  • ,VITAL
  • ,WHI
Training and test split not relevant to PGS
PSS000253 Colorectal adenocarcinoma located in the proximal colon confirmed by medical records, pathology reports, or death certificate
[
  • 1,670 cases
  • , 3,860 controls
]
,
0.0 % Male samples
European 6 cohorts
  • DACHS
  • ,DALS
  • ,HPFS
  • ,NHS
  • ,VITAL
  • ,WHI
Training and test split not relevant to PGS
PSS000254 Colorectal adenocarcinoma located in the proximal colon confirmed by medical records, pathology reports, or death certificate
[
  • 850 cases
  • , 2,442 controls
]
,
100.0 % Male samples
European 6 cohorts
  • DACHS
  • ,DALS
  • ,HPFS
  • ,NHS
  • ,VITAL
  • ,WHI
Training and test split not relevant to PGS
PSS000255 Colorectal adenocarcinoma located in the rectum confirmed by medical records, pathology reports, or death certificate
[
  • 713 cases
  • , 3,860 controls
]
,
0.0 % Male samples
European 6 cohorts
  • DACHS
  • ,DALS
  • ,HPFS
  • ,NHS
  • ,VITAL
  • ,WHI
Training and test split not relevant to PGS
PSS000256 Colorectal adenocarcinoma located in the rectum confirmed by medical records, pathology reports, or death certificate
[
  • 725 cases
  • , 2,442 controls
]
,
100.0 % Male samples
European 6 cohorts
  • DACHS
  • ,DALS
  • ,HPFS
  • ,NHS
  • ,VITAL
  • ,WHI
Training and test split not relevant to PGS
PSS000257 Colorectal adenocarcinoma confirmed by medical records, pathology reports, or death certificate
[
  • 380 cases
  • , 353 controls
]
,
0.0 % Male samples
European 6 cohorts
  • DACHS
  • ,DALS
  • ,HPFS
  • ,NHS
  • ,VITAL
  • ,WHI
Training and test split not relevant to PGS
PSS000258 Colorectal adenocarcinoma confirmed by medical records, pathology reports, or death certificate
[
  • 486 cases
  • , 516 controls
]
,
100.0 % Male samples
European 6 cohorts
  • DACHS
  • ,DALS
  • ,HPFS
  • ,NHS
  • ,VITAL
  • ,WHI
Training and test split not relevant to PGS
PSS000271
[
  • 1,316 cases
  • , 2,207 controls
]
,
40.85 % Male samples
Mean (Cases) = 58.34 years
Sd (Cases) = 12.85 years
East Asian
(Han Chinese)
NCRCC
PSS000259
[
  • 1,336 cases
  • , 2,744 controls
]
,
57.21 % Male samples
Range = [25.0, 90.0] years European
(Spanish)
MCC-Spain
PSS000086
[
  • 8,580 cases
  • , 13,050 controls
]
East Asian 8 cohorts
  • COLON
  • ,CORSA
  • ,DACHS
  • ,EPIC
  • ,HPFS
  • ,MGI
  • ,NHS
  • ,UKB
PSS000087
[
  • 12,952 cases
  • , 48,383 controls
]
European 8 cohorts
  • COLON
  • ,CORSA
  • ,DACHS4
  • ,EPIC
  • ,HPFS3
  • ,MGI
  • ,NHS3
  • ,UKB
PSS000260
[
  • 2,568 cases
  • , 2,932 controls
]
,
0.0 % Male samples
Mean (Cases) = 68.8 years
Sd (Cases) = 9.7 years
European 14 cohorts
  • CPSII
  • ,DACHS
  • ,DALS
  • ,HPFS
  • ,Hawaiian Colo2&3
  • ,KCCS
  • ,MCCS
  • ,MEC
  • ,MECC
  • ,NFCCR
  • ,NHS
  • ,PLCO
  • ,VITAL
  • ,WHI
PSS000261
[
  • 2,307 cases
  • , 2,359 controls
]
,
100.0 % Male samples
Mean (Cases) = 67.8 years
Sd (Cases) = 9.7 years
European 14 cohorts
  • CPSII
  • ,DACHS
  • ,DALS
  • ,HPFS
  • ,Hawaiian Colo2&3
  • ,KCCS
  • ,MCCS
  • ,MEC
  • ,MECC
  • ,NFCCR
  • ,NHS
  • ,PLCO
  • ,VITAL
  • ,WHI
PSS000262 Excluding participants with prevalent cancer at recruitment colorectal cancer was defined as ICD codes: C18 (except C18.1, Appendix), C19 and C20
[
  • 1,623 cases
  • , 359,920 controls
]
,
45.0 % Male samples
Mean = 57.0 years
Iqr = [50.0, 63.0] years
European UKB Follow-up time = 1,751,445 person years
PSS000263 Excluding participants with prevalent cancer at recruitment colorectal cancer was defined as ICD codes: C18 (except C18.1, Appendix), C19 and C20
[
  • 1,294 cases
  • , 285,583 controls
]
,
46.0 % Male samples
Mean = 57.0 years
Iqr = [50.0, 63.0] years
European UKB Follow-up time = 1,388,191 person years
PSS000274 Primary tumor samples from TCGA
[
  • 387 cases
  • , 0 controls
]
Mean = 68.0 years
Sd = 13.0 years
European TCGA
PSS000274
[
  • 0 cases
  • , 13,427 controls
]
European eMERGE
PSS000113 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 21041 - 21049, 21051, 21052, and 21060
[
  • 5,895 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB