PGS Publication: PGP000072

Publication Information (EuropePMC)
Title The added value of genetic information in colorectal cancer risk prediction models: development and evaluation in the UK Biobank prospective cohort study.
PubMed ID 30323197(Europe PMC)
doi 10.1038/s41416-018-0282-8
Publication Date Oct. 16, 2018
Journal Br J Cancer
Author(s) Smith T, Gunter MJ, Tzoulaki I, Muller DC.
Released in PGS: April 29, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
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

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
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
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]
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
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]
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

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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