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 Catalog: April 29, 2020

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:
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Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

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)
PGS000149
(CRC41)
 PGP000072 |
Smith T et al. Br J Cancer (2018)
 Colorectal cancer colorectal cancer 41
-
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000149/ScoringFiles/PGS000149.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
PPM000464 PGS000149
(CRC41)
 PSS000263|
European Ancestry|
286,877 individuals
 PGP000072 |
Smith T et al. Br J Cancer (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|
European Ancestry|
286,877 individuals
 PGP000072 |
Smith T et al. Br J Cancer (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|
European Ancestry|
361,543 individuals
 PGP000072 |
Smith T et al. Br J Cancer (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|
European Ancestry|
361,543 individuals
 PGP000072 |
Smith T et al. Br J Cancer (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|
European Ancestry|
361,543 individuals
 PGP000072 |
Smith T et al. Br J Cancer (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
PPM000465 PGS000149
(CRC41)
 PSS000263|
European Ancestry|
286,877 individuals
 PGP000072 |
Smith T et al. Br J Cancer (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
PPM000462 PGS000149
(CRC41)
 PSS000263|
European Ancestry|
286,877 individuals
 PGP000072 |
Smith T et al. Br J Cancer (2018)
 Reported Trait: Incident colorectal cancer in individuals without a family history — C-index: 0.57 [0.53, 0.6] — — —
PPM000461 PGS000149
(CRC41)
 PSS000263|
European Ancestry|
286,877 individuals
 PGP000072 |
Smith T et al. Br J Cancer (2018)
 Reported Trait: Incident colorectal cancer in individuals with a family history — C-index: 0.56 [0.55, 0.58] — — —
PPM000460 PGS000149
(CRC41)
 PSS000263|
European Ancestry|
286,877 individuals
 PGP000072 |
Smith T et al. Br J Cancer (2018)
 Reported Trait: Incident colorectal cancer — C-index: 0.57 [0.55, 0.58] — — —
PPM000456 PGS000149
(CRC41)
 PSS000262|
European Ancestry|
361,543 individuals
 PGP000072 |
Smith T et al. Br J Cancer (2018)
 Reported Trait: Incident colorectal cancer in individuals without a family history — C-index: 0.55 [0.52, 0.59] — — —
PPM000455 PGS000149
(CRC41)
 PSS000262|
European Ancestry|
361,543 individuals
 PGP000072 |
Smith T et al. Br J Cancer (2018)
 Reported Trait: Incident colorectal cancer in individuals with a family history — C-index: 0.57 [0.55, 0.58] — — —
PPM000454 PGS000149
(CRC41)
 PSS000262|
European Ancestry|
361,543 individuals
 PGP000072 |
Smith T et al. Br J Cancer (2018)
 Reported Trait: Incident colorectal cancer — C-index: 0.56 [0.55, 0.58] — — —

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
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