Polygenic Score (PGS) ID: PGS002013

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal cancer (EFO_0005842)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name portability-ldpred2_153
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 648,559
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
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
391,124 individuals European UK (+ Ireland) UKB

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)
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
PPM010978 PSS009272|
European Ancestry|
18,722 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Colorectal cancer Partial Correlation (partial-r): 0.0397 [0.0254, 0.054] sex, age, birth date, deprivation index, 16 PCs
PPM010979 PSS009046|
European Ancestry|
3,922 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Colorectal cancer Partial Correlation (partial-r): 0.0419 [0.0105, 0.0732] sex, age, birth date, deprivation index, 16 PCs
PPM010980 PSS008600|
European Ancestry|
6,241 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Colorectal cancer Partial Correlation (partial-r): 0.0234 [-0.0015, 0.0482] sex, age, birth date, deprivation index, 16 PCs
PPM010981 PSS008378|
Greater Middle Eastern Ancestry|
1,123 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Colorectal cancer Partial Correlation (partial-r): 0.0315 [-0.0276, 0.0904] sex, age, birth date, deprivation index, 16 PCs
PPM010982 PSS008154|
South Asian Ancestry|
6,010 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Colorectal cancer Partial Correlation (partial-r): 0.0275 [0.0021, 0.0528] sex, age, birth date, deprivation index, 16 PCs
PPM010983 PSS007942|
East Asian Ancestry|
1,719 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Colorectal cancer Partial Correlation (partial-r): 0.026 [-0.0215, 0.0735] sex, age, birth date, deprivation index, 16 PCs
PPM010984 PSS007724|
African Ancestry|
2,362 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Colorectal cancer Partial Correlation (partial-r): 0.0053 [-0.0352, 0.0458] sex, age, birth date, deprivation index, 16 PCs
PPM010985 PSS008826|
African Ancestry|
3,757 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Colorectal cancer Partial Correlation (partial-r): 0.0265 [-0.0056, 0.0585] sex, age, birth date, deprivation index, 16 PCs

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
PSS007942 1,719 individuals East Asian China (East Asia) UKB
PSS007724 2,362 individuals African American or Afro-Caribbean Carribean UKB
PSS009046 3,922 individuals European Poland (NE Europe) UKB
PSS008600 6,241 individuals European Italy (South Europe) UKB
PSS009272 18,722 individuals European UK (+ Ireland) UKB
PSS008378 1,123 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008154 6,010 individuals South Asian India (South Asia) UKB
PSS008826 3,757 individuals African unspecified Nigeria (West Africa) UKB