Polygenic Score (PGS) ID: PGS002013

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal cancer (MONDO_0005575)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
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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
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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 —