Polygenic Score (PGS) ID: PGS002019

Predicted Trait
Reported Trait Benign neoplasm of colon
Mapped Trait(s) benign colon neoplasm (MONDO_0002278)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_208
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 667,546
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
PPM011026 PSS009281|
European Ancestry|
19,812 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0716 [0.0577, 0.0854] sex, age, birth date, deprivation index, 16 PCs —
PPM011027 PSS009055|
European Ancestry|
4,121 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0761 [0.0456, 0.1065] sex, age, birth date, deprivation index, 16 PCs —
PPM011028 PSS008609|
European Ancestry|
6,617 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0659 [0.0418, 0.0899] sex, age, birth date, deprivation index, 16 PCs —
PPM011029 PSS008385|
Greater Middle Eastern Ancestry|
1,194 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0966 [0.0396, 0.153] sex, age, birth date, deprivation index, 16 PCs —
PPM011030 PSS008163|
South Asian Ancestry|
6,307 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0398 [0.0151, 0.0645] sex, age, birth date, deprivation index, 16 PCs —
PPM011031 PSS007950|
East Asian Ancestry|
1,800 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0601 [0.0137, 0.1063] sex, age, birth date, deprivation index, 16 PCs —
PPM011032 PSS007731|
African Ancestry|
2,469 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0409 [0.0012, 0.0803] sex, age, birth date, deprivation index, 16 PCs —
PPM011033 PSS008834|
African Ancestry|
3,905 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0603 [0.0289, 0.0916] 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
PSS007950 — — 1,800 individuals — East Asian China (East Asia) UKB —
PSS007731 — — 2,469 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009281 — — 19,812 individuals — European UK (+ Ireland) UKB —
PSS008385 — — 1,194 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009055 — — 4,121 individuals — European Poland (NE Europe) UKB —
PSS008609 — — 6,617 individuals — European Italy (South Europe) UKB —
PSS008834 — — 3,905 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008163 — — 6,307 individuals — South Asian India (South Asia) UKB —