Polygenic Score (PGS) ID: PGS002070

Predicted Trait
Reported Trait Anal and rectal polyp
Mapped Trait(s)
Additional Trait Information digestive
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_565.1
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 584,133
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
PPM011421 PSS009334|
European Ancestry|
19,196 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Anal and rectal polyp — — Partial Correlation (partial-r): 0.0342 [0.02, 0.0483] sex, age, birth date, deprivation index, 16 PCs —
PPM011422 PSS009108|
European Ancestry|
4,008 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Anal and rectal polyp — — Partial Correlation (partial-r): 0.0435 [0.0125, 0.0745] sex, age, birth date, deprivation index, 16 PCs —
PPM011423 PSS008662|
European Ancestry|
6,382 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Anal and rectal polyp — — Partial Correlation (partial-r): 0.0224 [-0.0022, 0.047] sex, age, birth date, deprivation index, 16 PCs —
PPM011424 PSS008436|
Greater Middle Eastern Ancestry|
1,135 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Anal and rectal polyp — — Partial Correlation (partial-r): 0.0438 [-0.015, 0.1022] sex, age, birth date, deprivation index, 16 PCs —
PPM011425 PSS008216|
South Asian Ancestry|
5,990 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Anal and rectal polyp — — Partial Correlation (partial-r): 0.0084 [-0.017, 0.0338] sex, age, birth date, deprivation index, 16 PCs —
PPM011426 PSS007997|
East Asian Ancestry|
1,770 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Anal and rectal polyp — — Partial Correlation (partial-r): 0.0501 [0.0032, 0.0967] sex, age, birth date, deprivation index, 16 PCs —
PPM011427 PSS007781|
African Ancestry|
2,363 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Anal and rectal polyp — — Partial Correlation (partial-r): 0.0457 [0.0052, 0.086] sex, age, birth date, deprivation index, 16 PCs —
PPM011428 PSS008885|
African Ancestry|
3,762 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Anal and rectal polyp — — Partial Correlation (partial-r): -0.0102 [-0.0422, 0.0219] 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
PSS007781 — — 2,363 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009108 — — 4,008 individuals — European Poland (NE Europe) UKB —
PSS008436 — — 1,135 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009334 — — 19,196 individuals — European UK (+ Ireland) UKB —
PSS008662 — — 6,382 individuals — European Italy (South Europe) UKB —
PSS008216 — — 5,990 individuals — South Asian India (South Asia) UKB —
PSS008885 — — 3,762 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007997 — — 1,770 individuals — East Asian China (East Asia) UKB —