Polygenic Score (PGS) ID: PGS002020

Predicted Trait
Reported Trait Benign neoplasm of other parts of digestive system
Mapped Trait(s) benign digestive system neoplasm (MONDO_0000385)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_211
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 503,832
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
PPM011034 PSS009282|
European Ancestry|
19,463 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of other parts of digestive system Partial Correlation (partial-r): 0.0199 [0.0059, 0.034] sex, age, birth date, deprivation index, 16 PCs
PPM011035 PSS009056|
European Ancestry|
4,074 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of other parts of digestive system Partial Correlation (partial-r): 0.0332 [0.0025, 0.064] sex, age, birth date, deprivation index, 16 PCs
PPM011036 PSS008610|
European Ancestry|
6,504 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of other parts of digestive system Partial Correlation (partial-r): 0.0281 [0.0038, 0.0524] sex, age, birth date, deprivation index, 16 PCs
PPM011037 PSS008386|
Greater Middle Eastern Ancestry|
1,178 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of other parts of digestive system Partial Correlation (partial-r): 0.0488 [-0.0088, 0.1061] sex, age, birth date, deprivation index, 16 PCs
PPM011038 PSS008164|
South Asian Ancestry|
6,243 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of other parts of digestive system Partial Correlation (partial-r): 0.0343 [0.0094, 0.0591] sex, age, birth date, deprivation index, 16 PCs
PPM011039 PSS007951|
East Asian Ancestry|
1,772 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of other parts of digestive system Partial Correlation (partial-r): 0.0236 [-0.0233, 0.0703] sex, age, birth date, deprivation index, 16 PCs
PPM011040 PSS007732|
African Ancestry|
2,441 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of other parts of digestive system Partial Correlation (partial-r): -0.0196 [-0.0594, 0.0202] sex, age, birth date, deprivation index, 16 PCs
PPM011041 PSS008835|
African Ancestry|
3,862 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Benign neoplasm of other parts of digestive system Partial Correlation (partial-r): 0.0027 [-0.0289, 0.0343] 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
PSS008164 6,243 individuals South Asian India (South Asia) UKB
PSS008610 6,504 individuals European Italy (South Europe) UKB
PSS007951 1,772 individuals East Asian China (East Asia) UKB
PSS007732 2,441 individuals African American or Afro-Caribbean Carribean UKB
PSS009282 19,463 individuals European UK (+ Ireland) UKB
PSS009056 4,074 individuals European Poland (NE Europe) UKB
PSS008386 1,178 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008835 3,862 individuals African unspecified Nigeria (West Africa) UKB