Polygenic Score (PGS) ID: PGS001812

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-PLR_211
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 801
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
PPM009396 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): 0.0232 [0.0091, 0.0372] sex, age, birth date, deprivation index, 16 PCs
PPM009397 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): 0.0262 [-0.0045, 0.057] sex, age, birth date, deprivation index, 16 PCs
PPM009398 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): 0.0186 [-0.0058, 0.0429] sex, age, birth date, deprivation index, 16 PCs
PPM009399 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): 0.0327 [-0.0249, 0.0902] sex, age, birth date, deprivation index, 16 PCs
PPM009402 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): -0.0065 [-0.0464, 0.0333] sex, age, birth date, deprivation index, 16 PCs
PPM009403 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): 0.0197 [-0.0119, 0.0513] sex, age, birth date, deprivation index, 16 PCs
PPM009400 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): 0.0246 sex, age, birth date, deprivation index, 16 PCs
PPM009401 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): 0.0436 [-0.0032, 0.0903] 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