Polygenic Score (PGS) ID: PGS001853

Predicted Trait
Reported Trait Appendiceal conditions
Mapped Trait(s) disorder of appendix (EFO_0009542)
Additional Trait Information digestive
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_540
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 19
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
PPM009715 PSS009102|
European Ancestry|
4,136 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0345 [0.0039, 0.0649] sex, age, birth date, deprivation index, 16 PCs
PPM009716 PSS008656|
European Ancestry|
6,660 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0198 [-0.0043, 0.0438] sex, age, birth date, deprivation index, 16 PCs
PPM009717 PSS008430|
Greater Middle Eastern Ancestry|
1,200 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): -0.0243 [-0.0813, 0.0328] sex, age, birth date, deprivation index, 16 PCs
PPM009718 PSS008210|
South Asian Ancestry|
6,331 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0024 [-0.0223, 0.0271] sex, age, birth date, deprivation index, 16 PCs
PPM009719 PSS007992|
East Asian Ancestry|
1,810 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0008 [-0.0455, 0.0471] sex, age, birth date, deprivation index, 16 PCs
PPM009720 PSS007775|
African Ancestry|
2,484 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): -0.0062 [-0.0457, 0.0333] sex, age, birth date, deprivation index, 16 PCs
PPM009721 PSS008879|
African Ancestry|
3,924 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): -0.0204 [-0.0517, 0.011] sex, age, birth date, deprivation index, 16 PCs
PPM009714 PSS009328|
European Ancestry|
20,000 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Appendiceal conditions Partial Correlation (partial-r): 0.0242 [0.0104, 0.0381] 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
PSS009102 4,136 individuals European Poland (NE Europe) UKB
PSS008430 1,200 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008656 6,660 individuals European Italy (South Europe) UKB
PSS008879 3,924 individuals African unspecified Nigeria (West Africa) UKB
PSS008210 6,331 individuals South Asian India (South Asia) UKB
PSS009328 20,000 individuals European UK (+ Ireland) UKB
PSS007992 1,810 individuals East Asian China (East Asia) UKB
PSS007775 2,484 individuals African American or Afro-Caribbean Carribean UKB