Polygenic Score (PGS) ID: PGS001785

Predicted Trait
Reported Trait Acute appendicitis
Mapped Trait(s) appendicitis (EFO_0007149)
Released in PGS Catalog: Sept. 8, 2022
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Terms and Licenses
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Score Details

Score Construction
PGS Name 1kgeur_gbmi_leaveUKBBout_AcApp_pst_eff_a1_b0.5_phiauto
Development Method
Name PRS-CS-auto
Parameters effective sample size and other defualt parameters
Variants
Original Genome Build GRCh37
Number of Variants 911,334
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000262
Citation (link to publication) Wang Y et al. medRxiv (2021) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 85.7%
East Asian: 11%
Additional Asian Ancestries: 3.2%
688,784 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 801 cases
  • , 75,085 controls
]
East Asian BioMe, BioVU, CCPM, MGI, UCLA
[
  • 28,224 cases
  • , 562,313 controls
]
European NR
[
  • 191 cases
  • , 22,170 controls
]
Asian unspecified BioMe, CCPM, UCLA

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
PPM009289 PSS007708|
European Ancestry|
359,031 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Acute appendicitis AUROC: 0.584 Nagelkerke's R2 (covariates regressed out): 0.00406 sex,age,age2,age*sex,age^2*sex, 20PCs

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
PSS007708
[
  • 2,985 cases
  • , 356,045 controls
]
European UKB