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Updated: May 23, 2025

Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization

Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization

Published on: July 27, 2021

Gene dosage architecture across complex traits.

Sayeh Kazem^{1,2,3,4,5,6,7,8,9}, Kuldeep Kumar^{1,2,3,4,5,6,7,8,9}, Martineau Jean-Louis^{1,2,3,4,5,6,7,8,9}

¹Centre de recherche Azrieli, CHU Sainte-Justine and University of Montréal, Canada.

Medrxiv : the Preprint Server for Health Sciences

|March 10, 2025

Summary

This summary is machine-generated.

Copy number variants (CNVs) significantly associate with 43 complex traits, with brain tissues showing high pleiotropy. Functional convergence between CNVs and other variant types is limited, highlighting distinct genetic architecture.

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Area of Science:

Genetics
Genomics
Complex Traits

Background:

Copy number variants (CNVs) have substantial impacts on complex traits but are rare and difficult to study.
Understanding the biological functions linking gene dosage to complex traits is limited.
It remains unknown if gene dosage-sensitive functions overlap with those affected by rare single nucleotide variants (SNVs) and common variants.

Purpose of the Study:

To develop and apply a functional burden analysis (FunBurd) to associate aggregated CNVs within functional gene sets with complex traits.
To compare CNV associations with those of common variants and loss-of-function SNVs.
To investigate the functional convergence and shared genetic contributions across different variant types.

Main Methods:

Developed FunBurd, a functional burden analysis method.
Applied FunBurd to 500,000 UK Biobank individuals, analyzing 43 complex traits and 172 gene sets.
Compared CNV findings with common variants and LoF SNVs using the same functional gene sets.

Main Results:

All 43 complex traits showed significant associations with CNVs.
Brain tissues and neuronal cell types exhibited the highest pleiotropy.
Shared genetic contributions were 2-fold higher for rare CNVs/SNVs than common variants, with limited functional convergence observed across variant types.

Conclusions:

CNVs are significantly associated with a wide range of complex traits, particularly those involving brain function.
The study provides methods to differentiate genetic constraint from gene function in CNV-trait associations.
Functional convergence between different variant types, including deletions and duplications, is limited, suggesting distinct genetic mechanisms for complex traits.