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Published on: July 11, 2025
A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci
Eric R Gamazon1, Dan L Nicolae, Nancy J Cox
1Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America.
Plos Genetics
|February 10, 2011
Summary
Copy number variants (CNVs) tagged by SNPs influence gene expression and are linked to human traits and diseases. Our findings suggest CNVs play a significant role in complex phenotypes, warranting further investigation.
Area of Science:
- Genetics
- Genomics
- Human Complex Traits
Background:
- Copy number variants (CNVs) are a source of genetic variation.
- The role of CNVs in complex human traits and diseases is not fully understood.
- Previous studies suggested limited impact of common CNVs on complex diseases.
Purpose of the Study:
- To investigate the functional relevance of CNVs by analyzing their effect on gene expression and association with human traits.
- To determine if CNV-tagging SNPs are more likely to be functional than frequency-matched SNPs.
- To create a resource of expression-associated CNVs (eCNVs).
Main Methods:
- Comprehensive analysis of CNVs well-tagged by single nucleotide polymorphisms (SNPs).
- Assessment of CNVs as trait-associated loci and expression quantitative trait loci (eQTLs).
- Utilized a population-based map of CNVs to identify expression-associated CNVs (eCNVs).
Main Results:
- CNV-tagging SNPs are significantly enriched for cis eQTLs.
- SNPs tagging CNVs are overrepresented in trait associations compared to frequency-matched SNPs.
- CNV-tagging SNPs are more likely to affect multiple expression traits.
Conclusions:
- CNVs are functionally relevant and contribute to complex phenotypes.
- It is premature to dismiss the role of common CNVs in complex diseases.
- An online resource of eCNVs is provided to facilitate future research.
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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