Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions

Copy-number variants (CNVs) form an abundant class of genetic variation with a presumed widespread impact on individual traits. While recent advances, such as the population-scale sequencing of human genomes, facilitated the fine-scale mapping of CNVs, the phenotypic impact of most of these CNVs rem...

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Bibliographic Details
Published in:Genome research 2011-12, Vol.21 (12), p.2004-2013
Main Authors: Schlattl, Andreas, Anders, Simon, Waszak, Sebastian M, Huber, Wolfgang, Korbel, Jan O
Format: Article
Language:English
Subjects:
DNA Copy Number Variations - physiology
Female
Gene Dosage - physiology
Gene Expression Regulation - physiology
Genotype
Humans
Male
Models, Genetic
Polymorphism, Single Nucleotide
Transcriptome - physiology
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Summary:Copy-number variants (CNVs) form an abundant class of genetic variation with a presumed widespread impact on individual traits. While recent advances, such as the population-scale sequencing of human genomes, facilitated the fine-scale mapping of CNVs, the phenotypic impact of most of these CNVs remains unclear. By relating copy-number genotypes to transcriptome sequencing data, we have evaluated the impact of CNVs, mapped at fine scale, on gene expression. Based on data from 129 individuals with ancestry from two populations, we identified CNVs associated with the expression of 110 genes, with 13% of the associations involving complex, multiallelic CNVs. Categorization of CNVs according to variant type, size, and gene overlap enabled us to examine the impact of different CNV classes on expression variation. While many small (
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.122614.111