Abstract
BackgroundCopy number variations (CNVs) are a significant source of genetic diversity and commonly found in mammalian genomes. We have generated a genome-wide CNV map for Cynomolgus monkeys (Macaca fascicularis). This crab-eating macaque is the closest animal model to humans that is used in biomedical research.ResultsWe show that Cynomolgus monkey CNVs are in general much smaller in size than gene loci and are specific to the population of origin. Genome-wide expression data from five vitally important organs demonstrates that CNVs in close proximity to transcription start sites associate strongly with expression changes. Among these eQTL genes we find an overrepresentation of genes involved in metabolism, receptor activity, and transcription.ConclusionThese results provide evidence that CNVs shape tissue transcriptomes in monkey populations, potentially offering an adaptive advantage. We suggest that this genetic diversity should be taken into account when using Cynomolgus macaques as models.
Highlights
Copy number variations (CNVs) are a significant source of genetic diversity and commonly found in mammalian genomes
CNVs in diverse Cynomolgus monkey populations Following the recent sequencing of the Cynomolgus monkey genome [21], we aimed at investigating CNVs among Cynomolgus monkey cohorts used in pharmaceutical research
We performed comparative genomic hybridization (CGH) using a Cynomolgus monkey specific high-resolution oligonucleotide tiling array with 4.2 million probes spanning the genome with a median spacing of 598 bp
Summary
Copy number variations (CNVs) are a significant source of genetic diversity and commonly found in mammalian genomes. We have generated a genome-wide CNV map for Cynomolgus monkeys (Macaca fascicularis). This crab-eating macaque is the closest animal model to humans that is used in biomedical research. More than 6.2 million different CNVs mapping to ~500’000 genomic regions have so far been identified [6]. They significantly contribute to genetic variation, covering more nucleotide content per genome than single nucleotide polymorphisms (e.g. approximately 0.8% of the length of the human genome differs between two human individuals) [7].
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