Distribution and functional impact of DNA copy number variation in the rat

Guryev, Victor; Saar, Kathrin; Adamović, Tatjana; Verheul, Mark; Heesch, Sebastiaan van; Cook, Stuart A.; Pravenec, Michal; Aitman, Timothy J.; Jacob, Howard J.; Shull, James D.; Hübner, Norbert; Cuppen, Edwin

doi:10.1038/ng.141

Cited by 184 publications

(191 citation statements)

References 42 publications

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“…That will make it straightforward to test suggestive breed-specific CNVs for particular disease associations. As was demonstrated in rats, is it also feasible to integrate genome-wide information on Quantitative Trait Loci, breed-specific CNV, and gene expression in order to identify candidate genes (Guryev et al 2008). Another use of CNV information is in comparative genetics.…”

Section: Org Downloaded Frommentioning

confidence: 99%

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Mapping DNA structural variation in dogs

Chen¹,

Swartz²,

Rush³

et al. 2008

Genome Res.

128

131

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DNA structural variation (SV) comprises a major portion of genetic diversity, but its biological impact is unclear. We propose that the genetic history and extraordinary phenotypic variation of dogs make them an ideal mammal in which to study the effects of SV on biology and disease. The hundreds of existing dog breeds were created by selection of extreme morphological and behavioral traits. And along with those traits, each breed carries increased risk for different diseases. We used array CGH to create the first map of DNA copy number variation (CNV) or SV in dogs. The extent of this variation, and some of the gene classes affected, are similar to those of mice and humans. Most canine CNVs affect genes, including disease and candidate disease genes, and are thus likely to be functional. We identified many CNVs that may be breed or breed class specific. Cluster analysis of CNV regions showed that dog breeds tend to group according to breed classes. Our combined findings suggest many CNVs are (1) in linkage disequilibrium with flanking sequence, and (2) associated with breed-specific traits. We discuss how a catalog of structural variation in dogs will accelerate the identification of the genetic basis of canine traits and diseases, beginning with the use of whole genome association and candidate-CNV/gene approaches.

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Section: Org Downloaded Frommentioning

confidence: 99%

“…Recent findings revealed that DNA structural variation (SV) is common in normal rodents (Graubert et al 2007;Guryev et al 2008) and primates (Iafrate et al 2004;Sebat et al 2007; Lee et al 2008; for review, see Freeman et al 2006). The term SV and its subset of copy number variation (CNV), refer to alterations from 1 kb to multi-Mb.…”

mentioning

confidence: 99%

Mapping DNA structural variation in dogs

Chen¹,

Swartz²,

Rush³

et al. 2008

Genome Res.

128

131

View full text Add to dashboard Cite

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“…Copy-number variations have been shown to be associated with complex traits in several species, including chimpanzee (Perry et al 2008), rat (Guryev et al 2008) and mouse (Adams et al 2005), and in livestock species such as cattle (Liu et al 2010;Hou et al 2011), goat (Fontanesi et al 2010), sheep (Fontanesi et al 2011) and horse (Dupuis et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide detection of copy-number variations in local cattle breeds

et al. 2019

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Abstract. The aim of the present study was to identify copy-number variations (CNVs) in Cinisara (CIN) and Modicana (MOD) cattle breeds on the basis of signal intensity (logR ratio) and B allele frequency of each marker, using Illumina's BovineSNP50K Genotyping BeadChip. The CNVs were detected with the PennCNV and SVS 8.7.0 software and were aggregated into CNV regions (CNVRs). PennCNV identified 487 CNVs in CIN that aggregated into 86 CNVRs, and 424 CNVs in MOD that aggregated into 81 CNVRs. SVS identified a total of 207 CNVs in CIN that aggregated into 39 CNVRs, and 181 CNVs in MOD that aggregated into 41 CNVRs. The CNVRs identified with the two softwares contained 29 common CNVRs in CIN and 17 common CNVRs in MOD. Only a small number of CNVRs identified in the present study have been identified elsewhere, probably because of the limitations of the array used. In total, 178 and 208 genes were found within the CNVRs of CIN and MOD respectively. Gene Ontology and KEGG pathway analyses showed that several of these genes are involved in milk production, reproduction and behaviour, the immune response, and resistance/susceptibility to infectious diseases. Our results have provided significant information for the construction of more-complete CNV maps of the bovine genome and offer an important resource for the investigation of genomic changes and traits of interest in the CIN and MOD cattle breeds. Our results will also be valuable for future studies and constitute a preliminary report of the CNV distribution resources in local cattle genomes.

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“…It is clear that copy number variability is a common feature of a wide range of species, from flies (Dopman and Hartl 2007) to maize (Schnable et al 2009), and including mice (Egan et al 2007;Graubert et al 2007;Cahan et al 2009), rats (Guryev et al 2008), dogs (Chen et al 2009), pigs (Ramayo Caldas et al 2010), goats (Fontanesi et al 2010), macaques , and chimpanzees . CNVs have been associated with traits of evolutionary interest, especially human disease-related traits (see, e.g., Craddock et al 2010, and references therein), but also traits in other species such as breed-specific features in dogs (Chen et al 2009), metabolic traits in mice (Orozco et al 2009), and, possibly, phenotypic differences in inbred lines of maize (Schnable et al 2009).…”

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confidence: 99%

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

Gazave¹,

Darré²,

Morcillo-Suárez³

et al. 2011

Genome Res.

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Copy number variants (CNVs) are increasingly acknowledged as an important source of evolutionary novelties in the human lineage. However, our understanding of their significance is still hindered by the lack of primate CNV data. We performed intraspecific comparative genomic hybridizations to identify loci harboring copy number variants in each of the four great apes: bonobos, chimpanzees, gorillas, and orangutans. For the first time, we could analyze differences in CNV location and frequency in these four species, and compare them with human CNVs and primate segmental duplication (SD) maps. In addition, for bonobo and gorilla, patterns of CNV and nucleotide diversity were studied in the same individuals. We show that CNVs have been subject to different selective pressures in different lineages. Evidence for purifying selection is stronger in gorilla CNVs overlapping genes, while positive selection appears to have driven the fixation of structural variants in the orangutan lineage. In contrast, chimpanzees and bonobos present high levels of common structural polymorphism, which is indicative of relaxed purifying selection together with the higher mutation rates induced by the known burst of segmental duplication in the ancestor of the African apes. Indeed, the impact of the duplication burst is noticeable by the fact that bonobo and chimpanzee share more CNVs with gorilla than expected. Finally, we identified a number of interesting genomic regions that present high-frequency CNVs in all great apes, while containing only very rare or even pathogenic structural variants in humans.

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Distribution and functional impact of DNA copy number variation in the rat

Cited by 184 publications

References 42 publications

Mapping DNA structural variation in dogs

Mapping DNA structural variation in dogs

Genome-wide detection of copy-number variations in local cattle breeds

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

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