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Copy number variation in the bovine genome.

Fadista J, Thomsen B, Holm LE, Bendixen C - BMC Genomics (2010)

Bottom Line: Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, have been shown to be associated with phenotypes of clinical relevance and to be causative of disease.About 10% of the human orthologous of these genes are associated with human disease susceptibility and, hence, may have important phenotypic consequences.Together, this analysis provides a useful resource for assessment of the impact of CNVs regarding variation in bovine health and production traits.

View Article: PubMed Central - HTML - PubMed

Affiliation: Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark.

ABSTRACT

Background: Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, have been shown to be associated with phenotypes of clinical relevance and to be causative of disease. Notwithstanding, little is known about the extent to which CNV contributes to genetic variation in cattle.

Results: We designed and used a set of NimbleGen CGH arrays that tile across the assayable portion of the cattle genome with approximately 6.3 million probes, at a median probe spacing of 301 bp. This study reports the highest resolution map of copy number variation in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. The CNVRs identified covered 0.68% (22 Mb) of the genome, and ranged in size from 1.7 to 2,031 kb (median size 16.7 kb). About 20% of the CNVs co-localized with segmental duplications, while 30% encompass genes, of which the majority is involved in environmental response. About 10% of the human orthologous of these genes are associated with human disease susceptibility and, hence, may have important phenotypic consequences.

Conclusions: Together, this analysis provides a useful resource for assessment of the impact of CNVs regarding variation in bovine health and production traits.

Show MeSH
CNV calling pipeline (details in Methods section). Data analysis procedure to discover copy number variations in array CGH data.
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Figure 2: CNV calling pipeline (details in Methods section). Data analysis procedure to discover copy number variations in array CGH data.

Mentions: After applying a stringent CNV calling pipeline with a theoretical 1.5 kb resolution for CNV detection (Figure 2 and Methods), 304 putative CNVRs were identified, averaging 47 CNVs per animal (Additional file 1, Table S1), with 70% (212) of the CNVRs observed in more than one animal. Although CNVRs detected in more than one animal of different families and/or breeds could be defined as frequent, the relationship between some of the animals precludes such classification (Additional file 2, Figure S1). The relatively poor breakpoint estimation also prevents information regarding whether these CNVRs are identical-by-descent (arisen before the divergence of these cattle breeds), or separate events occurred independently in different breeds (in putative structurally fragile genomic regions).


Copy number variation in the bovine genome.

Fadista J, Thomsen B, Holm LE, Bendixen C - BMC Genomics (2010)

CNV calling pipeline (details in Methods section). Data analysis procedure to discover copy number variations in array CGH data.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2902221&req=5

Figure 2: CNV calling pipeline (details in Methods section). Data analysis procedure to discover copy number variations in array CGH data.
Mentions: After applying a stringent CNV calling pipeline with a theoretical 1.5 kb resolution for CNV detection (Figure 2 and Methods), 304 putative CNVRs were identified, averaging 47 CNVs per animal (Additional file 1, Table S1), with 70% (212) of the CNVRs observed in more than one animal. Although CNVRs detected in more than one animal of different families and/or breeds could be defined as frequent, the relationship between some of the animals precludes such classification (Additional file 2, Figure S1). The relatively poor breakpoint estimation also prevents information regarding whether these CNVRs are identical-by-descent (arisen before the divergence of these cattle breeds), or separate events occurred independently in different breeds (in putative structurally fragile genomic regions).

Bottom Line: Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, have been shown to be associated with phenotypes of clinical relevance and to be causative of disease.About 10% of the human orthologous of these genes are associated with human disease susceptibility and, hence, may have important phenotypic consequences.Together, this analysis provides a useful resource for assessment of the impact of CNVs regarding variation in bovine health and production traits.

View Article: PubMed Central - HTML - PubMed

Affiliation: Group of Molecular Genetics and Systems Biology, Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark.

ABSTRACT

Background: Copy number variations (CNVs), which represent a significant source of genetic diversity in mammals, have been shown to be associated with phenotypes of clinical relevance and to be causative of disease. Notwithstanding, little is known about the extent to which CNV contributes to genetic variation in cattle.

Results: We designed and used a set of NimbleGen CGH arrays that tile across the assayable portion of the cattle genome with approximately 6.3 million probes, at a median probe spacing of 301 bp. This study reports the highest resolution map of copy number variation in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. The CNVRs identified covered 0.68% (22 Mb) of the genome, and ranged in size from 1.7 to 2,031 kb (median size 16.7 kb). About 20% of the CNVs co-localized with segmental duplications, while 30% encompass genes, of which the majority is involved in environmental response. About 10% of the human orthologous of these genes are associated with human disease susceptibility and, hence, may have important phenotypic consequences.

Conclusions: Together, this analysis provides a useful resource for assessment of the impact of CNVs regarding variation in bovine health and production traits.

Show MeSH