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Copy number variants in the sheep genome detected using multiple approaches

Gemma M Jenkins, Michael E Goddard, Michael A Black, Rudiger Brauning, Benoit Auvray, Ken G Dodds, James W Kijas, Noelle Cockett, John C McEwan
doi: https://doi.org/10.1101/041475
Gemma M Jenkins
1AbacusBio Limited, 442 Moray Place, PO Box 5585, Dunedin 9058, NEW ZEALAND
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  • For correspondence: gjenkins@abacusbio.co.nz
Michael E Goddard
2Victorian Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC 3083, AUSTRALIA
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Michael A Black
3Department of Biochemistry, University of Otago, 710 Cumberland St, Dunedin 9054, NEW ZEALAND
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Rudiger Brauning
4AgResearch, Invermay Agricultural Centre, PB 50034, Mosgiel 9053, NEW ZEALAND
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Benoit Auvray
3Department of Biochemistry, University of Otago, 710 Cumberland St, Dunedin 9054, NEW ZEALAND
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Ken G Dodds
4AgResearch, Invermay Agricultural Centre, PB 50034, Mosgiel 9053, NEW ZEALAND
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James W Kijas
5CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, 306 Carmody Road. St Lucia, QLD 4067, AUSTRALIA
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Noelle Cockett
6Utah State University, 1435 Old Main Hill, Logan, UT 84322-1435-1435, USA
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John C McEwan
4AgResearch, Invermay Agricultural Centre, PB 50034, Mosgiel 9053, NEW ZEALAND
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Abstract

Background. Background. Copy number variants (CNVs) are a type of polymorphism found to underlie phenotypic variation, both in humans and livestock. Most surveys of CNV in livestock have been conducted in the cattle genome, and often utilise only a single approach for the detection of copy number differences. Here we performed a study of CNV in sheep, using multiple methods to identify and characterise copy number changes. Comprehensive information from small pedigrees (trios) was collected using multiple platforms (array CGH, SNP chip and whole genome sequence data), with these data then analysed via multiple approaches to identify and verify CNVs.

Results. In total, 3,488 autosomal CNV regions (CNVRs) were identified from 30 sheep. The average length of the identified CNVRs was 19kb (range of 1kb to 3.6Mb), with shorter CNVRs being more frequent than longer CNVRs. The total length of all CNVRs was 67.6Mbps, which equates to 2.7% of the sheep autosomes. For individuals this value ranged from 0.24 to 0.55%, and the majority of CNVRs were identified in single animals. Rather than being uniformly distributed throughout the genome, CNVRs tended to be clustered. Application of three independent approaches for CNVR detection facilitated a comparison of validation rates. CNVs identified on the Roche-NimbleGen 2.1M CGH array generally had low validation rates, while whole genome sequence data had the highest validation rate.

Conclusions. This study represents the first comprehensive survey of the distribution, prevalence and characteristics of CNVR in sheep. Multiple approaches were used to detect CNV regions and it appears that the best method for verifying CNVR on a large scale involves using a combination of detection methodologies. The characteristics of the 3,488 autosomal CNV regions identified in this study are comparable to other CNV regions reported in the literature and provide a valuable addition to the small subset of published sheep CNVs.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 26, 2016.
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Copy number variants in the sheep genome detected using multiple approaches
Gemma M Jenkins, Michael E Goddard, Michael A Black, Rudiger Brauning, Benoit Auvray, Ken G Dodds, James W Kijas, Noelle Cockett, John C McEwan
bioRxiv 041475; doi: https://doi.org/10.1101/041475
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Copy number variants in the sheep genome detected using multiple approaches
Gemma M Jenkins, Michael E Goddard, Michael A Black, Rudiger Brauning, Benoit Auvray, Ken G Dodds, James W Kijas, Noelle Cockett, John C McEwan
bioRxiv 041475; doi: https://doi.org/10.1101/041475

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