Open Access Highly Accessed Research article

Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array

Yali Hou12, Derek M Bickhart1, Miranda L Hvinden3, Congjun Li1, Jiuzhou Song4, Didier A Boichard5, Sébastien Fritz6, André Eggen7, Sue DeNise3, George R Wiggans8, Tad S Sonstegard1, Curtis P Van Tassell1 and George E Liu1*

Author Affiliations

1 Bovine Functional Genomics Laboratory, ANRI, USDA-ARS, BARC-East, Beltsville, MD 20705, USA

2 Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

3 Pfizer Animal Genetics, 333 Portage Road, Building 300, Kalamazoo, MI 49007, USA

4 Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA

5 INRA UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas 78352, France

6 UNCEIA Genetics Team, Paris, 75595, France

7 Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA

8 Animal Improvement Programs Laboratory, ANRI, USDA-ARS, Beltsville, Maryland 20705, USA

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BMC Genomics 2012, 13:376  doi:10.1186/1471-2164-13-376

Published: 6 August 2012

Additional files

Additional file 1:

Table S1. Numbers of subspecies, breeds, animals and trios used to call CNVs genotyped by BovineHD assay. Table S2. The summary of CNVs or CNVRs for each specie/breed based on Btau_4.0. Table S4. The summary of CNVs or CNVRs for each specie/breed based on UMD3.1.

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Additional file 2:

Figure S1. Comparison of cattle copy number variations derived from BovineHD and BovineSNP50 assays on Batu_4.0.

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Additional file 3:

Table S3. Btau_4.0 CNV regions, their frequencies, corresponding gene contents, QTL, OMIM, and OMIA overlapping information.

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Additional file 4:

Table S5. UMD3.1 CNV regions, their frequencies, corresponding gene contents.

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Additional file 5:

Table S6. The summary of PCR results.

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Additional file 6:

Table S7. Over/Underrepresentation of PANTHER terms (molecular function, biological process, pathway, cellular component and PANTHER protein class) on Batu_4.0 and UMD3.1.

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Additional file 7:

Table S8: Network, Biological function and Pathway analyses using IPA on Batu_4.0 and UMD3.1.

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