Open Access Research article

Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses

Elisabeth Sundström12, Freyja Imsland2, Sofia Mikko3, Claire Wade456, Snaevar Sigurdsson4, Gerli Rosengren Pielberg2, Anna Golovko2, Ino Curik7, Monika H Seltenhammer8, Johann Sölkner9, Kerstin Lindblad-Toh24 and Leif Andersson12*

Author Affiliations

1 Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 597, SE-751 24, Uppsala, Sweden

2 Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23, Uppsala, Sweden

3 Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07, Uppsala, Sweden

4 Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA, 02142, USA

5 Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, 02114, USA

6 Faculty of Veterinary Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia

7 Animal Science Department, Faculty of Agriculture, University of Zagreb, Zagreb, HR-10000, Croatia

8 Clinical Department of Small Animal Surgery, University of Veterinary Medicine, Vienna, Austria

9 Department of Sustainable Agricultural Systems, University of Natural Resources and Applied Life Sciences, Vienna, A-1180, Vienna, Austria

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BMC Genomics 2012, 13:365  doi:10.1186/1471-2164-13-365

Published: 2 August 2012

Additional files

Additional file 1:

Lack of copy number variation outside and over the 5’breakpoint of the STX17 duplication in constitutional DNA from Grey horses.94 Grey Lipizzaner horses and one calibrator sample with a known copy number of 2 were included in the analysis. OUT = outside the duplicated sequence and BP n = the border between the 5’flanking sequence and the 5’end of the duplicated sequence. Error bars represent the copy number range from the CopyCaller™ Software analysis of quadruplicates in each assay.

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Additional file 2:

The late greying Connemara horses are heterozygous for the STX17 duplication.Copy number assay for the STX17 duplication from tests with four different probes using constitutional DNA from the late greying Connemara horses SP1, SP2, SP3. The sample denoted ‘Calibr’ is a g/g individual with a known copy number of 2, used as a calibrator in the IN, OUT and BP n analyses. Constitutional DNA from one G/g and one G/G horse was tested in the assay and the results are shown as a reference for the copy number expected from each genotype. The G/G reference sample was used as a calibrator in the BP d analysis. IN = inside the duplicated sequence, OUT = outside the duplicated sequence, BP n = the border between the 5’flanking sequence and the 5’end of the duplicated sequence and BP d = over the duplication breakpoint. Error bars represent the copy number range from the CopyCaller™ Software analysis of quadruplicates in each assay.

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Open Data

Additional file 3:

Primer sequences used for characterization of the region harbouring the Grey mutation in horses.

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Open Data