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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

Abstract

Background

Greying with age in horses is an autosomal dominant trait, associated with loss of hair pigmentation, melanoma and vitiligo-like depigmentation. We recently identified a 4.6 kb duplication in STX17 to be associated with the phenotype. The aims of this study were to investigate if the duplication in Grey horses shows copy number variation and to exclude that any other polymorphism is uniquely associated with the Grey mutation.

Results

We found little evidence for copy number expansion of the duplicated sequence in blood DNA from Grey horses. In contrast, clear evidence for copy number expansions was indicated in five out of eight tested melanoma tissues or melanoma cell lines. A tendency of a higher copy number in aggressive tumours was also found. Massively parallel resequencing of the ~350 kb Grey haplotype did not reveal any additional mutations perfectly associated with the phenotype, confirming the duplication as the true causative mutation. We identified three SNP alleles that were present in a subset of Grey haplotypes within the 350 kb region that shows complete linkage disequilibrium with the causative mutation. Thus, these three nucleotide substitutions must have occurred subsequent to the duplication, consistent with our interpretation that the Grey mutation arose more than 2,000 years before present.

Conclusions

These results suggest that the mutation acts as a melanoma-driving regulatory element. The elucidation of the mechanistic features of the duplication will be of considerable interest for the characterization of these horse melanomas as well as for the field of human melanoma research.

Keywords:
STX17; Melanoma; Hair greying; Copy number variation; Melanocytes