Data from: A SACS deletion variant in Great Pyrenees dogs causes autosomal recessive neuronal degeneration
Data files
Nov 03, 2025 version files 4.15 MB
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GP_Final.bed
874.51 KB
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GP_Final.bim
3.28 MB
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GP_Final.fam
780 B
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README.md
1.16 KB
Abstract
ARSACS (autosomal recessive spastic ataxia of Charlevoix-Saguenay) is a human neurological disorder characterized by progressive cerebellar ataxia and peripheral neuropathy. A recently recognized disorder in Great Pyrenees dogs is similarly characterized by widespread central nervous system degeneration leading to progressive cerebellar ataxia and spasticity, combined with peripheral neuropathy. Onset of clinical signs occurred in puppies as young as four months of age, with slow progression over several years. A multi-generation pedigree suggested an autosomal recessive mode of inheritance. Histopathology revealed consistent cerebellar Purkinje cell degeneration, neuronal degeneration in brainstem nuclei, widespread spinal cord white matter degeneration, ganglion cell degeneration, inappropriately thin myelin sheaths or fully demyelinated peripheral nerve fibers, and normal or only mild patterns of denervation atrophy in skeletal muscles. Genome-wide single nucleotide polymorphism (SNP) genotype data was collected from 6 cases and 26 controls, where homozygosity mapping identified a 3.3Mb region on CFA25 in which all cases were homozygous and all controls were either heterozygous or homozygous for alternate haplotypes. This region tagged the SACS gene where variants are known to cause ARSACS. Sanger sequencing of SACS in affected dogs identified a 4bp deletion that causes a frame shift and truncates 343 amino acids from the C terminus of the encoded sacsin protein (p.Val4244AlafsTer32). Our clinical and histopathological descriptions of this canine disorder contribute significantly to the description of human ARSACS and represents the first naturally-occurring large animal model of this disorder.
This dataset contains 170K Illumina canine SNP array data from 34 Great Pyrenees dogs. The data is formatted in binary files, ready to go into PLINK. Six dogs are affected with neuronal degeneration, with the remainder as controls (or phenotype uncertain, n = 2). A modified homozygosity mapping approach allowed the identification of a region segregating in an autosomal recessive manner with affected dogs.
Description of the data and file structure
The files are in standard binary format: .bim, .bed, and .fam, which are ready to go into PLINK.
GP_Final.bed
GP_Final.bim
The .bim and .bed files together (in PLINK) contain all of the SNP genotypes for each of the 34 dogs. These are raw files, and the SNP data has not been pruned for quality control.
GP_Final.fam
The .fam file is formatted in a typical linkage format, with the following columns: Family ID, Individual ID, Sire ID, Dam ID, Sex (1 = male, 2 = female) and Phenotype status (1 = unaffected, 2 = affected). The designation "-9" is used for two dogs with uncertain phenotypes.
- Ekenstedt, Kari J; Minor, Katie M; Shelton, G Diane et al. (2023). A SACS deletion variant in Great Pyrenees dogs causes autosomal recessive neuronal degeneration [Preprint]. Research Square Platform LLC. https://doi.org/10.21203/rs.3.rs-3163989/v1
- Ekenstedt, Kari J.; Minor, Katie M.; Shelton, G. Diane et al. (2023). A SACS deletion variant in Great Pyrenees dogs causes autosomal recessive neuronal degeneration. Human Genetics. https://doi.org/10.1007/s00439-023-02599-1
