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Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array

ABSTRACT: This study used the CanineHD genotyping array to investigate copy number variants in the dog genome in a total of 351 samples from 30 different breeds.

ORGANISM(S): Canis lupus familiaris

PROVIDER: GSE55134 | GEO | 2014/03/28

SECONDARY ACCESSION(S): PRJNA238616

REPOSITORIES: GEO

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Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array

Project description:This study used the CanineHD genotyping array to investigate copy number variants in the dog genome in a total of 351 samples from 30 different breeds. In total, 359 samples from 30 different breeds were genotyped on the CanineHD array. Signal intensities from the array were used to assess copy number variants and a supplied clusterfile from Illumina was used as reference file (downloadable at http://supportres.illumina.com/documents/downloads/productfiles/caninehd/caninehd_a.egt). Eight samples did not fulfill the quality criteria for CNV calling and therefore CNV calling was performed on 351 samples.

2014-03-28 | E-GEOD-55134 | biostudies-arrayexpress

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Project description:Osteosarcoma in dogs is a spontaneously occurring disease with a global tumor gene expression signature indistinguishable from human pediatric tumors and clinical progression is remarkably similar. Unlike human OS, canine OS is a highly heritable disease with some large and giant dog breeds at >10x increased risk. We did a genome wide association study of osteosarcoma using the Illumina CanineHD genotyping array in three breeds: greyhound (mortality from OS = 26%), rottweiler (17%) and Irish wolfhound (IWH, 21%) and identified 33 inherited risk loci explaining 55 to 85% of phenotype variance in each breed. Data created for a genome-wide association studio of heritable osteosarcoma risk factors in dogs, including 267 racing greyhounds (153 affected (A) + 114 unaffected (U)), 135 rottweilers (80 A + 55 U), 141 IWH (76 A + 65 U) and 19 AKC greyhounds using the Illumina CanineHD array (~170,000 SNPs genomewide)

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Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array.

Project description: Not available

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SNP genotyping of various breeds

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