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Genome-wide array comparative genomic hybridization (aCGH) profiling of copy number variations (CNVs) in various dog breeds in comparison to a reference sample

ABSTRACT: This study used the NimbleGen dog whole genome CGH 2.1M tiling array to assay copy number variants in the dog genome in multiple breeds and wolf.

ORGANISM(S): Canis lupus familiaris Canis lupus

PROVIDER: GSE40210 | GEO | 2012/08/21

SECONDARY ACCESSION(S): PRJNA173205

REPOSITORIES: GEO

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Genome-wide array comparative genomic hybridization (aCGH) profiling of copy number variations (CNVs) in various dog breeds in comparison to a reference sample

Project description:This study used the NimbleGen dog whole genome CGH 2.1M tiling array to assay copy number variants in the dog genome in multiple breeds and wolf. 53 samples of genomic DNA were hybridized to a reference sample. The dataset comprises 2 samples from each of 15 dog breeds, 10 samples from each of 2 dog breeds and 3 samples from gray wolf.

2012-08-21 | E-GEOD-40210 | biostudies-arrayexpress

Canine CNVs associated with canFam2 segmental duplications

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2010-05-17 | E-GEOD-13266 | biostudies-arrayexpress

Genome-wide array comparative genomic hybridization (aCGH) profiling of copy number variations (CNVs) in various dog breeds in comparison to a reference sample

Project description:Genome-wide array comparative genomic hybridization (aCGH) profiling of copy number variations (CNVs) in various dog breeds in comparison to a reference sample

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Diverse dog breeds genotyped on Affymetrix Canine v2 Arrays

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Diverse dog breeds genotyped on Affymetrix Canine v2 Arrays

Project description:Diverse dataset of 1247 dogs from many breeds and wolves used to investigate the origins of dog domestication DNA for 1228 dogs from 35 breeds and 19 wolves was extracted from whole blood samples and genotyped on the Affymetrix Canine v2 Arrays. Genotypes were called using Affymetrix's snp5-probeset-genotype software and the BRLMM-P calling algorithm. The included breed designations are owner reported.

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Project description: Not available

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Dataset #2 for genome-wide analysis of heritable dog osteosarcoma in 3 breeds

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.

2013-11-12 | GSE51976 | GEO

Dataset #1 for genome-wide analysis of heritable dog osteosarcoma in 3 breeds

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Project description:This study uses a custom made Nimblegen aCGH chip that targeted all segmental duplications in the canine genome to identify associated CNVs. A total of 23 hybridizations were performed in a panel of diverse dogs and a single wolf. This study focuses on the use a custom made Nimblegen aCGH chip to genotype 1,611 dog CNVs in 23 wolf-like canids (4 purebred dogs, one dingo, 15 gray wolves, one red wolf, one coyote and one golden jackal) to identify CNVs that may have arisen after domestication

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