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Analysis of structural diversity in wolf-like canids reveals post-domestication variants

ABSTRACT: 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.

ORGANISM(S): Canis rufus Canis latrans Canis lupus familiaris Canis aureus Canis lupus

PROVIDER: GSE58195 | GEO | 2014/06/05

SECONDARY ACCESSION(S): PRJNA251588

REPOSITORIES: GEO

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Analysis of structural diversity in wolf-like canids reveals post-domestication variants

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

2014-06-05 | E-GEOD-58195 | biostudies-arrayexpress

Canine CNVs associated with canFam2 segmental duplications

2008-10-31 | GSE13266 | GEO

Canine CNVs associated with canFam2 segmental duplications

Project description:This study centered on using a custom made Nimblegen aCGH chip that targeted all segmental duplications in the canine genome to identify associated CNVs. A total of 19 hybridizations were performed in a panel of diverse dogs and a single wolf. Using computational approaches all segmental duplications were identified in the canFam2 genome of the dog. A custom aCGH chip was then built that densely interrogated these segmental duplications for CNVs in a panel of diverse dog breeds and a single wolf.

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

Genome-wide CNVs within and between breeds

2011-03-31 | GSE26170 | GEO

Canine CNVs associated with canFam2 segmental duplications

Project description:Canine CNVs associated with canFam2 segmental duplications

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Genome-wide CNVs within and between breeds

Project description:This study used two different NimbleGen platforms to identify canine CNVs. The first identifies genome-wide CNVs while the second genotypes all known canine CNVs in a large panel of dogs from multiple breeds. The genome-wide microarray used was designed by NimbleGen. The genotyping chip was created by tiling all available probes to all known CNVs identified here and in previous studies.

2011-03-31 | E-GEOD-26170 | biostudies-arrayexpress

Computational detection and experimental validation of segmental duplications and associated copy number variants in river buffalo (Bubalus bubalis)

Project description:Duplicated sequences are the important source of gene innovation and structural variation within mammalian genomes. Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variants (CNVs) in water buffalo (Bubalus bubalis). Aligning to the UMD3.1 cattle genome, we estimated 44.6 Mb (~1.73% of cattle genome) segmental duplications in the autosomes and X chromosome using the sequencing reads of Olimpia (the sequenced water buffalo). 70.3% (70/101) duplications were experimentally validated using the fluorescent in situ hybridization. We also detected a total of 1344 CNV regions across 14 additional water buffalos as well as Olimpia, amounting to 59.8Mb of variable sequence or 2.2% of the cattle genome. The CNV regions overlap 1245 genes and are significantly enriched for specific biological functions such as immune response, oxygen transport, sensory system and signalling transduction. Additionally, we performed array Comparative Genomic Hybridization (aCGH) experiments using the 14 water buffalos as test samples and Olimpia as the reference. Using a linear regression model, significant and high Pearson correlations (r = 0.781) were observed between the digital aCGH values and aCGH probe log2 ratios. We further designed Quantitative PCR assays to confirm CNV regions within or near annotated genes and found 74.2% agreement with our CNV predictions.

2019-02-28 | GSE118117 | GEO

Array comparative genomic hybridization of canine diffuse large B-cell lymphoma (cDLBCL)

Project description:The aim of this work was to identify copy number variations (CNVs) by high-resolution array comparative genomic hybridization (aCGH) on 50 dogs with newly diagnosed DLBCL.

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Great Ape Copy Number Variation

Project description:Intra-specific polymorphism in copy number is documented in many organisms, including human and chimpanzee, but very little is known for other great apes. This study aims to provide CNVs data for orangutan, gorilla, bonobo and chimpanzee, and compare the CNV patterns among these species, as well as with human CNVs and segmental duplications from public databases.

2011-08-03 | GSE30559 | GEO

Analysis of CNVs in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies

Project description:Copy number variants (CNVs) are heritable gains and losses of genomic DNA in normal individuals. While copy number variation is widely studied in humans, our knowledge of CNVs in other mammalian species is more limited. We have designed a custom array-based comparative genomic hybridization (aCGH) platform with 385,000 oligonucleotide probes based on the reference genome sequence of the rhesus macaque (Macaca mulatta), the most widely studied non-human primate in biomedical research. We used this platform to identify 123 CNVs among 10 unrelated macaque individuals, with 24% of the CNVs observed in multiple individuals. We found that segmental duplications were significantly enriched at macaque CNV loci. We also observed significant overlap between rhesus macaque and human CNVs, suggesting that certain genomic regions are prone to recurrent CNV formation and instability, even across a total of ~50 million years of primate evolution (~25 million years in each lineage). Furthermore, for 8 of the CNVs that were observed in both humans and macaques, previous human studies have reported a relationship between copy number and gene expression or disease susceptibility. Therefore, the rhesus macaque offers an intriguing, non-human primate model organism for which hypotheses concerning the specific functions of phenotypically-relevant human CNVs can be tested. Keywords: array-based comparative genomic hybridization, oligonucleotide probes

2008-01-15 | GSE9220 | GEO

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