Canine CNVs associated with canFam2 segmental duplications
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ABSTRACT:
PROVIDER: PRJNA109559 | ENA |
REPOSITORIES: ENA
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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
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.
2008-10-31 | GSE13266 | GEO
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
Project description:This SuperSeries is composed of the following subset Series: GSE13884: INTER_specific hybs: A Burst of Segmental Duplications in the African Great Ape Ancestor GSE13885: INTRA_specific hybs: A Burst of Segmental Duplications in the African Great Ape Ancestor Refer to individual Series
2009-03-05 | E-GEOD-13934 | biostudies-arrayexpress
Project description:[original title] Identification of recurrent microdeletion on 17q23.2 flanked by segmental duplications associated with heart defects and limb abnormalities. Segmental duplications, are known to mediate non-allelic homologous recombination and have been suggested to be hotspots in chromosome evolution and human genomic instability. We report the identification by microarray-based comparative genomic hybridization (aCGH) of seven individuals with microdeletions of 17q23.1q23.2. The clinical information obtained from six individuals for whom medical records were available showed common features including mild to moderate developmental delay, postnatal growth retardation, eye anomalies, heart defects and hand/foot/limb abnormalities. The presence in the deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome.
2010-12-31 | GSE19932 | GEO
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.
2014-06-05 | GSE58195 | GEO
Project description:[original title] Identification of recurrent microdeletion on 17q23.2 flanked by segmental duplications associated with heart defects and limb abnormalities. Segmental duplications, are known to mediate non-allelic homologous recombination and have been suggested to be hotspots in chromosome evolution and human genomic instability. We report the identification by microarray-based comparative genomic hybridization (aCGH) of seven individuals with microdeletions of 17q23.1q23.2. The clinical information obtained from six individuals for whom medical records were available showed common features including mild to moderate developmental delay, postnatal growth retardation, eye anomalies, heart defects and hand/foot/limb abnormalities. The presence in the deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome. aCGH control vs. patient, total of 7 patients Lowest normalized log2 ratio = patient 1: -1.99; patient 2: -1.87; patient 3: -2.16; patient 4: -2.11; patient 5: -1.974802452; patient 6: -2.23; patient 7: -1.36.
2010-12-31 | E-GEOD-19932 | biostudies-arrayexpress
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
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.
2011-03-31 | GSE26170 | GEO
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