Project description:This SuperSeries is composed of the following subset Series: GSE24424: Copy number variation in inbred and wild mice GSE24640: Validation of a subset of copy number variants from GSE24424 by aCGH Refer to individual Series
Project description:This dataset was used to validate CNV predictions from GSE24424. We designed a custom CGH array to interrogate a total of 4,420 individual CNVs and their flanks predicted in 17 individuals. On the basis of a test that compares signals of probes located within to those mapping outside of CNVs (two-tailed P<0.05, Mann-Whitney U test), we could confirm about 77% of the tested predictions and thus establish a set of 3,383 validated CNVs. The vast majority of confirmed CNVs (3,299 of 3,383 or 97.5%) show a consistent direction of change between the initial array (GSE24424) and the custom array, suggesting a false-confirmation rate of approximately 5%.
Project description:This dataset was used to validate CNV predictions from GSE24424. We designed a custom CGH array to interrogate a total of 4,420 individual CNVs and their flanks predicted in 17 individuals. On the basis of a test that compares signals of probes located within to those mapping outside of CNVs (two-tailed P<0.05, Mann-Whitney U test), we could confirm about 77% of the tested predictions and thus establish a set of 3,383 validated CNVs. The vast majority of confirmed CNVs (3,299 of 3,383 or 97.5%) show a consistent direction of change between the initial array (GSE24424) and the custom array, suggesting a false-confirmation rate of approximately 5%. We interrogated a total of 4,420 individual CNVs and their flanks predicted in 17 individuals from the GSE24424 dataset by rehybridizing their DNAs on a high-resolution custom CGH array (median probe spacing 350 bp).
Project description:Custom exon aCGH analysis of copy number across the genomes of 16 horse breeds Two-condition experiment, All breed samples were compared to a single Thoroughbred reference, Reference was then compared to Twilight (DNA from horse used for reference genome assembly)
Project description:Custom exome aCGH analysis of copy number across the genomes of 16 canine breeds Two-condition experiment, All breed samples were compared to a single Boxer reference, Seizure samples were compared to breed and sex matched controls, and German Shepherds were compared to the Boxer reference
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.
Project description:Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform a genome-wide analysis of CNVs in the 12 diversified chicken genomes based on next-generation sequencing. We apply aCGH experiments to confirm our predicted CNVs. Results from aCGH agree well with our findings and the Pearson’s correlation values between the test and reference samples range from 0.644 to 0.722.