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Validation experiment of copy number variations identified by next-generation sequencing in chickens (part 2)

ABSTRACT: 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.

ORGANISM(S): Gallus gallus

PROVIDER: GSE54118 | GEO | 2015/05/14

SECONDARY ACCESSION(S): PRJNA235207

REPOSITORIES: GEO

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Validation experiment of copy number variations identified by next-generation sequencing in chickens (part 1)

2015-05-14 | GSE54117 | GEO

Validation experiment of copy number variations identified by next-generation sequencing in chickens (part 2)

2015-05-14 | E-GEOD-54118 | biostudies-arrayexpress

Validation experiment of copy number variations identified by next-generation sequencing in chickens (part 1)

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 0.395 to 0.740. The whole blood samples were collected from Beijing You (BY), Dongxiang (DX), Luxi Game (LX), Red Jungle Fowl (RJF), Shouguang (SG), Silkie (SK), Tibetan (TB), Wenchang (WC), and White Plymouth Rock (WR), and genomic DNA was isolated using standard phenol/chloroform extraction methods. Each test sample labeled with Cy3 was mixed with Red Jungle Fowl as reference sample labeled with Cy5. All process and analysis was performed in terms of standard NimbleGen procedure. However, due to some uncontrollable factors, none of results were obtained in three consecutive trials for CS, RIR and WL, so we had to choose a similar Agilent custom-designed 1*1.0 M array.

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2010-06-11 | GSE19469 | GEO

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Project description:Chromosomal segmental copy number variation (CNV) has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory regions. Compelling evidence indicates that CNVs impact genome functions. The chicken is a very important farm animal species which has also served as model animal for biological and biomedical research for hundreds of years. A map of CNVs in chickens could facilitate the identification of chromosome regions that segregate for important agricultural and disease phenotypes. NimbleGen 385k whole genome tiling arrays were used to map CNVs in the chicken. This study has identified 96 CNVs in three lines of chickens (broiler, Leghorn and Rhode Island red). These CNVs encompass 16 Mb (1.3%) of the chicken genome. Twenty six CNVs were found in two or more animals. Smaller sized CNVs mostly affect none coding sequences while larger CNV regions involve genes, for example prolactin receptor, aldose reductase and zinc finger proteins, suggesting chicken CNVs potentially affect agricultural or disease related traits. Blood DNA isolated from Cornish Rock, Leghorn and Rhode Island Red birds. Cy5 labeled DNA from a Cornish Rock male used as reference was mixed with Cy3 labeled DNA samples was then hybridized to the 385K chicken tiling array. Fluorescence intensity data were normalized with qspline algorithm and ratio data were analyzed with the circular binary segmentation algorithm from Olshen et al. Copy number variation calls were made if the averaged Log2 ratio of a segment was shifted by 0.3 from the baseline.

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