Comparative Genomic Hybridization using Oligonucleotide Microarrays and Total Genomic DNA Michael T. Barrett, Alicia Scheffer, Amir Ben-Dor, Nick Sampas, Doron Lipson, Robert Kincaid, Peter Tsang, Bo Curry, Kristin Baird, Paul S. Meltzer, Zohar Yakhini, Laurakay Bruhn, and Stephen Laderman. Proc. Natl. Acad. Sci. USA 101 (51): 17765-17770 (2004).
| Genome Coverage by Chromosome |
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Each 60-mer oligonucleotide probe is represented by a dot. Average probe spatial resolution is ~35KB. |
Detection sensitivity and reproducibity
The ability to detect a single copy loss is critical in identification of new tumor suppressor genes and microdeletions. The accuracy and detection sensitivity of the system is illustrated with hybridizations using 40, XY and 40, XX genomic DNA samples.
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Distribution of log2 ratio values of all X-chromosome oligo probes (blue) versus autosom oligo probes (red) in two dye-flip pairs of XY/XX hybridizations on the Mouse Genome CGH Microarray 44A (P/N G4414A). |
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CGH Analytics view of Chromosome X from two dye-flip pairs of an XY/XX experiment, demonstrating the reproducibility of the platform. |
Detection and mapping of a single-copy amplification
The Ts65Dn Down Syndrome mouse contains a specific translocation on Chromosome 16 just proximal to the App gene and is trisomic for the HSA21-homologous genes from App to the telomere. The genomic DNA obtained from Ts65Dn mice is used in two dye-flip pairs hybridization experiment, using 40, XY DNA as a common reference. |
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CGH Analytics chromosome view (left panel) and zoomed-in gene view (right panel) of Chromosome 16 and breakpoint in dye-flip plot (5 pt moving average). |
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