Preparation of genomic DNA for microarray-based comparative genome hybridization.
Genome-wide assessment of DNA gains and losses can be accomplished by comparative hybridization using a variety of microarray platforms that employ oligo, cDNA, BAC and other sequences as probes. Here we describe the preparation of genomic DNA for hybridization to a set of chicken cDNA probes spotted on glass slide microarrays. Method 1 can be used to assess DNA copy-number differences between two genomes, typically an experimental genome and a normal, diploid genome. We then present a specialized application of array CGH for detecting DNA amplifications containing long, inverted repeat structures (palindromes). Method 2 describes the procedure for palindrome enrichment and the internal controls used to distinguish direct versus inverted, long repeat structures using the cDNA microarray platform.
Kimmel
Robert
R
Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Icreverzi
Amalia
A
Neiman
Paul
P
D000818:Animals; D002645:Chickens; D016678:Genome; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis