Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays.
Array painting is a technique that uses microarray technology to rapidly map chromosome translocation breakpoints. Previous methods to map translocation breakpoints have used fluorescence in situ hybridization (FISH) and have consequently been labor-intensive, time-consuming and restricted to the low breakpoint resolution imposed by the use of metaphase chromosomes. Array painting combines the isolation of derivative chromosomes (chromosomes with translocations) and high-resolution microarray analysis to refine the genomic location of translocation breakpoints in a single experiment. In this protocol, we describe array painting by isolation of derivative chromosomes using a MoFlo flow sorter, amplification of these derivatives using whole-genome amplification and hybridization onto commercially available oligonucleotide microarrays. Although the sorting of derivative chromosomes is a specialized procedure requiring sophisticated equipment, the amplification, labeling and hybridization of DNA is straightforward, robust and can be completed within 1 week. The protocol described produces good quality data; however, array painting is equally achievable using any combination of the available alternative methodologies for chromosome isolation, amplification and hybridization.
Gribble
Susan M
SM
Human Genetics, Sulston Laboratories, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK. smg@sanger.ac.uk
Ng
Bee Ling
BL
Prigmore
Elena
E
Fitzgerald
Tomas
T
Carter
Nigel P
NP
D018929:Cell Culture Techniques; D002460:Cell Line; D002874:Chromosome Mapping / Q000379:methods*; D005434:Flow Cytometry; D015723:Gene Library; D006801:Humans; D021141:Nucleic Acid Amplification Techniques; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D014178:Translocation, Genetic