Representational Oligonucleotide Microarray Analysis: A High-Resolution Method to Detect Genome Copy Number Variation

Robert Lucito, John Healy, Joan Alexander, Andrew Reiner, Diane Esposito, Maoyen Chi, Linda Rodgers, Amy Brady, Jonathan Sebat, Jennifer Troge, Joseph A West, Seth Rostan, Ken C Q Nguyen, Scott Powers, Kenneth Q Ye, Adam Olshen, Ennapadam Venkatraman, Larry Norton, Michael Wigler

We have developed a methodology we call ROMA (representational oligonucleotide microarray analysis), for the detection of the genomic aberrations in cancer and normal humans. By arraying oligonucleotide probes designed from the human genome sequence, and hybridizing with "representations" from cancer and normal cells, we detect regions of the genome with altered "copy number." We achieve an average resolution of 30 kb throughout the genome, and resolutions as high as a probe every 15 kb are practical. We illustrate the characteristics of probes on the array and accuracy of measurements obtained using ROMA. Using this methodology, we identify variation between cancer and normal genomes, as well as between normal human genomes. In cancer genomes, we readily detect amplifications and large and small homozygous and hemizygous deletions. Between normal human genomes, we frequently detect large (100 kb to 1 Mb) deletions or duplications. Many of these changes encompass known genes. ROMA will assist in the discovery of genes and markers important in cancer, and the discovery of loci that may be important in inherited predispositions to disease.