Journal
GENOME RESEARCH
Volume 13, Issue 10, Pages 2291-2305Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.1349003
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Funding
- NCI NIH HHS [1R21-CA81674, 5R01-CA78544, K01 CA93634-01, R01 CA078544, K01 CA093634, 5R33-CA81674-04] Funding Source: Medline
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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 oligonucleoticle 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 I 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.
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