Representational oligonucleotide microarray analysis: A high-resolution method to detect genome copy number variation Journal Article
| Authors: | Lucito, R.; Healy, J.; Alexander, J.; Reiner, A.; Esposito, D.; Chi, M.; Rodgers, L.; Brady, A.; Sebat, J.; Troge, J.; West, J. A.; Rostan, S.; Nguyen, K. C. Q.; Powers, S.; Ye, K. Q.; Olshen, A.; Venkatraman, E.; Norton, L.; Wigler, M. |
| Article Title: | Representational oligonucleotide microarray analysis: A high-resolution method to detect genome copy number variation |
| Abstract: | 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. |
| Keywords: | controlled study; gene sequence; gene deletion; research design; accuracy; gene amplification; gene locus; genetic variability; cell line, tumor; mutational analysis; breast neoplasms; cancer genetics; gene number; homozygosity; oligonucleotide array sequence analysis; human genome; gene duplication; hemizygosity; models, genetic; dna microarray; gene dosage; nucleic acid hybridization; genetic predisposition; oligonucleotide; comparative genomic hybridization; aneuploidy; genetic marker; genome, human; diploidy; genes, neoplasm; variation (genetics); base composition; oligonucleotide probe; oligonucleotide probes; humans; male; female; priority journal; article |
| Journal Title: | Genome Research |
| Volume: | 13 |
| Issue: | 10 |
| ISSN: | 1088-9051 |
| Publisher: | Cold Spring Harbor Laboratory Press |
| Date Published: | 2003-10-01 |
| Start Page: | 2291 |
| End Page: | 2305 |
| Language: | English |
| DOI: | 10.1101/gr.1349003 |
| PUBMED: | 12975311 |
| PROVIDER: | scopus |
| PMCID: | PMC403708 |
| DOI/URL: | |
| Notes: | Export Date: 12 September 2014 -- Source: Scopus |
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