Representational oligonucleotide microarray analysis: A high-resolution method to detect genome copy number variation

Lucito, R., Healy, J., Alexander, J., Reiner, A., Esposito, D., Chi, M. Y., Rodgers, L., Brady, A., Sebat, J., Troge, J. E., West, J. A., Rostan, S., Nguyen, K. C. Q., Powers, S., Ye, K. Q., Olshen, A., Venkatraman, E., Norton, L., Wigler, M. H. (October 2003) Representational oligonucleotide microarray analysis: A high-resolution method to detect genome copy number variation. Genome Research, 13 (10). pp. 2291-2305. ISSN 1088-9051

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DOI: 10.1101/gr.1349003


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.

Item Type: Paper
Uncontrolled Keywords: GENE-EXPRESSION PATTERNS Gene-expression patterns BREAST CANCER Breast cancer CDNA MICROARRAY CDNA microarray HYBRIDIZATION Hybridization AMPLIFICATION Amplification CARCINOMA Carcinoma CLONING Cloning ARRAY Array
Subjects: bioinformatics > genomics and proteomics > analysis and processing > microarray gene expression processing
Investigative techniques and equipment > ROMA
CSHL Authors:
Communities: CSHL labs > Lucito lab
CSHL labs > Powers lab
CSHL labs > Wigler lab
Depositing User: Brian Soldo
Date: October 2003
Date Deposited: 29 Mar 2012 15:31
Last Modified: 07 Nov 2016 20:13
PMCID: PMC403708
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