Mouse genomic representational oligonucleotide microarray analysis: detection of copy number variations in normal and tumor specimens

Lakshmi, B., Hall, I. M., Egan, C., Alexander, J., Leotta, A., Healy, J., Zender, L., Spector, M. S., Xue, W., Lowe, S. W., Wigler, M. H., Lucito, R. (July 2006) Mouse genomic representational oligonucleotide microarray analysis: detection of copy number variations in normal and tumor specimens. Proc Natl Acad Sci U S A, 103 (30). pp. 11234-9. ISSN 0027-8424 (Print)

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DOI: 10.1073/pnas.0602984103


Genomic amplifications and deletions, the consequence of somatic variation, are a hallmark of human cancer. Such variation has also been observed between "normal" individuals, as well as in individuals with congenital disorders. Thus, copy number measurement is likely to be an important tool for the analysis of genetic variation, genetic disease, and cancer. We developed representational oligonucleotide microarray analysis, a high-resolution comparative genomic hybridization methodology, with this aim in mind, and reported its use in the study of humans. Here we report the development of a representational oligonucleotide microarray analysis microarray for the genomic analysis of the mouse, an important model system for many genetic diseases and cancer. This microarray was designed based on the sequence assembly MM3, and contains approximately 84,000 probes randomly distributed throughout the mouse genome. We demonstrate the use of this array to identify copy number changes in mouse cancers, as well to determine copy number variation between inbred strains of mice. Because restriction endonuclease digestion of genomic DNA is an integral component of our method, differences due to polymorphisms at the restriction enzyme cleavage sites are also observed between strains, and these can be useful to follow the inheritance of loci between crosses of different strains.

Item Type: Paper
Uncontrolled Keywords: Animals Crosses Genetic Gene Expression Regulation Neoplastic Genome Mice Mice Inbred BALB C Mice Inbred C57BL Neoplasms genetics Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis methods Oligonucleotides chemistry Polymorphism Genetic Species Specificity
Subjects: bioinformatics > genomics and proteomics > analysis and processing > microarray gene expression processing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > copy number variants
CSHL Authors:
Communities: CSHL labs > Lowe lab
CSHL labs > Lucito lab
CSHL labs > Spector lab
CSHL labs > Wigler lab
School of Biological Sciences > Publications
Depositing User: Editor Margaret Fantz
Date: 25 July 2006
Date Deposited: 21 Feb 2012 17:00
Last Modified: 16 Nov 2016 19:32
PMCID: PMC1544071
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