Open Access Research

Physical mapping of genes in somatic cell radiation hybrids by comparative genomic hybridization to cDNA microarrays

Johann Y Lin17, Jonathan R Pollack237, Fan-Li Chou1, Christian A Rees4, Allen T Christian6, Joel S Bedford6, Patrick O Brown35 and Mark H Ginsberg1*

Author Affiliations

1 Department of Vascular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA

2 Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA

3 Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA

4 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA

5 Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA

6 Department of Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA

7 These authors contributed equally to this work

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Genome Biology 2002, 3:research0026-research0026.7  doi:10.1186/gb-2002-3-6-research0026

Published: 14 May 2002

Abstract

Background

Somatic cell mutants can be informative in the analysis of a wide variety of cellular processes. The use of map-based positional cloning strategies in somatic cell hybrids to analyze genes responsible for recessive mutant phenotypes is often tedious, however, and remains a major obstacle in somatic cell genetics. To fulfill the need for more efficient gene mapping in somatic cell mutants, we have developed a new DNA microarray comparative genomic hybridization (array-CGH) method that can rapidly and efficiently map the physical location of genes complementing somatic cell mutants to a small candidate genomic region. Here we report experiments that establish the validity and efficacy of the methodology.

Results

CHO cells deficient for hypoxanthine:guanine phosphoribosyl transferase (HPRT) were fused with irradiated normal human fibroblasts and subjected to HAT selection. Cy5-labeled genomic DNA from the surviving hybrids containing the HPRT gene was mixed with Cy3-labeled genomic DNA from normal CHO cells and hybridized to a microarray containing 40,185 cDNAs, representing 29,399 genes (UniGene clusters). The DNA spots with the highest Cy5:Cy3 fluorescence ratios corresponded to a group of genes mapping within a 1 Mb interval centered near position 142.7 Mb on the X chromosome, the genomic location of HPRT.

Conclusion

The results indicate that our physical mapping method based on radiation hybrids and array-CGH should significantly enhance the speed and efficiency of positional cloning in somatic cell genetics.