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Development of NF2 gene specific, strictly sequence defined diagnostic microarray for deletion detection

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Abstract

Neurofibromatosis type 2 (NF2) is an autosomal dominant cancer syndrome caused by the biallelic inactivation of the neurofibromin 2 tumor suppressor gene (NF2). Current molecular diagnostic methods for NF2 involve the detection of point mutations and/or microdeletions across the 100-kb locus from 22q12. Despite the fact that NF2 gene inactivating deletions occur in 25–30% of NF2 patients, the available approaches for high-resolution and high-throughput detection of deletions are underdeveloped. This need for improved methodology for gene copy number analysis is especially apparent when compared to a variety of methods available for accurate detection of point mutations. The microarray-based form of comparative genomic hybridization has been previously applied in the high-resolution analysis of gene copy number variation across large genomic regions. In this study we apply a PCR-based, strictly sequence-defined, repeat-free approach for the preparation of a diagnostic microarray for the detection of disease-causing deletions in the NF2 gene. The methodology is based on the preselection of target DNA by excluding redundant sequence within the NF2 locus using bioinformatics. This approach allows a significant increase in the resolution of deletion detection. The current average resolution of analysis across the NF2 locus is 23 kb. Therefore this NF2 gene-specific microarray is the first high-resolution tool for detection of diagnostically significant gene copy number aberrations. This microarray should now be applied in the analysis of an extensive series of NF2 patients, and hence we would like to call for such samples.

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Abbreviations

ANILFR :

Average normalized interlocus fluorescence ratio

Array-CGH :

Microarray-based comparative genomic hybridization

CGH :

Comparative genomic hybridization

NF2 :

Neurofibromatosis type 2

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Acknowledgements

We thank Dr. Jessica Zucman-Rossi for cosmid clone 72c7, Dr. Pieter de Jong for providing the chromosome 22 specific cosmid libraries, and Dr. Anna Wedell and Isabel Tapia for critical review of the manuscript. This work was supported by grants from the United States Army Medical Research and Materiel Command, award no. DAMD17-00-1-0536, the Swedish Cancer Foundation, the Swedish Research Council, and Uppsala University to J.P.D.

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Authors and Affiliations

  1. Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjölds väg 20, 75185, Uppsala, Sweden

    Kiran K. Mantripragada, Patrick G. Buckley, Caroline Jarbo, Uwe Menzel & Jan P. Dumanski

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  1. Kiran K. Mantripragada
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  2. Patrick G. Buckley
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  3. Caroline Jarbo
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  4. Uwe Menzel
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  5. Jan P. Dumanski
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Correspondence to Jan P. Dumanski.

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K.K. Mantripragada and P.G. Buckley contributed equally to this work.

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Mantripragada, K.K., Buckley, P.G., Jarbo, C. et al. Development of NF2 gene specific, strictly sequence defined diagnostic microarray for deletion detection. J Mol Med 81, 443–451 (2003). https://doi.org/10.1007/s00109-003-0458-3

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  • DOI: https://doi.org/10.1007/s00109-003-0458-3

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