Published online before print September 18, 2009

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Copyright © 2009 American Society for Investigative Pathology
Journal of Molecular Diagnostics, doi:10.2353/jmoldx.2009.090064

Accepted for publication June 16, 2009.

Technical Advance

Detection and Characterization of NF1 Microdeletions by Custom High Resolution Array CGH

Eric Pasmant^*@, Audrey Sabbagh^*, Julien Masliah-Planchon, Véronique Haddad, Marie-José Hamel, Ingrid Laurendeau^*, Jean Soulier, Béatrice Parfait^*, Pierre Wolkenstein, Ivan Bièche^*, Michel Vidaud^*, and Dominique Vidaud^*

From the UMR745 INSERM,* Université Paris Descartes, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France; the Service de Biochimie et de Génétique Moléculaire, Hôpital Beaujon, Clichy, France; the UMR728 INSERM, Unité d'Immuno-Hématologie and Laboratoire d'Hématologie, Hôpital Saint-Louis, Paris, France; and the Service de Dermatologie, Hôpital Henri Mondor, Créteil, France

^@ To whom correspondence should be addressed. E-mail: eric.pasmant{at}etu.univ-paris5.fr.

	Abstract

In 5% to 10% of cases, neurofibromatosis type 1 is caused by microdeletions scattered across the entire NF1 gene and various neighboring genes. The phenotype appears to be more severe in patients with NF1 microdeletions than in patients with NF1 single point mutations. We have developed a new method for detecting and characterizing NF1 microdeletions based on a custom high-resolution oligonucleotide array comparative genomic hybridization by using the custom 8x15K Agilent array format. The array comprised a total of 14,207 oligonucleotide probes spanning the whole of chromosome 17, including 12,314 probes spanning an 8 Mb interval surrounding the NF1 locus. We validated this approach by testing NF1 microdeleted DNA samples previously characterized by means of microsatellites and real-time PCR methods. Our array comparative genomic hybridization provided enough information for subsequent long-range PCR and nucleotide sequencing of the microdeletion endpoints. Unlike previously described methods, our array comparative genomic hybridization was able to unambiguously differentiate between the three types of microdeletions (type I, type II, and atypical) and to characterize atypical microdeletions. Further comparative studies of patients with well-characterized genotypes and phenotypes and different microdeletions sizes and breakpoints will help determine whether haploinsufficiency of deleted genes and/or genes rearrangements influence clinical outcomes.