Genomic organization study of NF1 duplicon by high resolution FISH

In a recent study we have documented by high resolution FISH the duplication of NF1 gene and several flanking loci in 17q11.2. This evidence was in accordance with the previous identification of REPs in NF1 region by other groups and the increasing number of reports on novel identified LCRs clustered at pericentromeric regions. NF1 is duplicated in direct orientation and the distance between the two copies is estimated to be about 300 Kb. Locus-specific FISH and fiber FISH analyses by using both small (6-8 kb) and large (PACs/BACs) NF1 specific probes demonstrated a similar genomic organization of the duplicon. Further evidence was obtained for the presence of NF1 copies in 17q11.2 by deletion characterization of microdeleted NF1 patients. Following FISH with 7 locus-specific-probes, centered on the centromeric part of the NF1 gene (exon 1-intron 6), we observed a patient showing a decreased signal on one chromosome 17, while two comparable fluorescent signals for probes covering ex 10b-3’UTR were detected. As the centromeric NF1 probes on normal metaphases did not give evidence of any signal asymmetry , we concluded that only a part of an NF1 copy is deleted in our patient. Fiber-FISH experiments with BACs 82O19 and 23O13, specific for the centromeric and telomeric patient breakpoint respectively, evidenced adjacent signals, confirming the involvement of the centromeric NF1 copy in NF1 microdeletion. To assess the evolutionary history of the NF1 duplicon, we performed FISH analysis on stretched chromosomes and DNA fiber from chimpanzee, gorilla, orangutan, gibbon, macaque and mouse, that evidenced the presence of NF1 duplicon in all apes, but not in mouse. Further studies are necessary to characterize the structure and the functional activity of the 17q11.2 NF1 copy.