Molecular characterization and gene content of breakpoint boundaries in patients with neurofibromatosis type 1 with 17q11.2 microdeletions

Homologous recombination between poorly characterized regions flanking the NF1 locus causes the constitutional loss of similar to1.5 Mb from 17q11.2 c overing greater than or equal to 11 genes in 5%-20% of patients with neurof ibromatosis type 1 (NF1). To elucidate the extent of microheterogeneity at the deletion boundaries, we used single-copy DNA fragments from the extreme ends of the deleted segment to perform FISH on metaphase chromosomes from eight patients with NF1 who had large deletions. In six patients, these pro bes were deleted, suggesting that breakage and fusions occurred within the adjacent highly homologous sequences. Reexamination of the deleted region r evealed two novel functional genes FLJ12735 (AK022797) and KIAA0653-related (WI-12393 and AJ314647), the latter of which is located closest to the dis tal boundary and is partially duplicated. We defined the complete reading f rames for these genes and two expressed-sequence tag (EST) clusters that we re reported elsewhere and are associated with the markers SHGC-2390 and WI- 9521. Hybrid cell lines carrying only the deleted chromosome 17 were genera ted from two patients and used to identify the fusion sequences by junction -specific PCRs. The proximal breakpoints were found between positions 12527 9 and 125479 in one patient and within 4 kb of position 143000 on BAC R-271 K11 (AC005562) in three patients, and the distal breakpoints were found at the precise homologous position on R-640N20 (AC023278). The interstitial 17 q11.2 microdeletion arises from unequal crossover between two highly homolo gous WI-12393-derived 60-kb duplicons separated by similar to1.5 Mb. Since patients with the NF1 large-deletion syndrome have a significantly increase d risk of neurofibroma development and mental retardation, hemizygosity for genes from the deleted region around the neurofibromin locus (CYTOR4, FLJ1 2735, FLJ22729, HSA272195 (centaurin-alpha2), NF1, OMGP, EVI2A, EVI2B, WI-9 521, HSA272196, HCA66, KIAA0160, and WI-12393) may contribute to the severe phenotype of these patients.