BACKGROUND: Segmental duplications flanking the neurofibromatosis type 1 (NF1) 
gene locus on 17q11 mediate most gene deletions in NF1 patients. However, the 
large size of the gene and the complexity of the locus architecture pose 
difficulties in deletion analysis. We report the construction and application of 
the first NF1 locus specific microarray, covering 2.24 Mb of 17q11, using a 
non-redundant approach for array design. The average resolution of analysis for 
the array is approximately 12 kb per measurement point with an increased average 
resolution of 6.4 kb for the NF1 gene.
METHODS: We performed a comprehensive array-CGH analysis of 161 NF1 derived 
samples and identified heterozygous deletions of various sizes in 39 cases. The 
typical deletion was identified in 26 cases, whereas 13 samples showed atypical 
deletion profiles.
RESULTS: The size of the atypical deletions, contained within the segment 
covered by the array, ranged from 6 kb to 1.6 Mb and their breakpoints could be 
accurately determined. Moreover, 10 atypical deletions were observed to share a 
common breakpoint either on the proximal or distal end of the deletion. The 
deletions identified by array-CGH were independently confirmed using multiplex 
ligation-dependent probe amplification. Bioinformatic analysis of the entire 
locus identified 33 segmental duplications.
CONCLUSIONS: We show that at least one of these segmental duplications, which 
borders the proximal breakpoint located within the NF1 intron 1 in five atypical 
deletions, might represent a novel hot spot for deletions. Our array constitutes 
a novel and reliable tool offering significantly improved diagnostics for this 
common disorder.