Spectrum of single- and multiexon NFI copy number changes in a cohort of 1,100 unselected NFI patients

Neurofibromatosis type I (NFI), the most common tumor-predisposing disorder in humans, is caused by defects in the NFI tumor-suppressor gene. Comprehensive mutation analysis applying RNA-based techniques complemented with FISH analysis achieves mutation detection rates of similar to 95% in NFI patients. The majority of mutations are minor lesions, and similar to 5% are total gene deletions. We found 13 single- and/or multiexon deletions/duplications out of 1,050 detected mutations using our RNA-based approach in a cohort of 1, 100 NFI patients and confirmed these changes using multiplex ligation-dependent probe amplification (MLPA). With MLPA, we found another 12 novel multiexon deletion/duplications in 55 NFI patients for whom analysis with multiple assays had not revealed a NFI mutation, including 50 previously analyzed comprehensively. The extent of the 22 deletions and 3 duplications varied greatly, and there was no clustering of breakpoints. We also evaluated the sensitivity of MLPA in identifying deletions in a mosaic state. Furthermore, we tested whether the MLPA PI22 NFI area assay could distinguish between type I deletions, with breakpoints in low-copy repeats (NFI-LCRs), and type II deletions, caused by aberrant recombination between the JJAZ gene and its pseudogene. Our study showed that intragenic deletions and/or duplications represent only similar to 2% of all NFI mutations. Although MLPA did not substantially increase the mutation detection rate in NFI patients, it was a useful first step in a comprehensive mutation analysis scheme to quickly pinpoint patients with single- or multiexon deletions/duplications as well as patients with a total gene deletion who will not need full sequencing of the complete coding region. (c) 2005 Wiley-Liss, Inc.