NF1 microdeletion breakpoints are clustered at flanking repetitive sequences

Neurofibromatosis type 1 patients with a submicroscopic deletion spanning t he NF1 tumor suppressor gene are remarkable for an early age at onset of cu taneous neurofibromas, suggesting the deletion of an additional locus that potentiates neurofibromagenesis. Construction of a 3.5 Mb BAC/PAC/YAC conti g at chromosome 17q11.2 and analysis of somatic cell hybrids from microdele tion patients showed that 14 of 17 cases had deletions of 1,5 Mb in length. The deletions encompassed the entire 350 kb NF1 gene, three additional gen es, one pseudogene and 16 expressed sequence tags (ESTs). In these cases, b oth proximal and distal breakpoints mapped at chromosomal regions of high i dentity, termed NF1 REPs, These REPs, or clusters of paralogous loci, are 1 5-100 kb and harbor at least four ESTs and an expressed SH3GL pseudogene. T he remaining three patients had at least one breakpoint outside an NF1REP e lement; one had a smaller deletion thereby narrowing the critical region ha rboring the putative locus that exacerbates neurofibroma development to 1 M b. These data show that the likely mechanism of NF1 microdeletion is homolo gous recombination between NF1REPs on sister chromatids, NF1 microdeletion is the first REP-mediated rearrangement identified that results in loss of a tumor suppressor gene. Therefore, in addition to the germline rearrangeme nts reported here, NF1REP-mediated somatic recombination could be an import ant mechanism for the loss of heterozygosity at NF1 in tumors of NF1 patien ts.