Mapping of genes and ESTs assigned to 17q11.2 to a YAC contig centred on the NF1 gene

Abstract

Background The 17q11.2 cytogenetic band is partially covered by the WC17.3 YAC contig, but the position on this contig of many D-segments, genes and ESTs assigned to the region is not unambiguous. A major reference gene of the region is NF1, involved in neurofibromatosis type 1 and deleted with flanking genes in a subset of patients with NF1 microdeletion syndrome. Several genes of medical relevance also map to the 17q11.2 band.

Methods We assigned genes, markers and ESTs mapped to the 17q11.2 cytogenetic band to selected YACs and PACs by PCR screening and Southern hybridization of PFGE blots. YAC chimerism was detected by FISH which also allowed the refining of gene/marker order. New STSs were generated by cloning and sequencing Alu–Alu or Alu–vector fragments obtained from YACs.

Results A > 7 Mb contig centred on the NF1 gene and consisting of 26 YACs and 8 PACs has been built up to cover most of the 17q11.2 cytogenetic band. Within the contig, we ordered 11 known and 8 novel STSs, 18 ESTs and 11 known genes, a few of which are involved in genetic diseases. Additional genes loosely assigned to 17q11.2 could be located outside the contig. The contig clones with the wide panel of anchored STSs, genes and ESTs provide a tool for the FISH characterization of gross deletions in NF1 patients with complex phenotypes and any constitutional/somatic chromosomal rearrangement affecting 17q11.2. Crosslinking of the telomeric side of our contig to the centromeric side of the nearby chemokine contig has been established, thus providing a long-range integrated map for the isolation of disease genes and the construction of a transcription map.