Identification of duplicated genes in 17q11.2 using FISH on stretched chromosomes and DNA fibers

Recent evidence has been provided that links duplicons (REP-P and REP-M) in 17q11.2 flanking the neurofibromatosis type 1 (NF1) gene to the breakpoints of the NF1 microdeletion syndrome. The physical mapping and structural definition of duplicated regions is often impossible by conventional approaches, and so we have used high resolution fluorescence in situ hybridization (FISH) with locus-specific probes of limited size on chromosomes stretched to different degrees to identify novel duplicated genes and expressed sequence tags (ESTs) mapping to 17q11.2. This approach has allowed us to detect and map duplications of the BLMH and GOS28 genes, with one copy lying centromeric and one telomeric to the NF1 gene, and an SHGC30113 transcript with one copy being adjacent and the other distal to the NF1 3' untranslated region. Double-color FISH with a BLMH-specific probe on stretched chromosomes showed that the telomeric BLMH repeat lacked the 5' end of the gene and was 0.8 Mb from its centromeric copy. The distance between the SHGC30113 repeats was estimated as being 500 kb by double-color FISH on highly stretched chromosomes and DNA fibers. The latter approach revealed adjacent SHGC30113-BLMH-specific signals relating to the incomplete BLMH copy. The use of FISH on stretched chromosomes and, where applicable DNA fibers, is a powerful tool for identifying and finely characterizing duplicated regions whose mapping by the classical physical mapping approach is often precluded.