Precise mapping of the fragile site FRA12A on chromosome 12q13.1

Introduction A causative relationship has been reported between fragile site expression and disease for FRA12A, a rare, folate-sensitive fragile site on chromosome 12q13.1. FRA12A expression has been described in a number of patients with mental retardation, sometimes in combination with clinical abnormalities. In correspondence to the molecular mechanism of previously cloned, rare, fragile sites, it may be expected that FRA12A is caused by repeat expansion, affecting the expression of genes in the region. To identify the repeat and the associated gene, this paper reports the precise mapping of FRA12A on chromosome 12q12–13.

Methods Fluorescence in situ hybridization (FISH) techniques were used to map YAC and PAC clones in the neighbourhood of FRA12A. PAC DNA pools and PAC filters were screened to find additional PAC clones spanning the candidate region. Markers in the region were obtained via web searches and used to construct both PAC and YAC contigs.

Results and Discussion A single YAC clone that overspans the fragile site was identified and a complete YAC and PAC contig for the FRA12A region was constructed. The region contains several candidate genes, including a calcium ion channel (CACNLB3), a GTP-binding factor (ARF3), a gene involved in brain development (INT1) and two other genes involved in developmental processes (WNT10B and ALR). The FXR1 gene, a homologue of the FMR1 gene, that is associated with fragile X syndrome and that maps to chromosome 12q12–13, was ruled out as a possible candidate gene for the FRA12A site.