Two families of low-copy-number repeats are interspersed on Xp22.3: implications for the high frequency of deletions in this region.

The locations of two families of low-copy-number repeats (CRI-S232 and G1.3) in the physical and genetic maps of the distal short arm of the human X chromosome (Xp22.3) have been determined. Single-copy fragments flanking several repeat elements from each family have been cloned and assigned to specific intervals on a deletion map of Xp22.3. Physical distances between these loci and previously isolated Xp22.3 markers have been determined by pulsed-field gel electrophoresis (PFGE). The positions of some of these markers on the genetic map of the region have been established by segregation analysis in CEPH families. Four members of the CRI-S232 family have been localized within 3 Mb on Xp22.3, interspersed with two members of the G1.3 family. Both deletion and PFGE mapping data suggest that a CpG island localized in a specific position on the map might be associated with the Kallmann syndrome gene. Unlike the previously reported data on hyperpolymorphic minisatellite sequences, no increase in the recombination rate was detected around the CRI-S233 repeats. The presence of several repeat elements in a region with a very high frequency of deletions, such as Xp22.3, is highly suggestive of the occurrence of unequal crossovers between the various elements, leading to deletion events.