Ordering of Y-specific sequences by deletion mapping and analysis of X-Y interchange males and females.

We have used DNA from 23 patients with Y-chromosome aberrations and 25 patients with presumptive X-Y interchange to map 39 Yp restriction fragments and 37 Yq restriction fragments. In the majority of patients the results are consistent with a standard contiguous order of sequences along the Y chromosome. In 6 of 26 patients (23%) with Yp aberrations and 2 of 17 (12%) with Yq aberrations, exceptions to the consensus order have been observed. These can be accommodated by postulating the presence of inversion polymorphisms. Such variation may occur more commonly on the nonpairing part of the Y chromosome that in other chromosomes owing to the absence of homologous synapsis and recombination in male meiosis. The Y sequence most frequently present in X-Y interchange males was that recognized by GMGY3. 18 of 19 X-Y interchange males had this sequence suggesting that it is the nearest in the series to the TDF locus, and indicating that the latter maps to the distal end of Yp. Several techniques, including in situ hybridization and DNA measurement by flow cytometry, have been used to demonstrate that in X-Y interchange males there is transfer of Y sequences to the distal end of the X chromosome; no mechanism other than X-Y interchange has been demonstrated.