X-linked agammaglobulinemia is a primary immunodeficiency which arises as a result of a block in B cell differentiation and the subsequent prevention of antibody production by these cells. The disease locus has been previously mapped to Xq21.3-q22 by linkage studies. Pulsed field gel electrophoresis and radiation hybrid mapping were used to construct a physical map of Xq22. The map incorporated ten probes arranged into three unlinked submaps, and spanned 6 Mb of DNA. The physical map was consistent with genetic recombination frequency data for this part of the genome. PFGE was also used to screen unrelated XLA patients for deletions. The probe 212/9 (DXS178), which is closely linked to XLA, was found to be flanked by several restriction sites for infrequently cutting restriction enzymes which impaired attempts to span the distance separating the markers which flank the locus. A high resolution physical map was made around this marker which showed that the restriction sites were clustered. This indicated the presence of CpG islands, which are frequently associated with expressed sequences. A chromosome walk towards the CpG islands was instigated by screening a cosmid library with a subfragment of 212/9. Several clones were isolated and two were restriction mapped using infrequently cutting restriction enzymes. Comparison of the cosmid restriction maps with the genomic map around DXS178 indicated that the cosmids were a maximum of 20 kb from the nearest CpG island
