Order of genes on human chromosome 5q with respect to 5q interstitial deletions

Using (a) somatic cell hybrids retaining partial chromosome 5 and (b) clinical samples from patients with acquired deletions of the long arm of chromosome 5, combined with chromosome 5-linked DNA probes, some of which exhibited RFLPs, we have determined the order of a series of genes on chromosome 5. The order established is 5pter → MLVI-2 → cen → HEXB → DHFR → Pi227 → cp12.6 → (IL5,IL4) → IL3 → GMCSF → FGFA → (CSF1R,PDGFR) → (treC,ADRBR) → (ARH-H9,CSF1) → qter. The suggested order and orientation for the closely linked IL3/GMCSF gene pair is cen → 5' IL3 3' → 5' GMCSF 3' → qter, on the basis of analysis of the GMCSF rearrangement in HL60 DNA. The map position of the GRL locus, which was consistent with both somatic cell hybrid and 5q^- analyses, was telomeric to GMCSF and centromeric to CSF1R/PDGFR, near FGFA. Long-range restriction-enzyme analysis of 5q- DNAs did not detect rearrangements of 5q-linked probes except in HL60 DNA, but it did reveal putative long-range RFLPs of several loci. RFLPs for GRL, Pi227, cp12.6, IL3, and CSF1R can detect deletions in bone marrow and in leukemia cells from patients with acquired 5q deletions.