We show that chromosome-mediated gene transfer can provide an enriched source of DNA markers for predetermined, subchromosomal regions of the human genome. Forty-four human DNA recombinants isolated from a HRASI-selected chromosome-mediated gene transformant map exclusively to chromosome 11, with several sublocalizing to the Wilms tumor region at llpl3. We present a detailed molecular map of the deletion chromosomes 11 from five WAGR (Wilms tumor/aniridia/genitourinary abnormalities/ mental retardation) syndrome patients, three of which are at the limits of cytogenetic resolution but shown here to be molecularly distinguishable and overlapping. We can define ten distinct regions of the short arm of chromosome 11, five of which subdivide band lipl3. We also map two independent llpl3 translocation breakpoints to within the smallest region of overlap defined by the WAGR deletions. The first comes from a patient with familial aniridia, and the second from a patient with Potter facies and genitourinary dysplasia. The close similarities in map location and affected cell lineage for Wilms tumor and genitourinary dysplasia suggest that they may be alternative manifestations of mutation at the same locus.The association of aniridia, genitourinary abnormalities, and mental retardation with Wilms tumor (WAGR syndrome; genetic locus WAGR) is well established (1, 2). Cytogenetic analysis of independent WAGR syndrome patients has localized the relevant genetic region to band llpl3 (3). We (4) and others (5-8) have utilized available DNA probes and expressed protein markers to start to define the molecular extent of the various deletions. In most studies, only one patient has been examined (5-7) or the deletions have been large and therefore likely to show loss of markers that map some distance from the disease-related genes (8). We now attempt to distinguish the smaller deletions, those which take us beyond the resolving power of cytogenetic analysis towards defining the smallest region of overlap that is within reach of complete molecular analysis. We make use of five independent WAGR deletion hybrids, three of which are at the limit of cytogenetic resolution and involve only part of band llpl3.The short arm of human chromosome 11 (lip) is one of the better mapped regions of the genome (9, 10), but there is still a relative dearth of genetic markers that map within even the larger WAGR syndrome deletions (4, 8). The genes encoding erythrocyte catalase (CAT) and two cell surface markers, MIC4 and MIC11 (synonymous with MIC1), all map to band llpl3 and are closely associated with WAGR but not invariably deleted (4, 8). Most recently (8), the /3 subunit of follicle-stimulating hormone (FSHB) has been shown to map close to the aniridia and Wilms tumor genes. Of the anonymous DNA markers mapped to the short arm of chromosome 11, the majority derive from a somatic cell hybrid considered to retain lip material as the sole human component (11). However, none of these markers has been found to map as close to WAGR as CAT or F...