Nephropathic cystinosis is an autosomal recessive disorder resulting from defective transport of the amino acid cystine out of lysosomes. Difficulties inherent in purifying membrane transporters have prevented isolation of the cystinosis gene product, thus, we pursued a positional cloning approach for its study. The Cystinosis Collaborative Research Group mapped the cystinosis gene to human chromosome 17p13 (Nat Genet: 10, 246, 1995). The short arm of chromosome 17 is a gene dense region known to contain, among others, the genes for Miller-Dieker syndrome, Canavan disease, and autosomal retinitis pigmentosa. The physical mapping of large genomic clones and expressed sequences to this region will no doubt identify many disease genes and therefore is of broad interest to the medical community.

We identified two new polymorphic markers, D17S2167 and D17S2169, within the cystinosis region and determined their locations by radiation hybrid mapping. Recombination mapping narrowed the cystinosis region to an interval less than 500 kb (D17S1828 - D17S2167). We next identified a contig of BAC and P1 clones which appear to completely span this new interval. These clones are in turn being used to map cDNAs by a sample sequencing approach. Each BAC or P1 clone is converted to an M13 library from which 200 random clones are sequenced to an average of 500 base pairs. The sequence is compared to those in human genome databases to identify cDNAs. To date, 5 genes have been mapped to two genomic clones in the cystinosis region. One is expressed in all tissues examined, has no homology to known genes, and therefore is a candidate for the cystinosis gene. Sample sequencing of genomic clones has proven a rapid and efficient method for mapping and identifying transcripts in a defined region of interest.