Isolation of region specific single-copy probes from human chromosome 1q23-->1q25.

Single-copy sequences of chromosome bands 1q23-->1q25 were enriched by subtractive hybridization of digoxigenin oligonucleotide-labeled DNA from a somatic cell hybrid containing human chromosome 1 with DNA from a somatic cell hybrid containing a deleted human chromosome 1, del(1)(q23q25). These sequences were purified with an immobilized anti-digoxigenin antibody, amplified by polymerase chain reaction (PCR) and cloned. The majority of clones contained single-copy sequences, thus allowing direct screening of human genomic DNA. With pools of probes complex hybridization patterns as well as differences in hybridization patterns between genomes were observed in Southern blotting experiments. Nine clones containing independent single-copy sequences from chromosome bands 1q23-->1q25 were isolated and sequenced to generate sequence-tagged sites (STSs). Using PCR, region specific genomic clones containing large inserts were identified in human genomic lambda phage and cosmid libraries. Thus, region specific genomic probes generated by genomic difference cloning are useful for identifying deletions and rearrangements, for generating STSs and for isolating genomic clones containing large inserts of a particular chromosomal region.