IRS-Bubble PCR: An Effective Method for Representative Amplification of Human Genomic DNA Sequences from Complex Sources

Abstract A rate-limiting step in the analysis of large segments of genomic DNA is the generation of a set of representative short single-copy sequences that can be used for development of fine-structure maps. In direct response to this need, we have developed interspersed repetitive DNA sequence (IRS)-bubble PCR. IRS-bubble PCR was designed to amplify the human DNA content of somatic cell hybrids, yeast artificial chromosomes (YACs), BACs, PACs, cosmids, and λ phage and to result in greater complexity and representation than standard inter-IRS PCR. Here, we describe the application of IRS-bubble PCR to the generation of complex clone libraries for targeted STS development and the construction of robust hybridization probes for FISH mapping, “chromosome painting,” or the assembly of cosmid contigs representing the human DNA content of somatic cell hybrids or YACs.