Development of new tools for multiplex genetic analyses

Abstract: Several methods allowing the simultaneous interrogation of multiple qualities of nucleic acid samples have been developed recently. Although diverse in nature, many of these methods have common limitations. This thesis discusses new developments to overcome the problems of multiplex amplification of genomic sequences and design of sets of probes for multiplex assays.A novel molecular technique, termed the selector technique, is described. This method allows circularization of an arbitrary selection of restriction fragments from genomic DNA, and the subsequent amplification of these circular products in parallel using common primers. Furthermore, the PieceMaker software for selection of restriction enzymes and restriction fragments is described. These two developments will allow the selective amplification of subsets of genomes for further analyses.A general-purpose software tool for design of oligonucleotide probes is presented. The ProbeMaker software is a framework for design of sets of oligonucleotide probes composed of separate functional elements, and uses an extension mechanism to incorporate support for new probe types as needed. This platform enables rational design of large sets of probes for various types of multiplex genetic analyses, thus overcoming one of the major obstacles for the deployment of such assays.