The overall goal of this proposal is to develop a strategy towards clinical resequencing of the human genome which we define as the application of human genome resequencing to large clinical populations for disease gene discovery research as well as a clinical application that has diagnostic potential. Our strategy relies on """"""""third generation"""""""" single molecule DNA sequencing as utilized by the Pacific Biosciences platform. We anticipate that single molecule DNA sequencing technology will ultimately be the sequencer of choice given these systems'rapid collection of massive amounts of DNA sequences from patient samples with clinical outcome annotation, and cost-effective operation at a fraction of the current costs of other sequencing technologies. This first goal focuses on developing what we term an intermittent segment resequencing approach. A set of interspersed reads will be generated from a single DNA molecule, much the same way as mate paired sequence works, but having internal interval sequences rather than a terminal sequence pair as generated by paired-end approaches. The second goal involves testing in-solution based approaches to increase substantially the fold coverage of genomics regions of high clinical interest in combination with genome shotgun sequencing. Given their random distribution of sequences, shotgun genome sequencing efforts treat all regions of the genome equally. Increasing the fold-coverage of these regions of interest selectively, in comparison to the rest of the genome, would improve the detection of important clinical variants.
Creating a """"""""personalized"""""""" medicine strategy for each individual requires decoding the DNA sequence of a person's cancer that involves identifying genetic variations for any patient and discovering the clinical significance of these variants. The composition and spectrum of these variants can vary significantly from individual to individual, thus pointing out the importance of identifying all of the critical ones with clinical ramifications. New sequencing technologies have opened the way for creating personalized genetic signatures which can be used to tailor the clinical management of individuals but even more cost-effective approaches are needed given that thousands of individuals with specific disease have their genomes sequenced.
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