Subgenome fractionation for HT sequencing

New high throughput sequencing technologies offered e.g. by Life Sciences 454, Solexa and Applied Biosystems provide up to 100-fold improvements in cost and throughput compared with conventional Sanger sequencing. These techniques provide high accuracy and readouts up to the gigabase level by approaches of massive parallelization, and are especially suited for re-sequencing purposes like the detection of heterozygous variations. Although the readout of these techniques is not sufficient to re-sequence large numbers of complete mammalian genomes, they are an ideal tool to investigate multiple genomic regions in parallel. Therefore it is necessary to reduce DNA complexity from whole genomes to the regions of interest. Selection by hybridization to microarrays has been proposed as a cost effective approach and requires access to individual and flexible microarray-synthesis. We use a highly flexible microarray platform to establish the appropriate conditions including probe design, array synthesis, hybridization and sample processing that will allow for the parallel selection of equal target amounts needed for the available sequencing technologies. The work of the consortium includes further the evaluation of the selection technology concerning disease-relevant genome-regions and the development of dedicated “ready-to-use” analytical selection matrices. Intended applications are re-sequencing of coding sequence, promotor regions, CpG islands and candidate regions established by association and linkage studies. The technology is made applicable to detect germline mutations (in patients with inherited diseases) as well as somatic sequence alterations (in neoplasia) and is optimized to work with genomic DNA (searching for point mutations, insertions, deletions, and epimutations) and cDNA (searching for non-synonymous mutations, frame shifts, and alternative splicing forms).