Cancer genotyping in the clinical setting demands high coverage to achieve the analytical sensitivity for detecting low frequency variants in heterogeneous specimens. At the present time, this is only achievable in practice with sub-exome targeted gene panels. Elim have developed a broad, 1000 cancer gene panel for next generation sequencing based on enrichment by liquid phase hybridization and targeting all coding exons and intron-exon junctions of the selected genes. The design of the panel contains 3 tiers of genes related to cancer:
(1) known oncogenes and tumor suppressors that are clinically actionable,
(2) additional oncogenes and tumor suppressors for which clinical utility have not been demonstrated, and
(3) other cancer related genes, such as tyrosine kinase, phosphatase, and vascular genes.

The assay has been developed comprehensively as a library construction and capture kit (RightOn Cancer Sequencing Kit) which will accommodate small quantities of formalin-fixed paraffin-embedded clinical DNA samples. Performance of the assay shows minimum 100X coverage for more than 98% of the target bases at a sequencing throughput of 5 gigabase per sample. Such high on target coverage allows robust detection for single nucleotide variants, insertions/deletions, and copy number changes. The kit has been validated with a variety of clinical specimens previously genotyped by traditional single base genotyping, PCR sizing, and fluorescence in situ hybridization techniques. To our knowledge, this is the largest cancer gene panel developed so far with a focus on high coverage for sensitive detection of low frequency variants. In contrast to current commercially available exome capture kits which show incomplete coverage for many genes, this kitted assay offers a nearly complete and high coverage cancer sequencing option for clinical application and discovery.