Clinical validation of Duoseq, a Swiss army knife genomic approach to diagnosis of blood cancers

ABSTRACT DNAseq and RNAseq are powerful and complementary next generation sequencing (NGS) assays for characterizing cancers. Together, these assays can recapitulate nearly all the diagnostic workup of many tumors. However, significant barriers prevent its actual application in the routine diagnosis of cancers. First, these assays are complex and usually separate, with different workflows and timelines for sample preparation. Second, the bioinformatics analyses needed to interpret the data are complex and difficult to implement. Third, the turnaround time for NGS assays and analyses typically stretches over a week, making it difficult to incorporate into diagnostic workups. To overcome these limitations, we have developed Duoseq, a novel clinical approach for dual DNA and RNA sequencing from a single workflow. Duoseq also includes bioinformatics software that connects directly to the NGS sequencer to provide DNA mutations, copy number and translocation status, as well as expression data for markers recommended by standard clinical guidelines. We have initially developed Duoseq as a solution that uses DNA and RNA sequencing for the diagnosis of blood cancers. The average blood cancer biopsy is subjected to a battery of time-consuming diagnostic tests that require subjective interpretation by pathologists. Duoseq is currently available for clinical adoption as an assay that reports single nucleotide variants (SNVs), small insertions/deletions (indels) and translocation and fusion status. However, Duoseq has the potential to deliver many other essential molecular diagnostic readouts including (i) copy number alterations, (ii) immunoglobulin heavy chain variable region mutation status, (iii) viral infection status and (iv) diffuse large B cell lymphoma subtypes. Adding these applications would render Duoseq a comprehensive profiling assay that could replace a vast suite of different assays currently used in the clinic to determine these features, thus saving costs, time and precious biopsy material. In this Phase I proposal, we will perform the analytical and clinical validation of these extended Duoseq applications. These studies are necessary for an FDA application and will significantly advance Duoseq toward clinical implementation in blood cancer diagnostics.