Clinical Validation of Duoseq, a Novel Assay for Clinical DNA and RNA Sequencing

Next-generation sequencing (NGS) has become integral to the clinical workup of blood cancers. However, there remain barriers to implementing clinical NGS, including the separate workflows required for DNA and RNA sequencing, complex bioinformatics analyses, and long turnaround times. Duoseq has been developed as a comprehensive, kitted solution to these barriers and implemented as a genomic profiling tool for blood cancers to simultaneously detect single-nucleotide variants (SNVs), small insertions/deletions (indels), and structural variants (SVs; translocations and fusions). Additionally, Duoseq can evaluate numerous other blood cancer diagnostic markers, including gene expression, copy number alterations, cell of origin, oncogenic viral status (eg, Epstein-Barr virus), B-/T-cell receptor clonality, Ig heavy chain mutational status, and diffuse large B-cell lymphoma subtypes. Analytical and clinical validation of Duoseq was performed in parallel at two clinical institutions. Limit of detection was confirmed as 5% variant allele frequency for SNVs, 10% variant allele frequency for indels, and ≥20% tumor purity for SVs. Repeatability studies showed >99% intrarun and interrun positive predictive value and >96% percentage positive agreement. Duoseq was run on formalin-fixed, paraffin-embedded biopsy specimens (N = 197), using NGS and/or fluorescence in situ hybridization as orthogonal comparison. SNVs, indels, and SVs achieved accuracy of >95%. These results establish Duoseq as a genomic profiling tool for blood cancers that can enable laboratories to provide critical diagnostic information in a time- and cost-effective manner.