Establishing clinical performance characteristics for Duoseq, a new assay for DNA and RNA sequencing.
Authors: Thacker Elizabeth , Czader Magdalena , Wang Lin , Hsi Eric , Giauque Christopher , Sperling Matthew , Vrydaghs Andrea , Bouldin Jordan , Erno Robert , Happ Lanie , Parker Clay , Dave Sandeep 
Published: June 2023

e15059

Background: Despite advances in genomics and next generation sequencing (NGS), clinical implementation of NGS remains challenging. This challenge is critical in hematologic malignancies where NGS has become an essential part of the clinical workup. Many clinical labs resort to send-out testing that can delay appropriate treatment and drive up the cost of care. To address these issues, we have developed Duoseq as a unified approach for DNA and RNA NGS. Duoseq assesses mutations (single nucleotide variants [SNVs], insertions/deletions [indels] and splice site variants [SSVs]), structural variants, and gene expression using a panel of over 400 genes. It is supplied as a kit that enables preparation of DNA and RNA sequencing libraries in a single workflow performed at the point-of-care. It includes complete bioinformatics support that enables a clinical laboratory with an NGS instrument to perform the assay with a turn-around time of 2-3 days. Duoseq is optimized to work with formalin-fixed, paraffin embedded (FFPE) samples that are the standard fixation practice. Methods: We evaluated Duoseq on four dimensions critical to clinical performance: reproducibility, precision, analytical sensitivity (limit of detection, LoD), and analytical specificity. Identical experiments were run at clinical laboratories of two different institutions. Analytical validation samples included 4 FFPE cell lines and 2 synthetic DNA samples designed to harbor variants of interest at known allele frequencies. Results: We determined the LoD to be 5% mutant allele fraction (MAF) for SNVs, 10% MAF for indels/SSVs, and 10% tumor purity for SVs. Duoseq achieved 100% precision and reproducibility for each variant class for events at or above the LoD. Analytical specificity was 100%, indicating no instances of cross-contamination of samples within or across runs. We further evaluated Duoseq performance in 54 clinical cases of myeloid and lymphoid malignancies compared against clinical results provided by FoundationOne Heme NGS panel. Collectively, we assessed 119 SNVs and 49 indels/SSVs. Duoseq performed with 100% specificity for both SNVs and indels/SSVs. Duoseq achieved 98% sensitivity for SNVs and 96% for indels/SSVs. For example, Duoseq detected TP53 variants in 6 cases of myeloid neoplasms, which has relevance for the 2022 WHO and ICC classifications. Duoseq also identified therapeutically relevant variants in IDH1/2, EZH2, FLT3, KRAS and TET2. Conclusions: This study demonstrates performance characteristics that suggest Duoseq would perform well as a clinical-grade assay. Local laboratory factors that include staffing, case volumes, and reimbursement affect adoption and turnaround times in the individual clinical laboratory. However, we anticipate that Duoseq implementation will accelerate the diagnosis of hematologic malignancies and facilitate rapid, more cost-effective care to improve patient outcomes.