Project Grant R44CA298055

VALIDATION OF DUOSEQ AS A GENOMIC SWISS ARMY KNIFE FOR THE DIAGNOSIS OF LYMPHOMAS - 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 LYMPHOMAS. THE AVERAGE LYMPHOMA BIOPSY IS SUBJECTED TO A BATTERY OF TIME-CONSUMING DIAGNOSTIC TESTS THAT REQUIRE SUBJECTIVE INTERPRETATION BY PATHOLOGISTS. DUOSEQ IS ABLE TO DELIVER NEARLY ALL OF THESE ESSENTIAL MOLECULAR DIAGNOSTIC READOUTS INCLUDING (I) SINGLE NUCLEOTIDE VARIANTS, (II) SMALL INSERTIONS AND DELETIONS, (III) TRANSLOCATION AND FUSION STATUS, (IV) COPY NUMBER ALTERATIONS, (V) IMMUNOGLOBULIN HEAVY CHAIN VARIABLE REGION MUTATION STATUS, (VI) B AND T CELL CLONALITY, (VI) VIRAL INFECTION STATUS AND (VIII) DIFFUSE LARGE B CELL LYMPHOMA SUBTYPES. DUOSEQ THUS REPRESENTS 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 II PROPOSAL, WE WILL PERFORM A MULTI-SITE ANALYTICAL AND CLINICAL VALIDATION OF DUOSEQ. THESE STUDIES ARE NECESSARY FOR AN APPLICATION FOR FDA APPROVAL, WHICH WILL SIGNIFICANTLY ACCELERATE DUOSEQ ADOPTION BY CLINICAL LABS. WE ALSO PROPOSE OPTIMIZATION OF AN AUTOMATED, ROBOTICS-BASED VERSION OF THE DUOSEQ WORKFLOW THAT WILL LOWER THE BARRIER TO ENTRY FOR CLINICAL LABS THAT ARE LESS FAMILIAR WITH NGS ASSAYS. TOGETHER, THESE AIMS WILL SIGNIFICANTLY ADVANCE DUOSEQ TOWARD WIDESPREAD CLINICAL IMPLEMENTATION IN LYMPHOMA DIAGNOSTICS.