Development of a sample-to-answer sequencing pipeline for detection of viral infections and co-infections in immunocompromised transplant patients.

ABSTRACTNext generation sequencingNGShas the potential to revolutionize how infectious disease is diagnosed and treatedenabling the detection of a wide variety of pathogens in a single testHoweverdespite the increasing adoption of molecular diagnostics in clinical virology and microbiology labsNGS has not become widespread due to its costturnaround timeand the technical and computational expertise required to produce and analyze the dataTo overcome these challengesArc Bio is developing a suite of technologies that will enable clinical virology and microbiology labs to more easily implement NGS pipelinesThe Arc Bio product includes all the experimental protocols and software necessary to go from sample to answer for pathogen detection in clinical samplesincluding novel tools to make pathogen sequencing less expensivemore sensitiveand more accurateThese tools include a host DNA depletion technology that helps reduce costs and increase sensitivity by removing background human DNA RNA from sequencing librariesIn additionArc Bio has developed a unique bioinformatics pipeline that incorporates graph based analytics to deliver sensitive and specific strain identificationIn this projectwe propose to adapt this NGSbased pipeline to detecting common transplant related viral infectionsImmunocompromised solid organ and hematopoietic stem cell transplant recipients are uniquely susceptible to severe infection due to many common and opportunistic virusesWe will determine the performance of our pipeline onplasma samples containing five different known virusescytomegalovirusEpstein Barr virusBK virusadenovirusand human herpesvirusWe will also sequencenegative immunocompromised samples to determine baseline nucleic acid levelsWe will use these datasets to optimize our host depletion and bioinformatics technologies for this applicationand will examine the feasibility of simultaneously determining viral loaddrug resistanceand co infections from the same datasetCurrentlythere are no existing commercial diagnostic tests that deliver all of this information in a single assayIn the clinicthis test could significantly reduce morbidity and mortality by shortening time to diagnosisidentifying common co infectionsreducing hospital staysand limiting the number of transplant rejectionsThe result of this project will be a completevalidated pipeline that will include all protocols and software necessary to perform larger scale retrospective and prospective studies with our alpha partner clinical labs PROJECT NARRATIVE Next generation sequencing of clinical samples for pathogen detection is likely to replace many existing targeted molecular diagnostic tests in the near futureimproving our ability to detect and treat infectious diseaseHoweverbefore this replacement can occurthe technology must become less expensivefasterand more user friendlyIn the proposed workArc Bio will develop a streamlined sample to answer pipeline that will use its host depletion technology to reduce sequencing costs and increase sensitivity for transplant related infectionsand its proprietary bioinformatics software to enable rapidaccurateand scalable data analysis with a user friendly interface