Epi-seq: Multiplexed ChIP-seq for personalized medicine and drug discovery

SUMMARY Dysregulation of epigenetic mechanisms is known to play important roles in the development and progression several disease states including cancerautoimmuneneurological and inflammatory disordersIn cancer alonehigh frequency mutations in sixty epigenetic regulatory proteins have been identifiedLike genome sequencingepigenetic information can be elucidated across the entire genome and profiling can be used to find epigenetic abnormalities that cause or correlate with diseaseComputational integration of genome wide genetic and epigenetic profilesepi genotypinghas enabled identification of novel disease subgroupswith pediatric neuro oncology being a notable exampleDeveloping a systems solution that facilitates integration of epigenetic data sets is key to enabling personalized medicine solutions for pathologies with epigenetic dependenciesChromatin immunoprecipitationChIPis the primary method for genome wide mapping of DNA associated proteinsIn contrast to the tremendous advances in DNA sequencing technologieswhich are approaching the $genomeChIP has only had incremental improvements in work flowreduction of background and sample size requirementsThis SBIR Fast Track proposal intends to develop Epi Seqa high throughput multiplexing ChIP Seq platform to map functional alterations in the epigenome on a scale and time frame suitable for clinical and drug screening applicationsWith automation compatibility in mindEpi Seq combines sample preparation and solubilization of fixed chromatin using PIXULawell plate sonicator capable of shearingchromatin samples in less thanminuteswith TransposaseAssisted Multiplex ChIP SeqTAM ChIPto functionally annotate the entire genome in a high throughput formatMultiplexing is achieved with a panel of recombinant AbFlexChIP qualified antibodies targeting various hallmark features of the epigenetic landscapeeach of which has been conjugated to a transposasecompatible barcoded oligonucleotide via site directed conjugationPhase I feasibility will use PIXUL from human and mouse tissues in Aimand compare TAM ChIP enabled AbFlexantibodies for key DNA binding proteins and histone PTMs in traditional and TAM ChIP seq methodsPhase II product development efforts will optimize TAM ChIP target multiplexing in Aimand Aimefforts will adapt current workflows for automation compatibility such that a hands freesample to sequenceworkflow is achievedPhase II efforts will conclude with alpha testing by independent laboratories whose feedback will be integrated into subsequent commercialization efforts by Active MotifEpi Seq is an enabling technology with potential accelerate development of epigenetic diagnosticsprognostic and therapeutics for diverse human pathologies and will be offered both as a contract service and as a productsold independently or bundled with the PIXUL instrument ChIPchromatin immunoprecipitationis the keystone method for epigeneticsdefined as regulatory mechanisms which affect heritable changes in cellular phenotypes independent of DNA sequenceThis SBIR Fast Track proposal describes development of Epi seqan automation compatible systems solution which streamlines ChIPenabling simultaneous interrogation of multiple targets and provides for integration of complex bioinformatic datasetsThis technology will simplify epigeneticsand will accelerate its adoption in drug discovery and personalized medicine