TempO-Seq: A Multiplexed Gene Expression Profiling Platform

PROJECT SUMMARY The Phase I of this program met or exceeded the success criteriadeveloping and implementing the capture free TempO Seq assaycapable of measuring not just mRNAbut any nucleic acid targetverifying this platform with a whole human transcriptome assay and human surrogate transcriptome assayboth of which were launched as commercial productsThe surrogate assay is a subset of genes from the whole transcriptome that is capable of identifying every known pathwaycompound signaturesetcwithout having to measure the whole transcriptomeThe performance of these assays exceeded the success criteria and the original plans to implement assays of up tomRNA targetswith the whole transcriptome assay targetingRefSeq IDsAffymetrix microarrays target onlyand the surrogate measuringgenesThis Phase II falls under the NHGRI area of special interest Topic CGenomics tools ranging from new instruments to sophisticated molecular biology kitsIt will extend the validation and crossplatform studies for the human assaysextend the assay to mouse by establishing a mouse whole transcriptome TempO Seq assayvalidate the accuracy with which the human and mouse surrogate assays identify pathways and predict gene changes across the whole transcriptome by testing diverse samples in the Hu and Mu TempO Seq whole transcriptome assaysestablish and validate focused sets of genes derived from the whole transcriptome archives that investigators can use as is or selectively combine together or with the surrogate into a single assay customized for their researchimplement a kit permitting sequencing on the Ion Torrentand fully implement a TempO SeqR analysis package that investigators can use to process their data and derive a file from which to derive dose and time course graphsidentify differentially expressed genes and false positive ratesidentify expressed pathwaysand predictfrom the surrogatewhat genes across the whole transcriptome that are not directly measured are expected to be differentially expressedall without requiring a bioinformatics expertThe significance to investigators is that the TempO Seq assays can provide the same coverage and as good or better sensitivity to measure rare transcripts as RNA seq buttomore samples can be sequenced for the same costwhich is important because more samples can be run to provide higher quality data and more detailed insightsor to profile more compoundsor more time pointsor more patient samplesInvestigators can make their budgets go furtherand get faster turn around time such as running whole transcriptome assays on the MiniSeqan automated sequencer costing only $which otherwise cannot run whole transcriptome RNA seq assaysand get higher quality datawithout the bioinformatics expertise required for RNA seq