Rapid, cost-effective whole genome screening tools for cryptic inversions and translocations

ABSTRACT The proposed projectRapidcost effective whole genome screening tools for cryptic inversions and translocationswill advance a genomic approach to precision medicineenabling the discovery of diseasecausing genomic structural variations and reducing the risks associated with clinical gene editingStructural variations cause a wide range of diseases from rare diseases to cancersand can be precise and definitive biomarkersAlsobecause variations arise from the miss repair of DNA strand breaksoff target structural variations are a high risk byproduct whenever a genome is editedas in CRISPR Casapproaches to curing human diseasesFor these reasonscomprehensive detection of structural variations is a necessary step toward understandingdiagnosing and ultimately precisely treating genetic diseasesHoweverour collaborations with well respected sequencing centersand the experience of our partners and customersconfirms that structural variations such as inversions and translocations can be difficult to discover or even detect with NGSgenomic arraysor any technique that relies on pooled DNA and a bioinformatic interpretation of dataIn particulardetection of structural rearrangements that vary from cell to celloccur in a minority of the cell populationor are confounded by other mutations and aberrations in the same cellwill benefit from an approach that directly reads the genome structure in many individual cells instead of algorithmicallycalculatinga structure from pooled DNA or even the DNA of a single cellDirectional Genomic Hybridization is our hybrid cytogenetic genomic platform for directly reading the structure of a genome in individual cells by analyzing chromatid paint datadGH is capable of resolving very small inversions and translocations and easily identifies variablerarelow occurrence and multiple structural rearrangements in individual cellsIn a cytogenetic formatdGH is a commercial technique which we and our customers have applied across a range of applications from dosimetry to rare diseases to oncologyReaching the full potential of dGH to discover and detect structural rearrangementshoweverrequires applications to larger libraries and larger numbers of cells than can be supported by a traditional cytogenetic approachThe goal of this FastTrack SBIR is to provide high resolution structural rearrangement data to researchers who need to screen larger libraries of samplesoncologyinvestigate a very diverse patient populationrare diseasesor assay very large numbers of cells for complex rearrangementsgene editingTo accomplish thisKromaTiD proposes development of an automatedfull genome dGH screening method comprised of high density chromatid paints and image processing softwareThis novel method will detect inversions and translocations smaller thankb and will be applicable to screening both very large numbers of samples and large numbers of cells in individual samplesmaking the discovery and detection of even the most complex structural variations routinerobust and economical PROJECT NARRATIVE Modern genomics demands higher throughputhigher integrityand improved resolution of structural variations for precision medicine applications including discovery of disease drivers and control of off target effects in gene editing systems such as CRISPR CasHowevereven with recent advancesstructural variations such as translocations and inversions still cannot be definitively discovered or detected in complex cases involving random variationsvariable breakpoints or multiple variations per cellBy making the cell by cell discovery and detection of structural variations routine and reliable in the most complex casesthis projectRapidCostEffective Whole Genome Screening Tools for Cryptic Inversions and Translocationswill enable a deeper understanding of the roots of human diseasesprovide for the precision diagnosis of genetic diseasesand allow for the control of off target effects in clinical gene editing systems