The proposed project, “Rapid, cost-effective whole genome screening tools for cryptic inversions and
translocations”, will advance a genomic approach to precision medicine, enabling the discovery of disease-
causing genomic structural variations and reducing the risks associated with clinical gene editing.
Structural variations cause a wide range of diseases from rare diseases to cancers, and can be precise and
definitive biomarkers. Also, because variations arise from the miss-repair of DNA strand breaks, off-target
structural variations are a high-risk byproduct whenever a genome is edited, as in CRISPR-Cas9 approaches
to curing human diseases. For these reasons, comprehensive detection of structural variations is a necessary
step toward understanding, diagnosing and ultimately precisely treating genetic diseases.
However, our collaborations with well-respected sequencing centers, and the experience of our partners and
customers, confirms that structural variations such as inversions and translocations can be difficult to discover
or even detect with NGS, genomic arrays, or any technique that relies on pooled DNA and a bioinformatic
interpretation of data. In particular, detection of structural rearrangements that vary from cell to cell, occur in a
minority of the cell population, or are confounded by other mutations and aberrations in the same cell, will
benefit from an approach that directly reads the genome structure in many individual cells instead of
algorithmically “calculating” a structure from pooled DNA or even the DNA of a single cell.
Directional Genomic Hybridization is our hybrid cytogenetic/genomic platform for directly reading the structure
of a genome in individual cells by analyzing chromatid paint data. dGH is capable of resolving very small
inversions and translocations and easily identifies variable, rare, low occurrence and multiple structural
rearrangements in individual cells. In a cytogenetic format, dGH is a commercial technique which we and our
customers have applied across a range of applications from dosimetry to rare diseases to oncology.
Reaching the full potential of dGH to discover and detect structural rearrangements, however, requires
applications to larger libraries and larger numbers of cells than can be supported by a traditional cytogenetic
approach. The goal of this FastTrack SBIR is to provide high-resolution structural rearrangement data to
researchers who need to screen larger libraries of samples (oncology), investigate a very diverse patient
population (rare diseases) or assay very large numbers of cells for complex rearrangements (gene editing).
To accomplish this, KromaTiD proposes development of an automated, full genome dGH screening method
comprised of high-density chromatid paints and image processing software. This novel method will detect
inversions and translocations smaller than 10 kb and will be applicable to screening both very large numbers of
samples and large numbers of cells in individual samples, making the discovery and detection of even the
most complex structural variations routine, robust and economical.