Technical Overview

KromaTiD offers a full range of dGH and Pinpoint FISH products and services, ranging from targeted rearrangement assays to unbiased screening of the entire genome.

In addition to our standard probes and services, we specialize in quickly and efficiently designing custom assays to your specifications. You provide the samples—culture, tissue or blood—we design, validate, and execute the assays, providing you with comprehensive reporting and analysis every step of the way.

KromaTiD’s proprietary platform, directional Genome Hybridization (dGHTM), provides researchers and scientists:

  • Rapid assay development and data delivery
  • Cost effective discovery of any structural rearrangement throughout the genome, including inversions and translocations
  • Sequence, location and orientation from a single assay
  • High resolution screening of individual genes to the entire genome
From the de novo discovery of large rearrangements, to specific targets as small as 2kb, the versatility of dGH provides researchers and scientists with structural genomic insight at almost any level.

What is dGH?

KromaTiD’s directional Genomic Hybridization™ (dGH) technology combines bioinformatics driven design of unique single-stranded synthetic probes with strand-specific hybridization strategies, and is the only genomics approach capable of detecting DNA sequence, location and orientation in a single test.

With the ability to resolve very small inversions and translocations, dGH technology can be employed in both targeted and unbiased discovery studies, quickly providing data on new or variable rearrangements for your patient screening or target validation needs.

If a complete genetic profile is required, pair dGH with NGS on the same samples to build a comprehensive mutation profile.



dGH in-Site
Pinpoint FISH

How does it work?

dGH begins with bioinformatic analysis in order to identify probe target sequences.

Next, chromosomal directionality and repeat regions within the target sequence are identified. 

 The result is probes that are designed to hybridize solely to repeat free regions of the sequence of interest.

Once repeat-free target sequences are identified and dGH probes are designed, the innovative chromosomal preparation technique enables the identification of previously undetectable structural rearrangements, such as inversions.

How is it different

The dGH platform differs from traditional FISH as a result of its unique chromosomal preparation technique. Analog nucleotide incorporation during the DNA replication phase of the cell cycle enables exonuclease daughter strand degradation that leaves dGH prepped chromosomes single-stranded.

Single-stranded chromosomes allow for unidirectional dGH probe binding which enables the detection of orientation information that traditional FISH assays cannot provide.

Double stranded metaphase chromosome with an inverted segment.

Inversion differentiated as a result of single-stranded chromosome and unidirectional probe binding after dGH preparation and probe hybridization. 

The same inversion would not be visualized using traditional FISH methodology and probes. The double stranded DNA would result in probes binding to both strands of the metaphase chromosome, making it impossible to discern DNA orientation.

While the preparation conditions differ, dGH does not require additional laboratory equipment. dGH probes can be visualized using standard FISH equipment and fluorescence microscopes found in many labs, making visualization and analysis as simple as possible.

The dGH platform is available in three iterations, each designed specifically to cater to different research needs.

Unbiased Assays: dGH SCREEN

dGH Paints

This image provides an example of an assay using dGH chromatid paints to visualize inversions. The inversions, circled in white, are represented by fluorescent signal on the arm opposite to the painted side of the chromosome.

Chromatid ‘paints ‘ can be used to screen the entire genome, whole chromosomes, or even single regions of chromosomes for clinically important DNA rearrangements. dGH paints can be used for the de novo discovery of all manner of structural variations including inversions, sister chromatid exchanges, translocations, and copy number variants. dGH SCREEN has broad utility in multiple fields and can be used to identify structural abnormalities of varying sizes in any actively dividing human cells.

Targeted Assays: dGH in-Site

Targeted dGH

This image shows an example of a targeted dGH assay. As opposed to dGH paints, targeted dGH assays are designed to give strand specific structural data at a specific chromosomal region of interest. Normal chromosomes in this assay appear as a single pair of red and green dots. The aberrations circled here demonstrate a loss of genetic material in one chromosome (green dot without corresponding red dot) and a gain of genetic material in another chromosome (two red dots and a green dot).

Targeted dGH in-Site provides analysis and visualization of exogenous DNA plasmids or rearrangements occurring at specific loci of interest. With dGH in-Site, researchers can track events involving their edit sites or plasmids throughout the genome. Capable of illuminating sequences as small as 2kb, dGH in-Site is a versatile method that helps researchers gain a deeper understanding about any genomic region of interest.

Pinpoint FISH

Pinpoint FISH Assay

This pictures demonstrates a metaphase Pinpoint FISH assay designed to monitor two genomic loci near the telomeric ends of a pair of homologous chromosomes. No chromosomal aberrations are visible in this picture, the green and red probes are not displaced from their expected positions.

Pinpoint FISH was developed with precision and resolution in mind. With 3x the relative signal of BAC FISH probes, and the ability to hit targets as small as 4kb in length, Pinpoint FISH can be used to detect inversions, gene rearrangements, gene fusions, copy number variants, duplications or deletions at nearly any location of the genome.

Assays and benefits

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Quantitative Mutation Size and Location

 Since dGH assays are based on a defined library of calibrated genomic probes, they can precisely locate and quantitatively size rearrangements.

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Visual Orientation Data

When used on metaphase chromosomes, dGH is the only imaging technology capable of providing sequence, location and orientation information in a single assay.

The KromaTiD platform enables inversion detection with a resolution that is orders of magnitude greater than any competing technique.

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Chromosome and Chromatid Assay Format

Using the same probes in different test conditions, KromaTiD assays can query entire chromosomes (double-stranded applications like FISH) or individual chromatids (single-stranded applications) in interphase or metaphase cells.

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Unique Specificity

Our probes are designed to target unique genomic sequences, so KromaTiD assays require no blocking DNA (COT), exhibit no non-specific background, and demonstrate improved hybridization performance.

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The Broadest Assay Range

In a single assay, KromaTiD products detect the broadest possible spectrum of chromosome rearrangements, including those assayable by standard FISH technologies (e.g. translocations between chromosomes) as well as intra-chromosomal rearrangements such as cryptic inversions.

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Single Cell Analysis

dGH assays generate imaging data on a cell-by-cell basis so are ideal for determining mutation heterogeneity within mixed cell populations while simultaneously identifying recurrent rearrangements.

Get Started with KromaTiD’s Simple 3 Step Process:


Design Your Assay

Collaborate with KromaTiD’s experts

Identify scope and requirements

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Send Your Samples

Cell lines


Metaphase Spreads


Get Results

Use dGH probes to analyze your samples or

Send samples to KromaTiD for expert assay execution

Contact us today to learn more!