Optical Genome Mapping

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Optical Genome Mapping (OGM) is a technique used to analyze large-scale Structural Variations (SV) in genomes with high resolution and accuracy.

The technology is able to detect :

Aneusomies
Intersistial Variants
- Insertions
- Deletions
- Duplications
- Inversions
- Copy Number Variants
Interchromosomal fusions
Translocations
Copy number neutral Loss-Of-Heterozygosity (LOH)
Complex rearrangements
- Ring chromosomes
- Chromothripsis
- Chromoplexy

It is only possible to detect variations larger than 500 bp and at a minimum Variant Allele Frequency (VAF) of 5%

The techology is currenly only applied for detection of structural variations (SVs) in hematological malignancies but also for complex germline mutations (where karyotyping and/or array CGH were not conclusive).

The Optical Genome Mapping technology can be broken down in the following steps:

1. Ultra-High-Molecular-Weight DNA Extraction

The process begins by isolating ultra-long DNA molecules (ideally >150 kb) from cells or tissue.

This step is critical because OGM relies on intact, long DNA strands to map structural variations accurately.

This ultra-long DNA is also referred to as Ultra High Molecular Weight DNA (UHMW DNA).

2. DNA Labeling + staining

A specific sequence motif (the 6 bp CTTAAG sequence) is targeted and enzymatically labeled with fluorescent tags.

This creates a barcode-like pattern along each DNA molecule, which serves as a unique identifier for mapping to the 'known' reference genome.

Next to labeling the DNA, a stain is added to visualize the DNA backbone.

3. Linearization and Imaging

The labeled DNA molecules are loaded into nanochannel arrays that stretch them out in a linear fashion.

High-resolution imaging systems capture the fluorescent patterns along each molecule.

4. Digital Map Construction

The fluorescent patterns are converted into optical maps, which represent the physical arrangement of the 6-base motifs along the DNA.

These maps are aligned to a reference genome or assembled de novo to detect/identify the Structural Variations (SVs) or Copy Number Variations (CNVs)

5. Data Analysis

Specialized software (Bionano Access and VIA) compares the optical maps to reference genomes.

Structural variations are identified at kilobase to megabase scale, which is often missed by short-read sequencing.

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Sample types

Bone Marrow > UHMW DNA

Microtube*

Heparin/EDTA stabilized BMA aliquots (ca. 800 µl)

Dry ice

Blood > UHMW DNA

Microtube*

Heparin/EDTA stabilized Blood aliquots (ca. 650 µl)

Dry ice

Extra requirements

See test/application specific recommendations

More information can be found on the subpages (related tests)

Minimum amount of cells

Frozen blood (for UHMW DNA) - Diagnostic

Minimum: 1,5 M

Minimum volume of frozen Bone Marrow Aspirate (BMA)

Frozen BMA (for UHMW DNA) - Diagnostic

Minimum: 500 µl

Optimally, we receive >800 µl of frozen BMA

Minimum volume of frozen blood

Frozen blood (for UHMW DNA) - Diagnostic

Minimum: 600 µl

Optimally, we receive >650 µl of frozen blood

Sample types

Deliverables

Below, you can find the type of data files that can be retrieved for this test.

If you require more information or need a more custom output, please consult our Bioinformatics page.

Bioinformatics

Called variants - vcf file

Text file containing all detected variants as compared to the relevant reference genome

Diagnostic / RUO

Clinical report

Diagnostic report generated by Clinical Geneticist/ Pathologist / Hematologist

Diagnostic

Molecule Quality Report

Text (json) file containing all relevant quality metrics like Map rate, N50(>150kbp), NLV, PLV,...

RUO (on request)

Raw data - Molecules file

Raw data file generated by Bionano devices (.bnx file)

RUO (on request)

Raw data - bam file

Binary data file containing the aligned reads

RUO (on request)

Deliverables

Costs

Below, you can find indicative prices (excl. VAT) for all potential options you'd require to accomplish your project. If you are interested, please contact us to receive a tailored quotation.

Request quote

Update pending

Our prices are being updated. More info soon.

Costs

Documents & certificates

Validated

Documents

Plan Experiment

Plan experiment

For Diagnostics

This test is mainly performed as a diagnostic assay. In this case, please contact your General Practitioner, Pathologist, Haematologist or Clinical Geneticist (Centre for Medical Genetics / haematology department of choice) to get the diagnosis started.

For Research

This test can also be applied in context of research. For this, please get approval from your local ethical committee and/or make proper arrangements with your Biobank.

Please follow the steps below to start up an experiment with us.

Get in touch (ONLY FOR NEW PROJECTS)

Explain your project, so we can assist you to find the best solution.

Expect questions like :

What type of sample would you like to analyze?
How was the sample collected (eg. incl. time to freeze sample)?
How many samples would you like to process?
How fast do you need the results (TAT) and/or do we need to expedite?
If you deviate from our sample types, are there test samples available?
Are our standard deliverables ok?
...

1

Start here

Request quotation

Once you know which experiment you want to set up, fill out the 'Quote request' form, with the essential details of your project :

Coordinates of the person to whom to address the quotation
Which type of test you'd like to set up
Do you require a specific deliverable?
Do we need to expedite (comes at extra cost)?
...

2

Quotation

Submit your samples

Once you agree with our terms (quote / TAT / terms & conditions) :

Fill out our sample submission form
Send it via email : contact us
Print out the form and include it with your samples
Send your samples to us
Label your tubes/plates correctly : see details here
Adhere to the corresponding transport conditions listed under Sample types
Indicate if we can discard your samples after completion of project

3

Submission form

Your experiment starts

Now it is up to us... We will start your experiment as soon as possible.

When expedited, the turn-around-time (TAT) is 2 weeks
For standard requests the turn-around-time (TAT) is 2 months

The standard TAT is generally overestimated, but this extended timeframe allows us to : combine similar requests of multiple scientists and to repeat the experiment in case of issues.

Please refrain from contacting us in case the pre-agreed TAT didn't expire yet.