SNP ARRAY

ABOUT

 

Using a microarray technology, a wide range of applications can be serviced, where content/specificity is defined by the probes on the array. A grasp of the possible  applications :

  • Genotyping (multi-species)

  • Cytogenomics

  • Gene expression analysis

  • Methylation profiling

  • miRNA profiling

  • Pharmacogenetic testing

  • ...

With the advent of Massive Parallel Sequencing (MPS) or Next Generation Sequencing (NGS), array technologies are steadily getting abandonded, however for some applications (like methylation profiling and pharmacogenetics), they remain a - sometimes cost-beneficial - gold standard.

METHODOLOGY

 

For the Affymetrix technology, either DNA (genotyping/CNV assays) or cRNA (expression arrays) is terminally labelled and hybridized to short probes on  a wafer. The ability of the DNA/cRNA to hybridize to the specific probes correlates to the presence of the transcript, DNA target or SNV. Signal intensities are analyzed to quantify abundance of the target of interest.

The Illumina Infinium technology is based on the hybridization of DNA (target of interest) to bead-linked probes (1 type of probe per bead), where the beads on its turn are deposited in wells on a silica slide (1 bead/well).  Following successful hybridization of the target DNA to the probe, a single base extension of the probe is performed. As this base is labelled with either biotin (C and G) or dinitrophenyl (A and T), they can be stained differentially with a fluorescently labelled antibody for either biotin or dinitrophenyl. There are 2 types of probes, (1) the Infinium I probe where the last base of the probe overlaps with the SNV of interest and (2) the Infinium II probe where the last base of this probe is 1 base before the SNV of interest. So in case of the Infinium II probes, there will always be a signal, where the detected color correlates to the SNV. For the Infinium I probe, there will only be a color signal if the last base of the probe matches with the target of interest.

The principle of the Illumina Infinium technology is depicted in the movie below.

Basic principle of the Illumina Infinium technology

 

INSTRUMENTS

The following array devices are present in our premises.

Affymetrix GeneChip 3000

Medium throughput SNP array device, where 48 samples (1 sample/genechip) can be processed simultaneously per run.

Illumina iScan

Medium throughput SNP array device, where 4 beadchips can be scanned/loaded simultaneously. The amount of samples that can be loaded is dependent on the assay/beadchip.

SPECIFICATIONS

 

The specifications are subdivided in 2 sections : (1) the assay metrics and (2) applications & remarks.

More information can be found on the supplier page through the corresponding buttons in the 'Assay metrics' section. 

Assay metrics

Instrument

Sample type

Kits currently in use

Volume/input range

Throughput

Sensitivity (input)

Affymetrix GeneChip 3000

RNA

Various

Various

Various

1 sample / chip (x48)

Illumina iScan

DNA

HumanKaryomap-12
Infinium MethylationEPIC
Infinium GDA with Enhanced PGx

Single cell to 400 ng
>250 ng (500 ng standard)
>200 ng (500 ng standard)

x
50 µl (10 ng/µl)
2 x 5 µl (50 ng/µl)

12 samples / chip (x4)
8 samples / chip (x4)
8 samples / chip (x4)

Applications & remarks

Instrument

Applications (possible)

Applications (in use)

Remarks

Affymetrix GeneChip 3000

Genotyping (multi-species), Cytogenomics, Gene expression analysis, Methylation profiling, miRNA profiling

Gene expression analysis

Mainly used for expression analysis. Convenient workflow due to the automated washing and staining on the Fluidics stations and the carrousel for the automated loading of up to 48 arrays.
The flexibility of 1 sample/array is a benefit.

Illumina iScan

Genotyping (multi-species), Cytogenomics, Methylation profiling, miRNA profiling, Pharmacogenetic testing

Genotyping (multi-species), Cytogenomics, Methylation profiling, Pharmacogenetic testing

Highly used platform for Karyomapping (in context of PGT), methylation profiling and pharmacogenomics.
In order to minimize cost, the beadchips have to be fully loaded (more samples/array possible ; number of samples are array-specific).

 

CERTIFICATES

Under validation
Under validation

DOWNLOADS

 
Flyer2 GW testing white borders_edited.j
Analyses génomiques - Expert FR

2

Flyer2 GW testing white borders_edited.j
Genoomonderzoek in de genetica - Niet-expert NL

2

Flyer2 GW testing white borders_edited.j
Analyses génomiques - Non-experts FR

2

Flyer2 GW testing white borders_edited.j
Genoomonderzoek in de genetica - Expert NL

2

Flyer2 GW testing white borders_edited.j
Genome-wide genetic testing - Expert EN

2

Flyer2 GW testing white borders_edited.j
Genome-wide genetic testing - Non-expert EN

2

CONTACTS

 
pas14klein.jpg

BRIGHTcore general inquires

+32 (0)2 477 64 79 (sec)

UZ Brussel

BRIGHTcore

Laarbeeklaan 101

1090 Brussels

SAMPLE TYPES

 

We aim to keep te list with sample types updated. However, if you believe we offer this test on other sample types, of if you have a very specific sample type you'd like to evaluate : please contact us.

Tissue
Recipient
Quantity
Transport
Purpose / Extract
DNA from various tissues
Microtube* or 96 well plate
See test details/specifications
Room temperature
DNA
RNA from various tissues
Microtube* or 96 well plate
See test details/specifications
Ice (max. 20 min) or dry ice
RNA

* Microtube can be  a either a cryovial or eppendorf tube (0,5 ; 1,5 or 2 ml). Please consider the quality of the tube used (nuclease free ; free of RNA/DNA ; sterile ; LoBind) according to application needed.  

 

DELIVERABLES

Below, you can find the deliverable for this test.

If you require more information or need a more custom output, please contact us.

Deliverable
Description
Research or diagnostic
Affy raw data - CEL file
Normalized intensities from the DAT file as generated by the Affymetrix GeneChip
RUO (on request)
Affy raw data - DAT file
The exported intensity data generated by the Affymetrix GeneChip
RUO (on request)
iScan genotype calls - gtc file
The converted intensity data files (.idat) to actual genotypes (based on the .dmap file)
Diagnostic / RUO
iScan raw data - idat file
The exported intensity data generated by the iScan
Diagnostic / RUO
Run folder
The complete run folder can be transferred if it concerns a run reservation (private run)
RUO (on request)
 

PLAN EXPERIMENT

To set experiments up with us, please follow the steps below.

Get in touch (ONLY FOR NEW PROJECTS)

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

Expect questions like :

  1. What type of sample would you like to analyze?

  2. What is the aim of your experiment?

  3. How many samples would you like to process?

  4. How fast do you need the results (TAT) and/or do we need to expedite?

  5. If you deviate from our sample types, are there test samples available?

  6. Are our standard deliverables ok?

  7. ...

Call Center Headset

1

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 :

  1. Coordinates of the person to whom to address the quotation

  2. Which type of test you'd like to set up

  3. Do you require a specific deliverable?

  4. Do we need to expedite (comes at extra cost)?

  5. ...

Image by Andre Taissin

2

Submit your samples

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

  1. Fill out our sample submission form

    1. Send it via email : contact us

    2. Print out the form and include it with your samples 

  2. Send your samples to us​​

    1. Follow the instuctions given during the "Get in touch (1)" phase

    2. Label your tubes/plates correctly : see details here

    3. Adhere to the corresponding transport conditions listed under Sample types

  3. Indicate if we can discard your samples​ after completion of project

Blood Samples

3

Your experiment starts

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

  1. When expedited, the turn-around-time (TAT) is 2 weeks

  2. 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.

Alarm Clock

4