GENE PANELS
SAMPLE SWITCH VARIANT PANEL (SSW)
DETAILS
Version :
2
Status :
Size :
35 SNVs
Start date :
June 20, 2019
Website :
Extra info :
This assay concerns a homebrew method.
Method :
Multiplex locus-specific PCR to amplify the 35 targets of interest whilst incorporating a universal tag. A second barcoding PCR incorporates the sample/patient specific barcode/index.
CERTIFICATES
141-TEST (BRIGHTcore)
INSTRUMENTS
Illumina NovaSeq 6000
Our highest capacity short read sequencer. This device can generate reads up to 250 bp in length (on the SP flowcell) and generate up to 10B reads per flowcell (S4).
DOWNLOADS
Analyses génomiques - Expert FR
2
Genoomonderzoek in de genetica - Niet-expert NL
2
Analyses génomiques - Non-experts FR
2
Genoomonderzoek in de genetica - Expert NL
2
Genome-wide genetic testing - Expert EN
2
Verzendinstructies DNA stalen - NL
1
Genome-wide genetic testing - Non-expert EN
2
CONTACT
BRIGHTcore general inquires
+32 (0)2 477 64 79 (sec)
UZ Brussel
BRIGHTcore
Laarbeeklaan 101
1090 Brussels
SAMPLE TYPES
We aim to keep the list with sample types updated. However, if you believe we offer this gene panel on other sample types, or if you have a very specific sample type you'd like to evaluate : please contact the corresponding persons for either diagnostic or research purposes.
* 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.
Research portfolio
DNA from various tissues > DNA
Microtube* or 96 well plate
See test details/specifications
Room temperature
Diagnostic portfolio
DNA from various tissues > DNA
Microtube* or 96 well plate
See test details/specifications
Room temperature
Specific sample recommendations / requirements
Absorbance ratio A260/A230 - Minimum
Optimum : 1,5 [Acceptable range (-)]
DNA from various tissues
Lower values are indicative for indicative for EDTA, carbohydrate, chaotropic salts (and also protein) contamination
Absorbance ratio A260/A280 - Minimum
Optimum : 1,5 [Acceptable range (-)]
DNA from various tissues
Lower values are indicative for indicative for protein, phenol or other aromatic compound contamination
Elution buffer : nuclease free water, Tris-HCl or TE
Optimum : [Acceptable range (-)]
Please use nuclease free elution buffers, however this assay is compatible with either water, Tris-HCl as TE.
DNA from various tissues
Minimum volume
Optimum : 2 [Acceptable range (-)]
DNA from various tissues
A minimum volume of 2 µl is required. We prefer to receive at least 5 µl.
DELIVERABLES
Which data files can be retrieved from us for this specific gene panel?
Deliverable | Description | Research or diagnostic |
|---|---|---|
Called variants - vcf file | Text file containing all detected variants as compared to the relevant reference genome | Diagnostic / RUO |
Raw data - bam file | Binary data file containing the aligned reads | RUO (on request) |
Raw data - fastq file | Data file containing the raw (unaligned) reads | RUO (on request) |
Research report | Research report generated by Clinical Geneticist/ Pathologist / Hematologist | RUO |
PLAN EXPERIMENT
For Diagnostics
This test is mainly performed as a diagnostic assay. In this case, please contact your General Practitioner or Clinical Geneticist (Centre for Medical Genetics 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?
Which elution buffer did you use?
What are the expected concentrations of your samples?
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
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
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
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 1 month
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.
4
GENELIST
The following variants are interrogated (hg19):
chr1:144866643
chr1:179520506
chr2:227896976
chr4:5749904
chr5:82834630
chr5:140797630
chr6:146755140
chr8:68968166
chr8:94935937
chr10:45496120
chr11:16133413
chr12:993930
chr12:30823971
chr13:42772717
chr14:50769717
chr15:31229420
chr15:59347929
chr16:46773999
chr16:81249954
chr17:37884037
chr17:80377690
chr18:21413869
chr18:30092097
chr18:60562298
chr19:10267077
chr20:854940
chr21:31964916
chr21:34399401
chr22:21141300
chr22:49834747
chrX:49103224
chrX:135429503
chrX:153880830
chrY:14532067
chrY:21618583