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GENE PANELS

STHT - BRAIN PANEL

Engineering Plans

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Version :

3.1

Status :
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Size :

178 genes

Start date :

Website :

Extra info :
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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.  

Blood > DNA

EDTA tube

10 ml (min. 3 ml)

Room temperature

DNA from various tissues > DNA

Microtube* or 96 well plate

See test details/specifications

Room temperature

FFPE block of various tissues > DNA

Paraffin block (in cassette)

Representative block ; Tumor load preferentially >10% ; To be processed by our pathology department (microtome section needed)

Room temperature

FFPE section of various tissues > DNA

Microtube*

Min. 1x 10 µm section (up to 2 mm³ tissue) ; Tumor load preferentially >10%

Room temperature

Tissue of various origins > DNA

Cryovial containing stabilizer (eg. AllProtect) or tissue homogenized on lysis buffer

Application/tissue specific (contact us)

Dry ice

Extra requirements

Absorbance ratio A260/A230 - Minimum
DNA from various tissues

Minimum: 1,5

Lower values are indicative for indicative for EDTA, carbohydrate, chaotropic salts (and also protein) contamination

Absorbance ratio A260/A280 - Minimum
DNA from various tissues

Minimum: 1,5

Lower values are indicative for indicative for protein, phenol or other aromatic compound contamination

Elution buffer : nuclease free water, Tris-HCl or TE
DNA from various tissues

:

Please use nuclease free elution buffers, however this assay is compatible with either water, Tris-HCl as TE.

Minimum DNA concentration
DNA from various tissues

Minimum: 6 ng/µl

A minimum concentration of 6 ng/µl is required, however succesfull experiments are possible below this limit. Low concentrated samples are vacuum concentrated to increase library prep success rate.

Minimum DNA quantity
DNA from various tissues

Minimum: 10 ng

Below 10 ng input, success rate is very low. Please provide us with as much as material as possible (300 ng preferred).

Image by Mezidi Zineb
Sample types
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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.

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
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)
Run folder

The complete run folder can be transferred if it concerns a run reservation (private run)

RUO (on request)
Deliverables

Costs

For Diagnostic testing

When requested through your General Practitioner / Clinical Geneticist / Pathologist / Hematologist, costs will be covered through your health insurance. The costs involved will be those for your consultation and/or 'remgeld'.

For Research testing

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.

Update pending

Our prices are being updated. More info soon.

Euro Bill
Costs
Documents
Books

Documents & certificates

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141-MED (UZ Brussel)
Plan experiment

Plan experiment

  1. For Diagnostics

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


  1. 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 :

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

  2. Which elution buffer did you use?

  3. What are the expected concentrations of your samples?

  4. How many samples would you like to process?

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

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

  7. Are our standard deliverables ok?

  8. ...

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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. ...

Call Center Headset

2

Submit your samples

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

  1. Fill out our sample submission form

  2. Send it via email : contact us

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

  4. Send your samples to us

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

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

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

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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.

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4

Genelist
White Rocks

Genelist

ABL1
ACVR1
AKT1
AKT2
AKT3
ALK
APC
AR
ARAF
ARID1A
ARID2
ATM
ATRX
AURKA
BAP1
BRAF
BRCA1
BRCA2
BRIP1
BTK
CCM2 (MGC4607)
CCND1
CCND2
CCND3
CCNE1
CDH1
CDK4
CDK6
CDKN2A
CDKN2B
CHEK2
CIC
CRBN
CREBBP (CBP)
CRKL
CSF1R
CTNNB1
DAXX
DDR2
DNMT3A
EGFR
EGR1
EP300
EPHA3
ERBB2
ERBB3
ERBB4
ERCC2
ERG
ESR1
ESR2
EZH2
FBXW7
FGF3
FGFR1
FGFR2
FGFR3
FGFR4
FLT3
FOXO1
FUBP1
GATA3
GNA11
GNAQ
GNAS
H1-2 (HIST1H1C)
H1-5 (HIST1H1B)
H3-3A (H3F3A)
H3-3B (H3F3B)
HRAS
IDH1
IDH2
IGF1R
IL7R
JAK1
JAK2
JAK3
KCNG1
KDM5A
KDM5C
KDM6A
KDR
KIT
KLF4
KMT2C
KRAS
KRIT1
LRRK2
LTB
MAP2K1
MAP2K2
MAP2K4
MAPK1
MAPK3
MAX
MCL1
MDM2
MDM4
MED12
MEN1
MET
MITF
MLH1
MRE11 (MRE11A)
MSH2
MSH6
MTOR
MYC
MYCN
NBN
NF1
NF2
NKX2-1
NOTCH1
NOTCH2
NOTCH3
NRAS
NTRK1
NTRK2
NTRK3
NUTM1
PAK1
PALB2
PBRM1
PDCD10
PDGFRA
PHOX2B
PIK3CA
PIK3CB
PIK3R1
PMS1 (MLH2)
PMS2 (MLH4)
POLD1
POLE
POLR2A
PTCH1
PTEN
PTPN11
RAB35
RAC1
RAD50
RAD51
RAD51B
RAD51C
RAD51D
RAF1 (CRAF)
RB1
RET (MEN2)
RHOA
RNF43
ROBO1
ROBO2
SETD2
SF3B1
SLIT2
SMAD4 (MADH4)
SMARCA4
SMO
SPOP
SRC
STAG2
STK11
SUFU
SUZ12
SYK
TERT
TET2
TGFBR2
TP53
TRAF7
TSC1
TSC2
TSHR
U2AF1
USP13
VHL
WT1
XRCC2

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BRIGHTcore / T +32 (0)2 477 64 79 / F +32 (0)2 477 68 59

Photography / See our Colofon

Content & illustrations / Ben Caljon

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