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GENE PANELS

STHT - OTHER SOLID TUMORS

Engineering Plans

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Version :

3.1

Status :
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Size :

109 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

BELAC logo - UZ Brussel - Certificate Only.png
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

ACD
AKT1
AKT3
ALK
ANKRD26
ANTXR1
ANTXR2
APC
AR
ARAF
ARID1A
ATM
ATRX
AXIN1
BAP1
BARD1
BMPR1A
BRAF
BRCA1
BRCA2
CASP8
CDH1
CDK12
CDKN2A
CHEK1
CHEK2
COL2A1
CTNNB1
CUL4B
CYLD
CYSLTR2
DAXX
DCC
DDR1
DELEC1 (DEC1)
DICER1
DLC1
DMD
DNMT3A
DPH3
DPYD
EED
EGFR
EGLN1
EGLN2
ENG
EPAS1 (HIF2A)
EPCAM
ERBB2
ERBB3
ERBB4
EXT1
EXT2
FAT1
FAU
FBXW7
FGFR1
FGFR2
FGFR3
FH
FLCN
FLT4
FOXO1
GAB2
GLMN
GNA11
GNAQ
GNAS
HRAS
IDH1
IDH2
IL7R
JAK2
JAK3
KDR
KEAP1
KIF1B
KIT
KMT2D (MLL2)
KRAS
LATS1
LATS2
LEMD3
LSAMP
LYST
MAP2K1
MAP2K2
MAP3K8
MAX
MC1R
MDH2
MEF2B
MEN1
MET
MLH1
MSH2
MSH6
MTOR
MUTYH
MYB
MYOD1
NF1
NF2
NOTCH1
NRAS
NTRK1
NTRK2
NTRK3
PAK1
PDGFRA
PDGFRB
PHOX2B
PIK3CA
PIK3R1
PLCB4
PMS1 (MLH2)
PMS2 (MLH4)
POLD1
POLE
POT1
PPM1D
PPP2R2A
PPP6C
PRDM1
PRF1
PRKAR1A
PRKD2
PTCH1
PTEN
PTPN11
PTPRD
RAD51B
RAD54L
RAF1 (CRAF)
RB1
RET (MEN2)
RICTOR
ROBO1
ROBO2
ROS1
SDHA
SDHAF2
SDHB
SDHC
SDHD
SLC25A11
SLC29A3
SMAD4 (MADH4)
SMARCA4
SMARCB1
SMO
SPEN
STARD13
STK11
SUZ12
TEK
TENT5C (FAM46C)
TERF2IP
TERT
TMEM127
TP53
TPMT
TSC1
TSC2
UGT1A1
USP13
VHL
WAS (XLN/XLT)
WWOX
YEATS2

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