top of page

GENE PANELS

STHT - OTHER SOLID TUMORS - EXTENDED

DETAILS

Panel Details
Version :
3.2
Status :
Inactive.png
Size :
183 genes
Start date :
June 2, 2025
Website :
Extra info :
Method :

Capture based panel, using the Roche KAPA HyperPlus kit and KAPA HyperChoice probes

CERTIFICATES

Certificates
Validated
Validated

INSTRUMENTS

Instruments
MGI DNBSEQ-T7
MGI DNBSEQ-T7

Our highest capacity short read sequencer. This device can generate up to 5,8B reads per flowcell. We standardly run SE50 bp and PE150 bp runs, but read length can be flexibily adjusted (to >200 bp).

DOWNLOADS

Downloads
Flyer2 GW testing white borders_edited.j
Genelist STHT other solid tumors

3.2

Flyer2 GW testing white borders_edited.j
STHT subpanels overview

3.2

Flyer2 GW testing white borders_edited.j
Verzendinstructies DNA stalen - NL

1

CONTACT

Contacts
pas14klein.jpg

Secretariaat Medische Genetica

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

UZ Brussel

Centrum Medische Genetica

Laarbeeklaan 101

1090 Brussels

pas14klein.jpg

Freya Vaeyens

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

UZ Brussel

Centrum Medische Genetica

Laarbeeklaan 101

1090 Brussels

SAMPLE TYPES

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

Blood > cfDNA/ctDNA

Streck Cell-Free DNA BCT

9 ml

Room temperature

Blood > DNA

EDTA tube

10 ml (min. 3 ml)

Room temperature

Cells of various tissue origins > DNA

Microtube* with cell pellet or on lysis buffer

> 5 million cells

Dry ice

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

Plasma > cfDNA/ctDNA

DNA LoBind 5 ml tube

> 2ml

Dry ice

Tissue of various origins > DNA

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

Application/tissue specific (contact us)

Dry ice

Diagnostic portfolio

Blood (for DNA) - Diagnostic
Blood > DNA

EDTA tube

10 ml (min. 3 ml)

Room temperature

DNA tube & plate - Diagnostic
DNA from various tissues > DNA

Microtube* or 96 well plate

See test details/specifications

Room temperature

FFPE tissue block (for DNA) - Diagnostic
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 tissue sections (for DNA) - Diagnostic
FFPE section of various tissues > DNA

Microtube*

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

Room temperature

Tissue biopsy (for DNA) - Diagnostic
Tissue of various origins > DNA

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

Application/tissue specific (contact us)

Dry ice

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 DNA concentration

Optimum : 6 [Acceptable range (-)]

DNA from various tissues

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

Optimum : 10 [Acceptable range (-)]

DNA from various tissues

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

DELIVERABLES

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
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)

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. ...

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. ...

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

Call Center Headset

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.

Call Center Headset

4

Genelist

GENELIST

ACD
AKT1
AKT3
ALK
ANKRD26
ANTXR1
ANTXR2
APC
AR
ARAF
ARID1A
ARID2
ATM
ATR
ATRX
AXIN1
B2M
BAP1
BARD1
BMPR1A
BRAF
BRCA1
BRCA2
CASP8
CDH1
CDK12
CDK4
CDKN2A
CHEK1
CHEK2
COL2A1
CTNNB1
CUL4B
CYLD
CYSLTR2
DAXX
DCC
DDR1
DELEC1 (DEC1)
DICER1
DLC1
DMD
DNMT3A
DPH3
DPYD
EED
EGFR
EGLN1
EGLN2
EIF1AX
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
KDM5C
KDR
KEAP1
KIF1B
KIT
KMT2D (MLL2)
KRAS
LATS1
LATS2
LEMD3
LSAMP
LYST
LZTR1
MAP2K1
MAP2K2
MAP3K8
MAX
MC1R
MDH2
MEF2B
MEN1
MET
MLH1
MRE11 (MRE11A)
MSH2
MSH6
MTOR
MUTYH
MYB
MYOD1
NF1
NF2
NOTCH1
NRAS
NTRK1
NTRK2
NTRK3
PAK1
PBRM1
PDGFRA
PDGFRB
PHOX2B
PIK3CA
PIK3R1
PLCB4
PMS1 (MLH2)
PMS2 (MLH4)
POLD1
POLE
POT1
PPM1D
PPP2R2A
PPP6C
PRDM1
PRF1
PRKAR1A
PRKD2
PTCH1
PTEN
PTPN11
PTPRD
RAC1
RAD51B
RAD54L
RAF1 (CRAF)
RB1
RET (MEN2)
RICTOR
RNF43
ROBO1
ROBO2
ROS1
SDHA
SDHAF2
SDHB
SDHC
SDHD
SLC25A11
SLC29A3
SMAD4 (MADH4)
SMARCA4
SMARCB1
SMO
SPEN
SPOP
STARD13
STK11
SUZ12
TEK
TENT5C (FAM46C)
TERF2IP
TERT
TGFBR2
TMEM127
TP53
TPMT
TSC1
TSC2
UGT1A1
USP13
VHL
WAS (XLN/XLT)
WWOX
YEATS2

BUA white.png

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

Photography / See our Colofon

Content & illustrations / Ben Caljon

BRIGHTcore no text white.png
bottom of page