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GENE PANELS

STHT - LYMFOID

DETAILS

Panel Details
Version :
3.2
Status :
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Size :
147 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 lymfoid

3.2

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STHT subpanels overview

3.2

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

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CONTACT

Contacts
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Secretariaat Medische Genetica

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

UZ Brussel

Centrum Medische Genetica

Laarbeeklaan 101

1090 Brussels

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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

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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

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Genelist

GENELIST

ABL1
ADA2
AIRE
ANK2
ARID1A
ARID1B
ARID2
ARPC1B
ATM
B2M
BCL2
BCL6
BCL7A
BCOR
BTK
CARD11
CASP8
CASP10
CCND1
CCND2
CCND3
CD27
CD28
CD58
CD79A
CD79B
CDC27
CDK12
CDKN2A
CDKN2B
CDKN2C
CEBPA
CHEK1
CHEK2
CIITA
CREBBP (CBP)
CSF2RB
CSMD3
CTLA4
CXCR4
DDX3X
DDX41
DICER1
DIS3
DNMT3A
DOCK8
DUSP2
EP300
EZH2
FANCL
FAS
FASLG
FAT3
FBXW7
FCGBP
FGFR1
FGFR2
FGFR3
FOXL2
FOXO1
H1-4 (HIST1H1E)
H3C2 (HIST1H3B)
H3C3 (HIST1H3C)
HRAS
HSPG2
HYDIN
ID3
IDH1
IDH2
IGLL5
IKZF1
IL4R
IRF4
IRF8
JAK2
JAK3
JUNB
KDM6B
KLF2
KMT2C
KMT2D (MLL2)
KRAS
LRBA
LRP1B
LTB
LZTR1
MAP2K2
MEF2B
MSC
MYC
MYD88
NFKB1
NFKB2
NFKBIA
NFKBIE
NOL9
NOTCH1
NOTCH2
NRAS
NSD2
NUTM1
PBRM1
PDCD1
PDGFRA
PIK3CD
PIK3R1
PIM1
PLCG1
PLCG2
PRDM1
PRF1
PRKAR1A
PTPRD
RET (MEN2)
RHOA
RNF43
RPS15
RYR1
SF3B1
SGK1
SMARCA4
SOCS1
SRSF2
STAG2
STARD9
STAT1
STAT3
STAT5B
STAT6
SYNE1
TBL1XR1
TCF3
TERC
TERT
TET2
TNFAIP3
TNFRSF13B
TNFRSF14
TP53
TPMT
TRAF3
TRRAP
U2AF1
UBR5
VAV1
XPO1
ZRSR2

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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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