GENE PANELS
EXOME - SKELETAL DYSPLASIA (SKD)
DETAILS
CERTIFICATES
Validated
INSTRUMENTS
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
Analyses génomiques - Expert FR
2
Genome-wide genetic testing - Non-expert EN
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Analyses génomiques - Non-experts FR
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Genoomonderzoek in de genetica - Niet-expert NL
2
Genelist Exome - Skeletal Dysplasia (SKD)
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Genoomonderzoek in de genetica - Expert NL
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Genome-wide genetic testing - Expert EN
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Verzendinstructies DNA stalen - NL
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CONTACT
Secretariaat Medische Genetica
+32 (0)2 477 64 79 (sec)
UZ Brussel
Centrum Medische Genetica
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
Blood > cfDNA/ctDNA
Streck Cell-Free DNA BCT
9 ml
Room temperature
Blood > DNA
DBS / Guthrie card / Punch in microtube*
Min. 1 punch
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 > DNA
DBS / Guthrie card / Punch in microtube*
Min. 1 punch
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
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 : 7,7 [Acceptable range (-)]
DNA from various tissues
A minimum concentration of 7,7 ng/µl is required, however succesfull experiments are possible below this limit.
Minimum DNA quantity
Optimum : 200 [Acceptable range (-)]
DNA from various tissues
We prefer delivery of at least 1 µg of DNA
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
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.
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GENELIST
ABCC9
ABL1
ACAN
ACP4
ACP5
ACVR1
ADAMTS10
ADAMTS17
ADAMTSL2
AFF4
AGA
AGPS
AHDC1
AKT1
ALPL
ALX1
ALX3
ALX4
AMER1
ANKH
ANKRD11
ANO5
ANTXR2
APC
ARCN1
ARHGAP31
ARID1A
ARID1B
ARSB
ARSE
ASCC1
ASXL2
ATP6V0A2
B3GALT6
B3GAT3
B4GALT7
BGN
BHLHA9
BMP1
BMP2
BMPER
BMPR1B
BRIP1
C1R
C1S
C2CD3
CA2
CANT1
CASR
CC2D2A
CCDC8
CCNQ
CD96
CDC45
CDC6
CDH3
CDKN1C
CDT1
CEP120
CEP290
CHD7
CHST14
CHST3
CHSY1
CKAP2L
CLCN5
CLCN7
COG1
COL10A1
COL11A1
COL11A2
COL1A1
COL1A2
COL2A1
COL9A1
COL9A2
COL9A3
COMP
CPLANE1
CREB3L1
CREBBP
CRTAP
CSPP1
CTSA
CTSK
CUL7
CYP26B1
DDR2
DDX58
DDX59
DHCR24
DHODH
DLL3
DLX3
DLX5
DLX6
DMP1
DOCK6
DVL1
DVL3
DYM
DYNC2H1
DYNC2LI1
EBP
EDNRA
EFNA4
EFNB1
EFTUD2
EIF2AK3
EIF4A3
ELMO2
ENPP1
EOGT
EP300
ERCC4
ERF
ESCO2
EVC
EVC2
EXT1
EXT2
EZH2
FAM111A
FAM20C
FANCA
FANCB
FANCC
FANCD2
FANCE
FANCF
FANCG
FANCI
FANCL
FBLN1
FBN1
FBN2
FBXW4
FERMT3
FGF10
FGF16
FGF23
FGF3
FGF4
FGF8
FGF9
FGFR1
FGFR2
FGFR3
FIG4
FKBP10
FLNA
FLNB
FMN1
FN1
FREM1
FUCA1
FZD2
GALNS
GALNT3
GDF3
GDF5
GDF6
GJA1
GLB1
GLI3
GNAS
GNPAT
GNPTAB
GNPTG
GNS
GORAB
GPC3
GPC6
GPR68
GPX4
GREM1
GUSB
HDAC4
HDAC8
HES7
HOXA11
HOXA13
HOXD13
HPGD
HSPG2
HUWE1
IARS2
ICK
IDH1
IDH2
IDS
IFITM5
IFT122
IFT140
IFT172
IFT43
IFT80
IGF1R
IHH
IKBKG
IL11RA
IL1RN
IMPAD1
INPPL1
JAG1
KAT6B
KIF22
KIF7
KRAS
LBR
LEMD3
LFNG
LIFR
LMBR1
LMNA
LMX1B
LONP1
LPIN2
LRIT3
LRP4
LRP5
LTBP2
LTBP3
MAB21L2
MAFB
MAN2B1
MAN2C1
MAP3K7
MATN3
MEGF8
MEOX1
MESP2
MGP
MITF
MKS1
MMP13
MMP2
MMP9
MNX1
MSX2
MYCN
MYT1
NAGLU
NEK1
NEU1
NF1
NFIX
NIPBL
NKX3-2
NLRP3
NOG
NOTCH2
NPR2
NSD1
NSDHL
NTRK2
OBSL1
OFD1
ORC1
ORC4
ORC6
OSTM1
P3H1
P4HB
PALB2
PAM16
PANK2
PAPSS2
PCNT
PCYT1A
PDE3A
PDE4D
PEX7
PGM3
PHEX
PIGV
PIK3CA
PITX1
PLEKHM1
PLOD2
PLS3
POLR1A
POLR1C
POLR1D
POP1
POR
PPIB
PRKAR1A
PROK2
PTDSS1
PTH1R
PTHLH
PTPN11
PYCR1
RAB23
RAB33B
RAD21
RAD51C
RASGRP2
RBM8A
RBPJ
RECQL4
RMRP
RNU4ATAC
ROR2
RPGRIP1L
RSPO2
RSPRY1
RUNX2
SALL1
SALL4
SBDS
SEC24D
SERPINF1
SERPINH1
SETD2
SF3B4
SH3BP2
SH3PXD2B
SHOX
SKI
SLC17A5
SLC26A2
SLC29A3
SLC34A3
SLC35D1
SLC39A13
SLCO5A1
SLX4
SMAD3
SMAD4
SMARCA2
SMARCA4
SMARCAL1
SMARCB1
SMC1A
SMC3
SMO
SNRPB
SNX10
SOST
SOX6
SOX9
SP7
STAT3
SULF1
SUMF1
TBCE
TBX15
TBX3
TBX4
TBX5
TBX6
TBXAS1
TCF12
TCIRG1
TCOF1
TCTN3
TGDS
TGFB1
TGFB2
TGFBR1
TGFBR2
THPO
TMCO1
TMEM216
TMEM38B
TMEM67
TNFRSF11B
TP63
TRAPPC2
TREM2
TRIP11
TRIP4
TRPS1
TRPV4
TTC21B
TWIST1
TYROBP
UBE2T
WDR19
WDR34
WDR35
WISP3
WNT1
WNT10B
WNT3
WNT5A
WNT6
WNT7A
XYLT1
XYLT2
ZEB2
ZIC1
ZMPSTE24
ZSWIM6