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For the doctor

  

Apart from our routine diagnostic work, detailed below, we view the participation in specialized research projects as an integral part of our laboratory’s existence and development. Please contact as if you would like to discuss the possibility of undertaking joint research work or perform specialized genetic screening as part of a medical trial.


Haematology
Sample requirements: please send bone marrow, blood or other primary tissue in one of our own transport bottles containing isotonic media. If you do not have one of our own bottles, please send 1-2 ml of bone marrow in lithium heparin (for Cytogenetics) or EDTA (for molecular tests). Please send fresh lymph nodes in sterile saline or other isotonic medium. Do not use formalin.

Please dispatch the sample as soon as possible. Disease cells often senesce quickly and we may not be able to detect them in culture if they have been left many days in transport.

For remission and relapse cases that were studied in a different laboratory, it would be useful if all previous results are made known to us.

We aim to report urgent results within 3 days and routine results within 7-14 days. Urgent FISH results within 24 hours if possible.

Tests
Please click here for a more extensive list of our probes and our pdf price list , including special price packages.

G-banded

kari1

 

karyotype
Karyotype of a male patient with AML and t(15;17), characteristic of Acute Promyelocytic Leukaemia
 

FISH
pdf A selection of our probes is listed below.

Acute leukaemias/CML

  • BCR/ABL1 to detect t(9;22) and variants
  • PML/RARa to detect t(15;17)
  • MLL breakapart to detect rearrangements of 11q23
  • CBFb to detect inv(16) or t(16;16)
  • ETV6/RUNX1 (previously known as TEL/AML)
  • RUNX1T1/RUNX1 (previously known as ETO/AML)
  • EGR1 to detect -5/del(5q)
  • D7S522/CEP7 to detect -7/del(7q)
  • del(20q)
  • PDGFRa
  • PDGFRb
  • EVI1 breakapart (3q rearrangements)
  • p53 deletion

bcd

BCR/ABL dual colour, dual fusion showing a pattern consistent with a BCR/ABL1 gene rearrangement and an extra fusion signal (an extra Philadelphia  chromosome was seen by G-banded cytogenetics). Red signal = ABL gene, green signal = BCR gene.

CLL panel

p53, ATM, CEP12, D13S319 [del(13q)]

Multiple myeloma

  • IGH@ breakapart
  • p53 deletion
  • 13q14 deletion
  • IGH/MAF to detect the rearrangement t(14;16)
  • IGH/FGFR3 to detect the cryptic rearrangement t(4;14)
  • IGH/CCND1to detect the rearrangement  t(11;14)

B-cell lymphomas/leukaemia

  • IGH@ breakapart
  • IGH@/BCL2
  • IGH@/CCND1
  • IGH@/MYC
  • MYC breakapart
  • MALT1 breakapart

T-cell leukaemias
TCRdelta

T-cell lymphomas
ALK breakapart

RT-PCR
For all common rearrangements, e.g. BCR/ABL1, PML/RARa, etc.

Mutation analysis

  • EGFR
  • K-RAS
  • FLT3
  • NPM1
  • C-KIT
  • JAK2

Array-CGH/expression arrays: this is a new technology in cancer that will help us to discover exactly what is happening at the DNA level during the cancer process and ultimately provide more targeted cancer therapies. At present, we use this technology at a research level, but we anticipate that this technology will become part of our diagnostic toolkit in the next few years.

 

gene

Gene expression arrays (from Agilent) 
 


B. Oncology
Sample requirements
Please send paraffin embedded tissue sections mounted on coated slides. The optimal thickness is 3µm. Please send one section per FISH test required and one spare section.

Paraffin embedded tissue is our preferred tissue for testing, although we can accept fresh material also for culture or touch preps.

Specialized oncology tests

  • Breast cancer

HER2 amplification screen: In some forms of breast cancer, a gene called HER2/neu on chromosome 17, is amplified, i.e. it is present in several copies instead of the normal 2. Patients with HER2/neu amplification have been shown to respond to the drug Herceptin® (trastuzumab). Presence or absence of HER2 amplification does not give any prognostic information. The overall prognosis is dependent on many other factors.

FISH is the test of choice for archival specimens of primary tumours and biopsies with an IHC score of 2+, as well as for confirming 3+ status.

CYP2D6: patient with reduced CYP2D6 enzymatic activity tend to have lower levels of endoxifen, a metabolite necessary for the metabolism of the drug tamoxifen. Patients with CYP2D6 mutations may have reduced efficacy in being able to metabolise tamoxifen and may therefore show grossly reduced response to the drug. We require 5-10 ml of peripheral blood in EDTA to carry out the CYP2D6 mutation screen.
RRM1: mutations of the RRM1 gene are associated with a better response to the drug gemcitabine.
Please contact the lab for further details.

 

fdfd

An amplified (right) compared to a normal (left) HER2 copy number.
Red signal = HER2 gene, green signal = centromere
17 control

 


  • Melanoma screen

Paraffin sections of melanoma lesions are examined to look for changes in copy number of 3 different genetic regions on chromosomes 6 and 11. Melanomas, the most aggressive form of skin cancer harbour one or more genetic changes. The morphologically similar Spitz nevus on the other hand, shows no genetic changes and is a benign tumour with a good prognosis. . We require 2 x 3μm paraffin sections for this test.


CCND1, MYB, RREB1, ratio MYB/CEP6: copy number changes in one or more of these regions would confirm the diagnosis of malignant melanoma, especially in cases of equivocal macroscopic morphology.

BRAF: mutations of the BRAF gene (mutation V600E) are seen in approximately 60% of all lesions and are associated with a higher probability for metastasis in the liver and other organs.
Please contact the lab for further details.

  • Soft tissue sarcoma

We provide FISH tests with:

  • EWSR1
  • SYT
  • CHOP

on soft tissue sarcoma biopsy for the diagnosis of Ewing sarcoma, synovial sarcoma, desmoplastic small round cell tumour and others.
Please contact Genomedica for more details.

  • Liposarcoma (fat tissue sarcoma)

In some types of fat tissue tumours we find an amplification of the gene MDM2. Amplification of MDM2 is seen in well-differentiated liposarcomas and dedifferentiated liposarcomas, which tend to be more aggressive forms of tumour, but is not seen in lipomas and spindle cell tumours.  We perform the MDM2 screen at Genomedica.   We require 2 x 3μm paraffin sections for this test.
Please contact the lab for further details.

ghghfgh

MDM2 gene amplification in a patient with aggressive de-differentiated liposarcoma.
Red signal = MDM2 gene, green
signal = centromere 12 control

  • Lung cancer

Approximately 70-75% of all lung cancers are known as non-small cell lung carcinomas. Mutations in the EGFR (epidermal growth factor receptor) gene have been associated with a favourable prognosis in early stage lung carcinoma. Early studies suggest an improved survival in patients with EGFR mutations when treated with the drug gefitinib. We perform the mutation analysis of EGFR at Genomedica.


EGFR (Epidermal Growth Factor Receptor gene): patients that harbour an EGFR mutation respond better to therapy with tyrosine kinase inhibitors and are therefore suitable for treatment with the drug gefitinib (Iressa) and erlotinib (Tarceva).

ALK: the ALK-NPM fusion product is well documented in T-cell large anaplastic lymphomas and arises most frequently from the translocation t(2;5). A subset of patients with non-small cell lung carcinoma has been identified with an ALK-EML4 rearrangement. These patients respond favourably to kinase inhibitors. The ALK FISH probe is available in our laboratory to identify the presence of an ALK rearrangement from paraffin embedded sections of lung biopsy.

ERCC1 and RRM1: reduced expression of these 2 genes is associated with a better response to cisplatin-based adjuvant therapy, while cisplatin-based agents are not recommended for patients with upregulated expression of these genes.

Please contact the lab for further details.
 

  • Prostate cancer

Currently, men with symptoms of prostate cancer are screened for PSA (prostate specific antigen), a protein present in the blood stream. However, this test is not very accurate for the diagnosis of prostate cancer and can give misleading results.

 

Although still under trial, there are strong indications that a new genetic test for the gene PCA3 (prostate cancer antigen 3) provides a much more accurate marker of prostate cancer than PSA. The PCA3 gene is overexpressed in prostate cancer cells found in urine, thus providing a marker of malignancy in prostate cells. Please contact the lab for further details.

  • Brain gliomas 

Combined loss of the chromosome regions 1p and 19q has been shown to be associated more strongly with a diagnosis of oligodendroglioma and to confer a better prognosis than intact 1p/19q. We provide FISH testing for 1p/19q deletion status. Please send 3 x 3µ paraffin sections with the area of highest infiltration marked on the slide..

MGMT: methylation of the MGMT gene is strongly associated with 1p/19q co-deletion status and an independent prognostic marker that is associated with a better response to the drug temozolomide.
Please contact the lab for further details


glioma
Oligodendroglioma showing loss of the 1p36 region.
Red signal = 1p36, green signal = 1q25 control
  • Colorectal cancer
KRAS και BRAF: mutations in these two genes are associated with poor response to anti-EGFR therapy, such as panitumumab and cetuximab.

TS (TYMS) and DPD (DYPD): mutations in the genes TYMS and DYPD are associated with TS and DPD enzyme deficiency, respectively, thus resulting in increased toxicity with 5-FU (5-fluorouracil) therapy.

ERCC1: reduced expression of this gene is associated with a better response to cisplatin-based adjuvant therapy, while cisplatin-based agents are not recommended for patients with upregulated expression of ERCC1.

MSI (microsatellite instability): increased microsatellite instability is known to be associated with an incomplete DNA repair mechanism. Patients with increased MSI respond better to drugs that inhibit thymidylate synthase, such as 5-FU, which inhibit DNA transcription.
Please contact the lab for further details
  • Gastrointestinal stromal tumours (GIST)
C-KIT and PDGFRα: mutations of the genes C-KIT, in exons 9 and 11 and less frequently 13 and 17, as well as PDGFRα are associated with a more favourable response to the drug Imatinib mesylate (Glivec).

HER2/neu: as in the case with breast carcinoma, amplification of the gene HER2/neu identified in GIST biopsy, identifies a subgroup of patients with a favourable response to the drug trastuzumab (Herceptin®).
Please contact the lab for further details
  
  • Bladder caner
Copy number change of chromosomes 3, 7, 17 and 9p21: this test identifies genetic changes that are associated with disease progression to higher grade tumours. They can also be used in lower grade tumours as a predictive marker of disease progression. This test can be carried out on bladder biopsies as well as urine samples (Cytospin).
Please contact the lab for further details
 
   
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