Document 15387

Issue 4
KREATECH NEWS
IN THIS ISSUE…
TWENTY-FOUR CHROMOSOME FISH
IN HUMAN IVF EMBRYOS REVEALS
PATTERNS OF POST-ZYGOTIC
CHROMOSOME SEGREGATION
AND NUCLEAR ORGANIZATION
Dimitris Ioannou, Gothami Fonseka, Eric
Meershoek, Alan Thornhill, Adulmawla
Abogrein, Michael Ellis and Darren
K. Griffin
University of Kent, Kreatech, Digital Scientific
and London Bridge Fertility, Gynaecology and
Genetics Centre.
In the May issue of Chromosome Research
this year, Dimitris Ioannou and .......
Read more on page 5
P53 / MPO “ISO 17Q” FISH PROBE IN
CHRONIC LYMPHOCYTIC LEUKEMIA
ROUTINE DIAGNOSTICS
DETECTION OF NUP98 GENE
REARRANGEMENTS BY FLUORESCENT
IN SITU HYBRIDIZATION
Lana Harder, MD, PhD
Institute of Tumour Genetics North, Kiel,
Germany
Susana Lisboa, Manuel R. Teixeira
Department of Genetics, Portuguese Oncology
Institute, Porto, Portugal
REPEAT-FREE™ POSEIDON™
BCR/ABL1 t(9;22) PRODUCT RANGE
Read more on page 8
Chronic lymphocytic leukemia (CLL) is a
disease with a highly heterogeneous clinical
course. Aberrations of the P53 pathway are
increasingly recognized as one of the most
important biological risk factors. Deletions
of the short arm of chromosome 17 resulting
in loss of one P53 allele occur in 8-10% of
German CLL patients [1]. In other populations,
the incidence can be higher, up to 16% [2].
Furthermore, P53 deletions were detected
by FISH in 7% of multiple myeloma [3], in
approximately 5% of myelodysplastic syndromes [4] and in up to 40% of complex
aberrant acute myeloid leukemias [5]. In
addition, P53 aberrations are recurrent abnormalities in almost all solid and hematologic cancers [6].
Read more on page 2
Nucleoporin 98 gene (NUP98) rearrangements
have been identified in a wide range of
hematologic malignancies, including acute
myeloid leukemia (AML), acute lymphoblastic
leukemia (ALL), chronic myeloid leukemia
in blast crisis (CML-bc), myelodysplastic
syndrome (MDS) and bilineage/ biphenotypic
leukemia [1]. So far, NUP98 has been found to
be rearranged with up to 28 different partner
genes, resulting in in-frame fusion genes [1,
2]. The clinical course of patients with NUP98
gene rearrangements seems to be aggressive
and presents a poor outcome [1], thus being
important to recognize patients harboring
such rearrangements.
Read more on page 4
DEVELOPMENT AND VALIDATION OF
A REPEAT-FREE™ DNA-FISH ASSAY
TO DETECT FGFR1 GENE LOCUS
AMPLIFICATION
Read more on page 12
OTHER NEWS
Please contact us or your local distributor
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IN THIS ISSUE
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CHILDHOOD
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B-CELL PRECU
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RSOR ACUTE
TIC LEUKA
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By Prof.
Christine
J Harris
Schwab,
Dr. Amy Erhorn on, Ms. Claire
Leukaemia
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Research
Cytogenetics
Newcastle
University,
Group,
Newcastle-up
on-Tyne, UK
The abnorm
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the most
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treatment
and manag
childhood
ement of
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acute lymph
leukaemia
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t(9;22)(q34;q
MLL-AFF1
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risk stratifi
Read more
cation…...
on page 2
GATA 4 (8p23
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DEFECT &
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KREATECH
CATALOGUE DIAGNOSTICS
2011
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KREATECH
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DIAGNOSTICS
TUMORS
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KREATECH
[email protected]
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Published Januari 2011
Reader,
CANCER
PROSTATE
IN AML
CANCER
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© 2011 KREATECH Diagnostics
FISH DIAGNOSTICS
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DIAGNOSTICS
DIAGNO
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RF™ POSEIDON™
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IN THIS
ISSUE
ALK
REARRANGEMENT
ANDROGEN
MLL
RECEPTOR IN LUNG
TRANSLOCATIONS
IN
Dear
CATALOGUE
CAT
ATALOGUE 2011 - 2012
ATALOGUE 2011 - 2012
CAT
CATALOGUE
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™ POSEIDON™
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12.
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KREATECH
CH DIAGNOSTICS
KREATECH DIAGNOSTICS
RF™
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CATALOGUE 2011 - 2012
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issue
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Yours sincerely, Kreatech Diagnostics
Diagnost
We are very grateful to these authors for their contribution to this
newsletter and we hope that you will enjoy it.
KREATECH
Translocations involving the MLL gene and one of its numerous
partner genes belong to the recurring cytogenetic aberrations
in Acute Myeloid Leukemia. MLL translocations exert prognostic
influence on response to induction therapy and survival. The
effect depends strongly on the partner gene. Therefore clarifying
exactly the aberration partner is of importance for further therapy
decisions. Continued on page 7
KREATECH DIAGNOSTICS
CATALOGUE 2011 - 2012
2
Promising results have been
b
obtained with ALK inhibitors
such as
Crizotinib (PF-02341066)
(PF-0234106 for treatment
of non-small cell lung cancer
(NSCLC) patients carrying
carry the fusion gene ALK-EML4.
“Fluorescent
In Situ Hybridization is most
likely the best adapted method
for
the diagnosis of ALK rearrangement
in NSCLC” cited by Dr. Just
Pathology Department,
Departme Hôpital Cochin,
Paris. Read more on page 2
FISH4U
All prostate cancers become essentially within a few years resistant
to endocrine therapy. This stage of disease is known as CastrationResistant Prostate Cancer (CRPC). Remarkably in approx. 30% of the
CRPC cases the most important mechanism seems Androgen Receptor
(AR) overexpression caused by high level amplification of the AR gene.
Read more on page 5 on The Role of the Androgen Receptor in Prostate
Cancer by Prof. Trapman, Erasmus Medical Centre, Rotterdam.
Pleasee contact us or your local distributor for
2011-2012.
our Patholog
Pathology Brochure and Catalogue
gue 2011
-2012
-2012.
You can also visit our website: www.kreatech
w.kreatech.com
.co
www.kreatech.com
IN THIS
ISSUE
FISH IN
BIOCHIPS
IT TAKES
TWO
FISH4
U
We are proud to present
a selection of informative
articles from
opinion leaders in Europe.
Europe To give you a preview
on these articles:
Promising results have been obtained with ALK inhibitors such as
Crizotinib (PF-02341066) for treatment of non-small cell lung cancer
(NSCLC) patients carrying the fusion gene ALK-EML4. “Fluorescent
In Situ Hybridization is most likely the best adapted method for
the diagnosis of ALK rearrangement in NSCLC” cited by Dr. Just
Pathology Department, Hôpital Cochin, Paris. Read more on page 2
Issue
ALK REARRANGEMENT
NTT INN LLUNG CANCER
ANDROGEN RECEPTOR
ORR INN PROSTATE CANCER
MLL TRANSLOCATIO
TRANSLOCATIONS
ONNS
NS IN AML
Dear Reader,
Welcome to our latest edition
of the Kreatech Newsletter.
In this
issue we present our latest
rreleases of REPEAT-FREE
POSEIDON
FISH DNA probes and our
F
FISH4U
Custom Probe Service which
provides you with the probe
of choice.
We are proud to present a selection of informative articles from
opinion leaders in Europe. To give you a preview on these articles:
FISH DIAGNOSTICS
RF™ POSEIDON™
FOR HEMATOLOGY
SOLUTIONS
Issue 1
IN THIS ISSUE
ALK REARRANGEMENT IN LUNG CANCER
ANDROGEN RECEPTOR IN PROSTATE CANCER
MLL TRANSLOCATIONS IN AML
Dear Reader,
Welcome to our latest edition of the Kreatech Newsletter. In this
issue we present our latest releases of REPEAT-FREE POSEIDON
FISH DNA probes and our FISH4U Custom Probe Service which
provides you with the probe of choice.
i
prevvioouss issue
r for the previous
or your local distributo
hure..
Please contact us
OGY Brochure
and for the HEMATOL
of KREATECH NEWS
tech.com.
our website: www.krea
You can also visit
Issue 3
KREATECH
NEWS
Issue 2
KREATECH
NEWS
© 2011
FGFR1 (8p11) / SE 8 probe hybridized to SCC NSCLC and BC tissue
KREATECH NEWS
P53 / MPO “ISO 17Q” FISH PROBE IN CHRONIC
LYMPHOCYTIC LEUKEMIA ROUTINE DIAGNOSTICS
Lana Harder, MD, PhD
Institute of Tumour Genetics North, Kiel,
Germany
CLINICAL BACKGROUND OF CLL WITH
P53 DELETIONS
Chronic lymphocytic leukemia (CLL) is
a disease with a highly heterogeneous
clinical course. Aberrations of the P53
pathway are increasingly recognized as
one of the most important biological
risk factors. Deletions of the short arm
of chromosome 17 resulting in loss of
one P53 allele occur in 8-10% of German
CLL patients [1]. In other populations, the
incidence can be higher, up to 16% [2].
Furthermore, P53 deletions were detected
by FISH in 7% of multiple myeloma [3],
in approximately 5% of myelodysplastic
syndromes [4] and in up to 40% of complex
aberrant acute myeloid leukemias [5]. In
addition, P53 aberrations are recurrent
abnormalities in almost all solid and
hematologic cancers [6].
Lana Harder, MD, PhD in her new practice (founded January 1st, 2012 at the Institute of Tumour Genetics
North).
It is well established that deletions of P53 are known to be associated
with poor response to therapy (with purine analog refractory),
aggressive disease and shorter survival [1, 7, 8, 9]. Therefore, estimation
of genetic risk parameters has become increasingly important [10].
In CLL patients with loss/mutation of P53, so-called “high risk CLL”
an allogeneic stem cell transplantation (SCT) should be considered
[9]. Nowadays, P53 status in CLL patients should be identified prior
to treatment [9, 11]. Cytogenetic analyses and fluorescence in situ
hybridization (FISH) are helpful tools for investigation of the P53
status at initial diagnosis, at follow up, and especially during disease
progression [12]. P53 can be lost due to pure intrachromosomal
deletions in 17p, monosomy 17, unbalanced translocations involving
the short arm of chromosome 17 and formation of an isochromosome
17q. Unbalanced translocations involving 17p and isochromosomes
17q with breakpoints between 17p10 and 17p11.2 are recurrent events
triggered by low-copy DNA repeats located in 17p10 to 17p12 [13].
2
DESIGN OF P53 FISH PROBES
The commonly used FISH probe for detecting the P53 gene locus is the
P53 probe combined with the centromeric region of chromosome 17.
We prefer the use of the FISH probe P53 in combination with the MPO
probe at 17q22. The P53 / MPO probe combination has the advantage
that the MPO gene locus probe displays more or less similar signal
intensity as the specific P53 probe, whereas any commercially available
FISH probe for P53 and the centromeric region of chromosome 17 can
give a stronger signal of the centromeric region due to the repetitive
character of this region. In our hands the P53 / MPO probe is easier
to use, especially in tumor samples with poor cell morphology as one
can better distinguish a true P53 deletion from a reduced signal of P53
which possibly could lower the amount of false positive results. A second
advantage of the P53 / MPO probe combination is the possibility to
detect isochromosomes 17 very easily by FISH: An isochromosome 17q
results in a deletion of the short arm of chromosome 17 resulting in a
loss of one P53 gene signal and a gain of the long arm of chromosome
17 leading to an additional MPO gene signal. Using the two diagnostic
criteria, loss of one P53 signal and gain of one MPO signal, gives a high
sensitivity for detection of a tumor clone with an isochromosome 17q.
Issue 4
p53 (17p13) / MPO (17q22) “ISO 17q” probe hybridized to peripheral blood of a CLL
patient with a 17p- deletion (1 green and 2 red signals).
FISH PROBE EVALUATION
Every lab should establish their own cut off levels for the detection of
a P53 deletion as well as for the gain of the MPO locus in interphase
cells. In our lab, blood samples from five healthy persons served as
negative controls. For each blood sample 200 interphase nuclei were
evaluated for the determination of the diagnostic thresholds of the P53
and MPO probes. Cut off levels for a loss or gain of the P53 and MPO
gene locus were calculated as mean of false positive nuclei plus three
standard deviations, respectively.
REFERENCES
[1] Döhner H. et al. 2000, Genomic aberrations and survival in chronic
lymphocytic leukemia. N Engl J Med 343:1910-1916.
[2] Xu W. et al. 2008, Prognostic significance of ATM and TP53
deletions in Chinese patients with chronic lymphocytic leukemia.
Leuk Res 32:1071-1077.
[3] Walker BA. et al. 2010, A compendium of myeloma-associated
chromosomal copy number abnormalities and their prognostic value.
Blood 116:56-65.
[4] Haase D. et al. 2007, New insights into the prognostic impact of
the karyotype in MDS and correlation with subtypes: evidence from
a core dataset of 2124 patients. Blood 110:4385-95.
[5] Rücker FG. et al. 2012, TP53 alterations in acute myeloid leukemia
with complex karyotype correlate with specific copy number
alterations, monosomal karyotype, and dismal outcome. Blood
119:211421-21.
[6] Swerdlow SH. et al. 2008, WHO classification of Tumors of
hematopoietic and lymphiod tussue. IARC: Lyon.
[7] Cordone I. et al. 1998, p53 expression in B-cell chronic lymphocytic
leukemia : a marker of disease progression and poor prognosis. Blood
91:4342-4249.
[8] Haferlach C. et al. 2010, Toward a comprehensive prognostic
scoring system in chronic lymphocytic leukemia based on a
combination of genetic parameters. Genes Chromosomes Cancer
49:851-9.
[9] Zenz T. et al. 2012, Risk categories and refractory CLL in the era
of chemoimmunotherapy. Blood 119:4101-4107.
p53 (17p13) / MPO (17q22) “ISO 17q” probe hybridized to peripheral blood of a CLL
patient with an isochromosome 17 (1 green and 3 red signals).
[10] Gonzalez D. et al. 2011, Mutational status of the TP53 gene
as a predictor of response and survival in patients with chronic
lymphocytic leukemia: results from the LRF CLL4 trial. J Clin Oncol
29:2223-9.
[11] Pettitt AR. et al. 2012, Alemtuzumab in combination with
methylprednisolone is a highly effective induction regimen for
patients with chronic lymphocytic leukemia and deletion of TP53:
final results of the national cancer research institute CLL206 trial. J
Clin Oncol 30:1647-55.
[12] Delgado J. et al. 2012, Chronic lymphocytic leukaemia with 17p
deletion: a retrospective analysis of prognostic factors and therapy
results. Br J Haematol 157:67-74.
[13] Fink SR. et al. 2006, Loss of TP53 is due to rearrangements
involving chromosome region 17p10 approximately p12 in chronic
lymphocytic leukemia. Cancer Genet Cytogenet. 167:177-81).
To try out our P53 probes
please contact your local representative
17p13
D17S2151
D17S960
17q22
330 KB
P53
17
D17S634
MPO
400 KB
SHGC-144222
17
Ordering information
Tests
Cat#
ON p53 (17p13) / MPO (17q22) “ISO 17q”
10
KBI-10011
ON p53 (17p13) / SE 17
10
KBI-10112
ON p53 (17p13) / SE 17
20
KBI-12112
ON p53 (17p13) / ATM (11q22)
10
KBI-10114
ON p53 (17p13) / SE 17 (tissue)
10
KBI-10738
3
KREATECH NEWS
DETECTION OF NUP98 GENE REARRANGEMENTS
BY FLUORESCENT IN SITU HYBRIDIZATION
Susana Lisboa, Manuel R. Teixeira
Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
11p15
SHGC-84145
530 KB
RH75370
GAP 455 KB
Nucleoporin 98 gene (NUP98) rearrangements have been
identified in a wide range of hematologic malignancies,
including acute myeloid leukemia (AML), acute lymphoblastic
leukemia (ALL), chronic myeloid leukemia in blast crisis
(CML-bc), myelodysplastic syndrome (MDS) and bilineage/
biphenotypic leukemia [1]. So far, NUP98 has been found to
be rearranged with up to 28 different partner genes, resulting
in in-frame fusion genes [1, 2]. The clinical course of patients
with NUP98 gene rearrangements seems to be aggressive
and presents a poor outcome [1], thus being important to
recognize patients harboring such rearrangements.
Fluorescent in situ hybridization (FISH) using a dual color, break
apart probe flanking the NUP98 gene is a rapid method that allows
detection of rearrangements involving this gene, regardless of the
fusion partner. We have used the REPEAT-FREE™ (RF) POSEIDON™
NUP98 (11p15) Break Probe (cat# KBI-10311) to test for the
presence of NUP98 gene rearrangements in two AML cases with
11p15 abnormalities as detected by karyotype analysis and one
AML case, previously published by our group [3], harboring a NUP98
gene fusion. As a normal control, we used three samples obtained
from peripheral blood cell culture of normal donors. Slides were
prepared fresh from cultured cells fixed with methanol:acetic acid
and were pretreated with 2 x SSC/ 0.5% Igepal at 37 °C for 20
minutes (min). Co-denaturation was performed at 80 °C for 8 min
followed by hybridization at 37 °C in humidified chamber for 16
hours. Post- hybridization washes were done using 0.4 x SSC/ 0.3%
Igepal at 74 °C for 2 min and 2 x SSC/ 0.1% Igepal for one min, at
room temperature. DAPI was applied as a counterstain and results
were evaluated with a Zeiss Axioplan 2 fluorescence microscope.
For each sample, 100 intact non-overlapping nuclei were scored. We
have detected a normal signal pattern (two fusion signals) in all the
NUP98
D11S4525
410 KB
SHGC-79113
11
Ordering information
Tests
Cat#
ON NUP98 (11p15) Break*
10
KBI-10311
* Available soon
control samples. The two cases with 11p15 karyotype abnormalities
and the case with a known NUP98 gene rearrangement presented
abnormal signal patterns, shown by the presence of a fusion signal
and isolated green and red signals.
The use of the break apart NUP98 FISH probe allows the screening
of patients for rearrangements involving this gene, therefore making
it possible to better characterize and monitor such patients.
REFERENCES
[1] Gough SM. et al. 2011, NUP98 gene fusions and hematopoietic
malignancies: common themes and new biologic insights. Blood 118:
6247-6257.
[2] Nebral K. et al. 2005, Screening for NUP98 rearrangements in
hematopoietic malignancies by fluorescence in situ hybridization.
Haematologica 90: 746-752.
[3] Cerveira N, Correia C, Dória S, Bizarro S, Rocha P, Gomes P, Torres
L, Norton L, Borges BS, Castedo S, Teixeira M. 2003, Frequency of
NUP98-NSD1 fusion transcript in childhood acute myeloid leukaemia.
Leukemia 17: 2244-7.
RF POSEIDON NUP98 (11p15) Break Probe hybridized to AML patient sample showing a rearrangement of 11p15 involving the NUP98 gene (1 Fusion, 1 Red, 1 Green signal).
4
Issue 4
TWENTY-FOUR CHROMOSOME FISH IN HUMAN IVF EMBRYOS
REVEALS PATTERNS OF POST-ZYGOTIC CHROMOSOME
SEGREGATION AND NUCLEAR ORGANIZATION
Dimitris Ioannou, Gothami Fonseka, Eric Meershoek, Alan Thornhill, Adulmawla Abogrein, Michael Ellis and
Darren K. Griffin
University of Kent, Kreatech, Digital Scientific and London Bridge Fertility, Gynaecology and Genetics Centre.
INTRODUCTION
In the May issue of Chromosome Research this year, Dimitris
Ioannou and colleagues from Darren Griffin’s lab at the
University of Kent published a manuscript describing the use
of a 24 chromosome screen, previously described in Ioannou
et al (2011), which makes use of Kreatech fluorescence in situ
hybridization (FISH) probes, on human in vitro fertilization
(IVF) embryos (Ioannou et al 2012). Darren Griffin was in fact
involved in the first introduction of FISH as a tool in the IVF
world in the early 1990s as a means of determining sex for
preimplantation genetic diagnosis (PGD) to treat couples at
risk of transmitting sex-linked disorders such as Duchenne
Muscular Dystrophy. FISH was later used for the diagnosis of
unbalanced chromosome translocations and for screening for
aneuploidy. The latter became the infamous preimplantation
genetic screening (PGS) that courted much controversy in
both the scientific and popular press. This is because early
indications that PGS would be effective were challenged by
controlled and randomized trails that suggested that PGS
actually made IVF success rates worse. In part due to this bad
press, FISH-based technologies were replaced by microarraybased technologies for PGS.
FISH analysis can still be valuable, however in analyzing embryos
not used to establish a pregnancy, as it gives valuable information
on the accuracy of the original PGS result and an insight into very
early human development. Although it is theoretically possible
to use microarray technologies cell-by-cell on early IVF embryos,
such an approach would prove to be very costly. Thus any “followup” analysis by microarrays would be done on the whole embryo
thereby neglecting individual cell analysis and limiting any analysis
of chromosome mosaicism. FISH is a very good tool for investigating
mechanisms of both mitotic chromosome segregation errors and
chromosome position. In this regard the message is “the more
chromosomes analysed the better” with all 24 chromosomes being
optimal.
TABLE 1 THE PROBES USED AND THEIR LOCI IN EACH OF THE MULTI-COLOUR PROBE MIXES
FLUOROCHROME
LAYER A:
CENTROMERICPROBES
LAYER B:
LAYER C:
LAYER D: UNIQUE
CENTROMERIC PROBES CENTROMERIC PROBES SEQUENCE PROBES
PlatinumBright™ 405
Dark blue
SE7 (7p11-q11)
SE11 (11p11-q11)
SE18 (18p11-q11)
CD37 (19q13)
PlatinumBright ™ 415
Light blue(aqua)
SE1 (1q12)
SE9 (9q12)
SE16 (16p11-q11)
PDGFRB (5q33)
PlatinumBright ™ 495
Green
SE6 (6p11-q11)
SE20 (20p11-q11)
SE2 (2p11-q11)
DSCR (21q22)
PlatinumBright ™ 547
Light red/orange
SE8 (8p11-q11)
SE12 (12p11-q11)
SEX (Xp11-q11)
BCR (22q11)
PlatinumBright ™ 590
Dark red
SE3 (3p11-q11)
SE10 (10p11-q11)
SEY (Yp11-q11)
RB (13q14)
PlatinumBright ™ 647
Far red
SE4 (4p11-q11)
SE17 (17p11-q11)
SE15 (15p11-q11)
IGH (14q32)
The fluorescent dyes with which they were labelled and the order in which they were hybridised is given (A, B, C, then D). Probes for chromosomes 1 and 9
were for highly repetitive heterochromatic regions below the centromere. SE satellite enumeration —the Kreatech trade name
5
KREATECH NEWS
As mentioned, the authors (Ioannou et al. 2011) recently described
the development of a 24 chromosome assay involving a series
of six Kreatech fluorochrome-labeled probes and four rounds of
hybridization. As proof of principle, they demonstrated that it could
be used on lymphocytes, sperm and IVF embryo nuclei. Here, they
demonstrate further that this approach has a dual applicability for
the determination of aneuploidy and nuclear position of mostly
centromeric loci on every chromosome in human IVF embryos at
around days 5–6 of development. The main aims of the study were
firstly to confirm or refute former studies that indicated mitotic
non-disjunction was not the mechanism leading to post-zygotic
aneuploidy, rather is was independent chromosome loss and gain.
Second to ask which chromosomes are more likely to undergo gain
or loss in preimplantation embryos, and finally to assay the nuclear
positions of the loci recognized by the Kreatech probes.
MATERIALS AND METHODS
Material used in this study was mostly “follow up” aneuploid PGS
cases, the collaborating clinics were the London Bridge Fertility
Centre and the Lister Fertility Clinic. The Ioannou et al (2011) paper
described a protocol that involved six Kreatech fluorochromes,
namely PlatinumBright™405 (dark blue), 415 (light blue/aqua), 495
(green), 547 (light red/orange), 590 (dark red), 647 (far red) plus the
DAPI counterstain in a four-stage probing and re-probing strategy.
All probes for this protocol were synthesized by Kreatech Diagnostics
using the Universal Linkage System (ULS™) for labeling, including
six unique sequence targets for chromosomes 5, 13, 14, 19, 21 and
22 and the remaining 18 centromeric probes (See table 1).
Human IVF embryo nuclei were fixed to slides by standard protocols.
Then slides were washed in PBS for 2 minutes (min) and dehydrated
and dried using an ethanol series. Pepsin treatment removed
excess protein (1 mg/ml pepsin in 0.01 M HCl, 20 min at 37 °C),
then the slides were rinsed in distilled water and PBS, followed by a
paraformaldehyde (1% in PBS) fix at 4 °C for 10 min, then another
PBS and distilled water wash and an ethanol dehydration and dry.
The four probe combinations described by Ioannou et al. 2011 were
dissolved in hybridization mix of Kreatech. It was important to predenature the probes at 73 °C for 10 min before application on the
slide. Then co-denaturation of probe and chromosomes at 75 °C for 90
seconds (s) in a “Thermobrite-StatSpin” went ahead of hybridization
at 37 °C. The hybridization period for the first three rounds of
hybridization (centromeric probes) was for 30 min, whereas for the
final round, it was overnight. Post-hybridization washes were for 1
min 30 s in 0.7× SSC, 0.3%Tween 20 at 72 °C followed by a 2 min
in 2×SSC at room temperature. Slides were mounted in Vectashield
containing 0.1 ng/μl of DAPI (Vector labs) before microscopy and
image analysis. After analysis and image capture, slides were washed
in 2×SSC at room temperature to remove the coverslip and then
washed for 30 s in distilled water (72 °C) to remove the bound probe.
An ethanol series preceded air-drying before continuation to the next
round of hybridization. The protocol was the same for the second,
third and final rounds with the following exceptions: The overnight
hybridization time for the final round (previously mentioned), pepsin
and paraformaldehyde treatment were only required for the first
round; the post-hybridization wash time was reduced with every round
from 90 s (first round of hybridization) to 50–60 s (second round)
to 30 s (third and final rounds). Microscopy analysis was performed
on an Olympus BX-61 epifluorescence microscope equipped with
a cooled CCD camera (by Digital Scientific—Hamamatsu Orca-ER
C4742-80) and using the appropriate filters. To enable analysis of
the fluorochromes for image acquisition two communicating filter
wheels (Digital Scientific UK) with the appropriate filters were used.
The recommended filters by the probe manufacturer can be found
here: http://www.kreatech.com/rest/customer-service-support/
technical-support/fluorophores-and-filter-recommendation.html and
the image capture system was SmartCapture (Digital Scientific UK).
Fig.1Blastomere nucleus after four rounds of hybridisation, scales bars=10μm. a DAPI only, showing retention of nuclear structure b Same nucleus with final probe set signals shown—
chromosome 19 in blue, chromosome 5 in aqua,chromosome 21 in green, chromosome 22 in yellow, chromosome 13 in red, chromosome 14—far red fluorochrome pseudocoloured
purple. c Same nucleus with probes from the other three rounds super imposed in Adobe Photoshop—note position and copy number of chromosomes 5, 13, 14, 19, 21and 22 can still be
observed.
6
Issue 4
RESULTS AND DISCUSSION
Analysis of 17 embryos by this newly developed approach gave strong
signals for all chromosomes; it revealed chromosome copy number
for each human chromosome per nucleus for each embryo and the
nuclear positions of all the loci that were probed. As all embryos were
‘follow-up” (and most had a prior abnormal PGS result) the expected
high levels of chromosome abnormalities were seen and no single
nucleus displayed a normal chromosome complement. Moreover
all showed evidence of mosaicism. There were certain patterns
that emerged however. For instance chromosome loss appeared
more common than both chromosome gain and apparent mitotic
nondisjunction (thus confirmation of the first initial hypothesis).
Next, in terms of chromosome position, the centromeric probes
tended preferentially to occupy the nuclear centre. Where we had
a prior day 3 biopsy PGS result, it was confirmed, at least partly, by
24 colour FISH in the majority of instances. In conclusion, therefore,
the authors presented a new approach for assessing aneuploidy and
chromosome position in human IVF embryo nuclei that retains the
advantages of FISH while circumventing its former limitations (i.e. it
could previously only assay a small number of chromosomes).
The great value is its application for the providing insight into the
cytogenetics of early human development. Some of the advantages
over microarray array-based approaches lie in the fact that it is, in
comparison to microarrays, inexpensive, and it gives a cell by cell
analysis, which, while possible by microarrays, is practically and
financially not feasible given the numbers of nuclei that need to
be analysed. The added benefit is that the approach provides extra
insight into the role of chromosome position (nuclear organization)
in early human development.
REFERENCES
[1] Ioannou D, Fonseka KGL, Meershoek EJ, Thornhill AR, Abogrein
A, Ellis M, Griffin DK, 2012, Twenty-four chromosome FISH in
human IVF embryos reveals patterns of postzygotic chromosome
segregation and nuclear organisation, Chromosome Research
20: 447-60.
[2] Ioannou D, Meershoek EJ, Thornhill AR, Ellis M, Griffin DK, 2011,
Multicolour interphase cytogenetics: 24 chromosome probes,
6 colours, 4 layers. Molecular and Cellular Probes 25:199–
205.
PRODUCT AND ORDERING INFORMATION
Product
Description
Tests Cat#
PreimpScreen PolB (13,16,18,21,22) Five-color FISH-mix consisting of DNA probes specific for chromosomes 13, 16, 18, 21, and 22
20
KBI-40050
PreimpScreen Blas (13,18,21,X,Y)
Five-color FISH-mix consisting of DNA probes specific for chromosomes 13, 18, 21, X, and Y
20
KBI-40051
MultiStar 24 FISH
FISH probe panel for visualizing all 24 chromosomes (including the four panels KBI-40061,
KBI-40062, KBI-40063, and KBI-40064)
10
KBI-40060
MultiStar FISH Panel 1
FISH panel of centromeric probes for chromosomes 1, 3, 4, 6, 7, and 8
10
KBI-40061
MultiStar FISH Panel 2
FISH panel of centromeric probes for chromosomes 9, 10, 11, 12, 17, and 20
10
KBI-40062
MultiStar FISH Panel 3
FISH panel of centromeric probes for chromosomes 2, 15, 16, 18, X, and Y
10
KBI-40063
MultiStar FISH Panel 4
FISH panel of unique sequence probes for chromosomes 5, 13, 14, 19, 21, and 22
10
KBI-40064
7
KREATECH NEWS
REPEAT-FREE™ POSEIDON™ BCR/ABL1 t(9;22)
PRODUCT RANGE
The Philadelphia chromosome (Ph) is an abnormal chromosome 22 (der22) involved in a translocation with chromosome 9.
The presence of the Ph chromosome is characteristic of Chronic Myelogenous Leukemia (CML), found in 95% of the cases.
However, the presence of this characteristic t(9;22) BCR-ABL1 reciprocal chromosomal translocation is not solely specific for
CML as it is also shown in about 25-30% of adult Acute Lymphoblastic Leukemia (ALL) cases and 2-10% of childhood ALL and
occasionally in Acute Myelogenous Leukemia (AML).
In the formation of the Ph translocation, the c-abl oncogene 1
(ABL1) on chromosome 9 and the breakpoint cluster region (BCR)
on chromosome 22 fuse, generating two fusion genes: BCR-ABL1
on the Ph chromosome 22 and ABL1-BCR on the chromosome 9
(figure 1). The chimeric BCR/ABL1 fusion gene encodes a deregulated
constitutively activated protein tyrosine kinase with profound effects
on cell cycle, adhesion, and apoptosis. Understanding this process has
led to the development of the drug imatinib mesylate (Gleevec™), a
tyrosine kinase inhibitor.
BCR-ABL1
BCR 22q11
der(22)
22
9
ABL 9q34
ABL1-BCR
A
In BCR there are three breakpoint regions, the major breakpoint
cluster region (M-BCR), between exons 12 and 16 leading to the
creation of the oncogene p210 BCR-ABL1 and the minor breakpoint
cluster region (m-BCR), which maps the first intron of BCR and
leads to the creation of the oncogene p185 BCR-ABL1. In CML,
the breakpoint in BCR is mostly in the M-BCR located. Breaks in
the m-BCR are most frequently associated with Ph-positive ALL.
The micro BCR is very rare and only described in a few cases
Fluorescence in situ hybridization (FISH) is used to confirm the
presence of a BCR-ABL1 gene in the initial diagnosis of CML or
Ph-positive ALL or AML. FISH has the advantage that it may detect
cryptic BCR-ABL1 rearrangements not picked up by karyotyping and
also possible deletions in the derivative 9 (der (9)) chromosome. FISH
is also a valuable tool in determining the percentage patient's blood
or bone marrow cells harboring the Ph chromosome and to monitor
response to treatment and disease recurrence.
der(9)
Figure1: BCR/ABL1 t(9;22) Dual-Fusion Assay
The REPEAT-FREE POSEIDON portfolio contains five different designs of the BCR/ABL1 t(9;22) probe each providing different details.
BCR/ABL t(9;22) Dual-Color, Dual-Fusion
BCR/ABL t(9;22) Triple-Color, Dual-Fusion
BCR/ABL t(9;22) Dual-Color, Single-Fusion
8
BCR/ABL t(9;22) Dual-Color, Single-Fusion,
Extra Signal
Mm-BCR/ABL t(9;22) Dual-Color, Single-Fusion,
Extra Signal
Issue 4
BCR/ABL t(9;22) Dual-Color, Dual-Fusion - Cat# KBI-10005 is designed to detect the t(9;22)(q34;q11) reciprocal translocation.
The der(9) and the der(22), the Ph chromosome will be observed as 2 yellow (red/green) fusion signals. This design will also detect cryptic
insertions of ABL1 into the BCR region and therefore diagnosed as Ph-negative. A cryptic insertion of ABL1 in the BCR gene region will show
a yellow (red/green) fusion signal and an additional small remaining red signal at the der(9).
Normal Cell
t(9;22) positive
Cryptic insertion 9q34 to 22q11
D22S940
IGLC1
340 KB
SHGC-147754
ASS
340 KB
BCR
ABL
1000 KB
1000 KB
22q11
NUP214
9q34
D9S1991
IGLL1
SHGC-107450
9
22
BCR/ABL t(9;22) Triple-Color, Dual-Fusion - Cat# KBI-10006 is designed from the same regions as the Dual-Color, Dual-Fusion probe
but with the proximal BCR region labeled in blue. The probe is designed to detect both rearranged chromosomes. The der(22), which will be
observed as purple (red/blue) fusion signal and der(9) which will show a yellow (red/green) fusion signal. Deletions of 9q or 22q can also be
observed with this design. A deletion at the proximal 5’ site of ABL1 (9q34) will lead to lack of a red signal and a single green signal for 3’
distal sequences of the BCR gene region, deletions at the 3’ site of the BCR (22q11) gene will lead to lack of a green signal.
Normal Cell
t(9;22) positive
t(9;22) positive with del(22q11)
t(9;22) positive with del(9q34)
D22S940
IGLC1
340 KB
SHGC-147754
ASS
340 KB
BCR
ABL
1000 KB
1000 KB
22q11
NUP214
9q34
9
D9S1991
IGLL1
SHGC-107450
22
9
KREATECH NEWS
BCR/ABL t(9;22,) Dual-Color, Single-Fusion, Extra Signal - Cat # KBI-10008 is designed to detect the t(9;22)(q34;q11) reciprocal
translocation. By adding an additional region proximal to the breakpoints on chromosome 9q34, this probe will provide a smaller extra red
signal at the der(9).The der(22) is visualized by a yellow (red/green) fusion signal.
IGLC1
SHGC-147754
D22S940
ASS
340 KB
22q11.2
340 KB
ABL
1000 KB
Normal Cell
t(9;22) positive
22
BCR
NUP214
9q34
IGLL1
D9S1991
9
SHGC-107450
BCR/ABL t(9;22) Dual-Color, Single-Fusion - Cat# KBI-10009 is a simple design solely for the detection of the der(22), visible as one
yellow (red/green) fusion signal while the der(9) will show no signal.
IGLC1
SHGC-147754
D22S940
ASS
22q11.2
340 KB
ABL
1000 KB
Normal Cell
t(9;22) positive
22
BCR
NUP214
9q34
IGLL1
D9S1991
9
SHGC-107450
Mm-BCR/ABL t(9;22) Dual-Color, Single-Fusion, Extra Signal - Cat# KBI-10013 is designed to detect the der(22) with a break in
the major breakpoint region (M-BCR) by one yellow (red/green) fusion signal. A smaller extra red signal will identify the der(9). Breaks in the
minor breakpoint region (m-BCR) will be identified by two yellow (red/green) fusion signals. No smaller extra red signal should be visible.
Normal Cell
t(9;22) BCR/ABL with m-BCR
t(9;22) BCR/ABL with M-BCR
1
IGLC1
m-BCR
D22S940
SHGC-147754
ASS
22q11.2
420 KB
480 KB
ABL
22
620 KB
NUP214
9q34
9
10
D9S1991
HUMUT7039
BCR
IGLL1
SHGC-107450
2
3
4
6
5
7
8
9 10
11 12
13 14
15
16
b1
b2
b3
b4
b5
M-BCR
HUMUT7039
17
19
21
23
18
20
22
Issue 4
REFERENCES
[1] Dewald et al., 1998, Blood 91: 3357-3365
[2] Huntly et al., 2003, Blood 102: 1160-1168
[3] Kolomietz et al., 2001, Blood 97: 3581-3588
[4] Mian et al., 2012, Haematol. 97: 251-257
[5] Sharma et al., 2010, Ann Hematol., 89: 241-7
[6] Tkachuk et al., 1990, Science 250: 559-562
To try our BCR/ABL probes
please contact your local representative.
ORDERING INFORMATION
Probe name
Tests
Cat#
BCR/ABL t(9;22) Dual-Color, Dual-Fusion
10
20
KBI-10005
KBI-12005
BCR/ABL t(9;22) Triple-Color, Dual-Fusion
10
KBI-10006
BCR/ABL t(9;22) Dual-Color, Single-Fusion, Extra Signal
10
KBI-10008
BCR/ABL t(9;22) Dual-Color, Single-Fusion
10
KBI-10009
Mm-BCR/ABL t(9;22) Dual-Color, Single-Fusion, Extra Signal
10
KBI-10013
11
KREATECH NEWS
Development and validation of a REPEAT-FREE™ DNA-FISH
assay to detect FGFR1 gene locus amplification
Dimitri Pappaioannou1,3, Saskia Schoenmakers1, Birgit Rupp2, Isabell Dolznig2, Richard Ackbar2, Marcus Otte2,
Sandor Snoeijers1
1 KREATECH Diagnostics, Vlierweg 20, 1032 LG, The Netherlands, 2 ORIDIS Biomarkers GmbH, Stiftingtalstrasse 5, A-8010 Graz, Austria,
3 Author for correspondence ([email protected])
* This article is edited from a paper that has been presented by the authors during the ADAPT (Accelerating Development & Advancing Personalized Therapy) meeting, September 19-21, Washington DC.
INTRODUCTION
METHOD
Amplification of the fibroblast growth
factor receptor type 1 gene (FGFR1) has
been observed in numerous cancer types
including Squamous Cell Carcinoma (SCC)
Lung Cancer and Breast Cancer (BC)[1].
With the development of new therapeutic
strategies, FGFR1 amplification might act
as a valuable biomarker for R&D and can
provide an attractive approach for clinical
stratification[2].
PHASE 1
Design selection
A series of probe designs specific for the
FGFR1 gene locus (8p11) was constructed
In Silico.
Criteria for Probe design:
• REPEAT-FREE™ design (no need for Cot-1
DNA) / In Silico Design
• Free of segmental duplications in genomic
regions covered
• Optimize size of gene locus probe regions
for desired signal intensity
• Balance between signal strength of gene
specific region probe and control probe
Here we describe the development process of
a REPEAT-FREE™ (RF) DNA-FISH assay tested
for the detection of FGFR1 amplification.
The process was divided into four phases: 1)
design selection and assay development, 2)
candidate selection, 3) batch testing of final
design and, 4) validation on a cohort of 100
FFPE patient samples.
Assay Development
Candidate probes were tested on human
cell lines (verified for FGFR1 amplification
by real-time PCR). Using the REPEAT-
FREE™-FGFR1/SE8 probe, FGFR1 gene locus
amplification was considered positive with
an FGFR/SE8 signal ratio ≥ 2.0. Polysomy
of chromosome 8 was identified by an SE8/
nucleus ratio ≥ 2.0.
PHASE 2
Candidate Selection
From the initial probe designs, 2 designs were
selected for further development. The probes
were compared using various hybridization
protocols and results between KREATECH
and ORIDIS labs were compared as an
indication of reproducibility. This resulted in
selection ofthe final probe design (fig. 2).
PHASE 3
Batch Testing
Three batches of the final design were
produced and tested for batch to batch
TABLE 1. SCORING SCHEME FOR FGFR1 GENE PROBE COMPARISON ON TMA SECTIONS RECORDED FOR EACH PROBE BATCH
12
SCORE
SAMPLE EVALUABILLITY
SIGNAL INTENSITY
(NUMBER OF CELLS)
BACKGROUND SIGNAL
INTENSITY
PATTERN EVALUATION
1
> 40
Excellent
None to minimal
Correct FGFR1 pattern
2
≤ 40
Good
Acceptable
Correct FGFR1 pattern
3
≤ 25
Weak
Disturbing
Correct FGFR1 pattern
4
≤ 10
Lack of signals
Hampers analysis
Wrong FGFR1 pattern
Issue 4
variability on a TMA (core Ø = 0.6mm)
according to criteria described in Table 1.
PHASE 4
Validation on patient cohort
Hybridization efficacy was tested on FFPE
samples from 100 SCC NSCLC patients
from 4 different sites in Europe and the US.
Efficacy was determined by evaluation of
signal intensity, background intensity and
evaluability of sample and pattern. Repeated
hybridizations were carried out to investigate
the robustness and reproducibility of the
assay. Evaluation was conducted by three
independent observers. In addition, the
assay was further tested on a cohort of BC
samples. This study was approved by the
local ethical review board of the Medical
University of Graz.
RESULTS
PHASES 1 & 2
Design selection, Assay Development &
Candidate Selection
The final design of the REPEAT-FREE™
FGFR1 amplification probe is shown in
figure 2.
RH46977
8p11
SE8
FGFR1
540KB
D8S414
8
Fig. 2. Graphic display of the final design of the REPEATFREE™ FGFR1 amplification probe (not to scale).
A] SCC NSCLC
C] unamplified
B] BC
D] amplified
E] polysomy
Fig. 3. Panels A] and B]: FGFR1 (8p11) / SE 8 probe hybridized to SCC NSCLC and BC tissue. Panels C],
D] and E]: examples of FGFR1 copy numbers observed in tissue samples
PHASE 3
Batch Testing
Three production batches of FGFR1 probe
were compared side by side and evaluated
by 3 independent observers (see table 1
for evaluation criteria). Although variations
occurred between observers, no variability
between batches was observed (see table
2). In total 16 patient samples (8 NSCLC and
8 BC) and 12 cell lines were analyzed. FGFR1
gene status was known for all samples and
this was confirmed for all three batches by
all three observers.
PHASE 4
Validation on Patient Cohort
Finally, FGFR1 FISH was validated on TMAs
containing a cohort of NSCLC samples
(n = 100), selected for FGFR1 gene locus
amplification, polysomy of chromosome
8, normal gene status and tissues lacking
evaluable signal. Amplification of FGFR1,
polysomy and normal gene status (fig. 3)
were correctly identified for all samples.
Furthermore evaluation was possible in 5/20
samples previously lacking detectable FISH
signal with the optimized FGFR1 assay.
CONCLUSIONS
The REPEAT-FREE™-FGFR1 amplification
assay allows clear detection of amplification
and allows discrimination between
amplification and polysomy, with high
degrees of sensitivity, specificity and
hybridization efficacy. The REPEAT-FREE™FGFR1 amplification assay fulfills all
criteria for a clinical research tool aimed at
patient stratification. The described assay
development process is highly effective for
probe design selection and testing of assay
robustness and reproducibility and can be
generally applied in the development of
further FISH assays.
TABLE 2. CONTINGENCY TABLE FOR EVALUATION OF INTENSITY
COMPARED AT INDIVIDUAL SAMPLE LEVEL FOR ALLE THREE BATCHES
OBSERVER 1
OBSERVER 1
OBSERVER 1
Batch 1
Score: 1
Score: 2
Score: 1
Batch 2
Score: 1
Score: 2
Score: 1
Batch 3
Score: 1
Score: 2
Score: 1
REFERENCES
[1] Weiss et al., Sci. Transl. Med. 2(62):
62ra93 (2010)
[2] Brooks et al., Clin. Can. Res. 18(7):
1855-62 (2012)
13
KREATECH NEWS
®
THERMOBRITE ELITE
AUTOMATED LABORATORY ASSISTANT
AUTOMATED SAMPLE PREPARATION WITH REPEAT-FREETM
POSEIDONTM FISH PROBES
The ThermoBrite Elite provides total automation for the pre- and
post-hybridization steps in FISH testing and provides on-board
denaturation and hybridization.
The ThermoBrite Elite can process up to 12 slides per run.
You can also denature and hybridize slides on your ThermoBrite
slide denaturation and hybridization system, in order to have the
ThermoBrite Elite system available for additional runs.
Perfect Solution for Pathology
The pre-installed validated KREATECH FISH protocols allow for easy
selection of the correct program for your solid tumor, bone marrow
and blood samples. Just load your slides and walk away. Minimal
hands-on time frees time for other important projects. Adding the
probe and placing the coverslip are the only manual steps. After
denaturation and hybridization, the system will complete the posthybridization steps. Just add the DAPI / antifade and coverslip and
you are ready to image your slides.
Interactive easy-to-use software
The intuitive easy-to-use software allows you to run standard
validated KREATECH protocols for blood, bone marrow and solid
tumor FFPE samples. The system allows input of 10 different
reagents. It has 3 independent waste ports. You can also control
the functions in each of the 3 chambers (4 slides per chamber)
allowing for small batches or running of 12 slides at one time.
Features
•
•
•
•
•
14
Automatedd fluidic system
Accurate temperature control to + 1°C
Controlledd agitation and mixing
User-friendly
dly Graphical User Interface
Validated KREATECH protocols
pre-installed
Key Benefits
• Improves consistency and
reproducibility
• Reduces hands-on time
• Flexible and easy-to-use
• Saves time and money
Applications in FISH
• Pathology (Solid tumor/ FFPE)
• Hematology (Blood/bone marrow)
• Cytology (Fluids)
Issue 4
NOTES
15
KREATECH NEWS
Events
CONTACT
The following events will be attended by members of KREATECH Diagnostics in
the coming months. Please come and talk to us if you are at any of these events:
16 Nov
Landelijke Analistendag Genoom Diagnostiek
Media Plaza, Utrecht, The Netherlands
19 Nov
–
23 Nov
Carrefour Pathologie
INTERNATIONAL
KREATECH Diagnostics
Vlierweg 20
1032 LG Amsterdam
The Netherlands
Phone: +31 (0)20 691 9181
Fax: +31 (0)20 630 4247
E-mail: [email protected]
Paris, France
BENELUX
2013
7 Jan
Satellite Meeting:
New techniques in Molecular Pathology
Utrecht, The Netherlands
8 Jan
–
9 Jan
Winter Meeting
Joint Meeting with the Dutch Pathological Society
Utrecht, The Netherlands
18 Jan
–
20 Jan
15. Bamberger Morphologietage 2013
Bamberg, Germany
27 Mar
–
29 Mar
Société Française d'Hématologie (SFH) Meeting
CNIT Paris - La Défense, France
KREATECH Diagnostics
Vlierweg 20
1032 LG Amsterdam
The Netherlands
Phone: +31 (0)6 4850 0107
Fax: +31 (0)35 656 4826
E-mail: [email protected]
France
KREATECH Diagnostics
20 Avenue de la Paix
67080 Strasbourg Cedex
France
Phone: +33 (0)1 4372 0079
Fax: +33 (0)1 4348 8244
E-mail: [email protected]
Germany
KREATECH Diagnostics
Vlierweg 20
1032 LG Amsterdam
The Netherlands
Phone: +49 (0)223 3713 5979
Fax: +31 (0)20 630 4247
E-mail: [email protected]
For more information on events and for more KREATECH news
please scan the QR code below or go to
http://www.kreatech.com/news-media/events.html
United Kingdom
KREATECH Diagnostic
52 New Town, Uckfield
East Sussex, TN22 5DE
United Kingdom
Phone: +44 (0)208 350 5430
Fax: +44 (0)208 711 3132
E-mail: [email protected]
www.kreatech.com
Disclaimer Marketing Materials:
The content of this brochure is explicitly not meant for the North American region. If you are a resident in this region
please contact the North American sales office to obtain the appropriate product information for your country of residence.
For more information please visit our website: www.kreatech.com.
16
©2012 KREATECH Diagnostics
Published October 2012