European Human Genetics Conference 2007 June 16 – 19, 2007 ...

Cancer genetics
Po04. Cancer genetics
P0490. QMPSF : A novel method for detection of 1p19q deletions
in gliomas
S. Monnot 1 , D. Fontaine 2 , F. Vandenbos 3 , P. Paquis 2 , J. Michiels 3 , J. Lambert 1 ,
V. Paquis-Flucklinger 1,4 ;
1 Department of Medical Genetics, Nice, France, 2 Department of Neurosurgery,
Nice, France, 3 Department of Anatomopathology, Nice, France, 4 UMR CNRS
6543, Medicine School, Nice, France.
Gliomas are the most common primary cerebral malignancies. Deletions
of 1p and 19q chromosomes have shown to be predictors of
chemotherapeutic response and better survival in oligodendrogliomas.
Different techniques are available for the detection of these alterations
including LOH, FISH and CGH. Despite good concordance exists in
terms of sensitivity and specificity between these methods, all have
specific limitations. The aim of our study was to describe a reliable
novel technique for the detection of 1p/19q deletions in gliomas. For
each chromosome arm (1p and 19q), we devised a multiplex PCR assay
of fluorescent fragments corresponding to exons, which belong to
genes located in the minimal deleted region. A control gene, located
on chromosome 1q or 19p, is simultaneously amplified in each assay.
PCR products are analysed on an automated sequencer and electropherograms
generated from control and tumor samples are superimposed.
We have searched for 1p/19q deletions by LOH and QMPSF
(Quantitative Multiplex PCR of Short Fluorescent fragments) in a series
of 50 patients with a glioma. We found that QMPSF, which does
not require constitutional DNA, is a simple, rapid and reliable method
to detect 1p/19q deletions. There was a good concordance with LOH
data in (88% for 1p deletion and in 83% for 19q deletion). Furthermore,
we show that QMPSF has a higher sensitivity than LOH and allows the
detection of 1p/19q duplications.
In conclusion, QMPSF can be routinely used in diagnosis laboratories
for the detection of 1p/19q rearrangements in glial tumors.
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P0491. Amplification of ABL1 gene without BCR/ABL1 fusion in
two children with acute lymphoblastic leukemia
S. Berker Karauzum 1 , Z. Cetin 1 , S. Yakut 1 , G. Tezcan 2 , T. Tulumen 3 , V. Hazar 2 ,
T. Sipahi 3 , G. Luleci 1 ;
1 Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz
University, ANTALYA, Turkey, 2 Department of Pediatric Haematology and Oncology,
Faculty of Medicine, Akdeniz University, ANTALYA, Turkey, 3 Department
of Pediatric Haematology, Faculty of Medicine, Süleyman Demirel University,
Isparta, Turkey.
The ABL1 proto-oncogene, located on chromosome band 9q34 is the
known translocation partner of the BCR gene on chromosome band
22q11, giving rise to t(9;22)(q34;q11). This is the most common chromosomal
abnormality in Chronic Myeloid Leukemia (CML) and adult
Acute Lymphoblastic Leukemia (ALL) patients. Otherwise, frequency
of this translocation is only 3-5 % in childhood ALL patients. Amplification
of ABL1 gene is a rare event, that only 7 cases reported in the
literature.
In this study, conventional cytogenetics (CC) and Flourescence In Situ
Hybridization (FISH) studies were performed on two ALL patients. In
the first case, which is a seven-year-old girl, amplification of ABL1
gene, without BCR/ABL1 fusion, was observed in 27% interphase nuclei
in FISH analysis while metaphases were not found in CC. In the
second case which is a ten year old boy, translocation of t(9;15) was
detected in CC and interphase cytogenetic analysis by FISH showed
the presence of the 10% ABL1 gene amplification without t(9;22) translocation.
Our results indicate that, amplification of ABL1 gene without BCR/
ABL1 fusion can be shown by FISH methods. This amplification might
play role in leukomogenesis of pediatric ALL and may be used for disease
monitoring
P0492. Oligo array CGH on 1, 5 and 10 year old FFPE breast
cancer samples
A. De Witte 1 , I. Bukholm 2 , V. Kristensen 3 , A. Borresen-Dale 3 , E. Klok 4 , J. Collins
1 ;
1 Agilent Technologies, Santa Clara, CA, United States, 2 Department of Surgery,
Akershus University Hospital, Nordbyhagen, Norway, 3 Department of Genetics,
Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Cen-
ter, Montebello and the Faculty of Medicine University of Oslo, Oslo, Norway,
4 Kreatech Biotechnology B.V., Amsterdam, The Netherlands.
Microarray-based comparative genomic hybridization (array CGH) has
become a powerful technique for studying DNA sequence copy number
changes in breast tumors. The ultimate goal of these efforts is
the identification of genomic markers that correlate with prognosis and
prediction of clinical outcome. For many of these retrospective studies,
formalin-fixed, paraffin-embedded (FFPE) tissues are the only samples
available. DNA extracted from FFPE tissue can present challenges as
it is often degraded and damaged. In this study, we extracted DNA
from 24 FFPE breast tumor samples (mostly ductal invasive cancers):
ten 1 year, eight 5 year, and six 10 year old. Traditional enzymatic
labeling of degraded DNA samples can decrease the DNA fragment
length still further and moreover can result in the introduction of enzymatic
biases. Therefore, we chose a non-enzymatic labeling method
- the Universal Linkage System (ULS, Kreatech Biotechnology).
Analysis of these samples on Agilent Human CGH arrays showed that
the average probe-to-probe log ratio noise (DLRSD) was 0.33 for the
1 and 5 year old FFPE samples, indicating that high quality, reliable
biological data were obtained. While the 10 year old FFPE samples
showed higher average DLRSD values (0.53), the 60 mer probes
still enabled detection of aberrations with a high level of confidence.
Previously known aberrations associated with breast cancer, such as
HER-2 (human epithelial receptor 2), PIK3CA (phosphatidylinositol 3kinase)
and CCND1 (cyclin D1) were detected in several samples. We
conclude that the method described here is well suited for analysis of
archival pathology specimens for biomarker discovery.
P0493. Cytogenetic findings in a group of patients with acute
lymphoblastic leukemia
H. G. Karabulut, B. Saglam, T. Tuncalı, N. Y. Kutlay, H. I. Ruhi, K. Yararbas, I.
Akalın, F. Sadeghi, A. Vicdan, A. Tükün;
Ankara University, Ankara, Turkey.
Cytogenetic analysis in bone marrow samples of acute lymphoblastic
leukemia (ALL) patients have both pathophysiologic and prognostic
significance. In this retrospective study, we present the results of cytogenetic
analysis of 348 ALL patients (243 children and 105 adults).
Cytogenetic abnormalities were found to be more frequent in adults
than in children, 23,8 % and 13,6 %, respectively. Structural abnormalities
were more frequent than numerical abnormalities in childhood
ALL (61.5 % vs 38.5 %) while numerical abnormalities were observed
more frequently than structural abnormalities in adults (56 % vs 44 %).
Overall, the most frequent cytogenetic abnormality in both childhood
and adult ALL patients was t(9;22)(q34;q11) with a frequency of 12,3
% and 8,2 %, respectively. Monosomy 22 and trisomy 21 was the most
frequent second and third cytogenetic abnormality in childhood ALL,
followed by -7 and +8 at fourth place. On the other hand, - 21 was the
most frequent second cytogenetic abnormality in adults, followed by
-13, -15 and -20 at third place each with equal frequencies.
P0494. Cytogenetics in AML: results of 589 patients
N. Yurur-Kutlay, T. Tuncali, H. G. Karabulut, F. Sadeghi, B. Saglam, I. Akalın,
K. Yararbas, H. Ilgın Ruhi, A. Vicdan, A. Tukun;
Ankara University Faculty of Medicine Department of Medical Genetics, Ankara,
Turkey.
The role of cytogenetics in diagnosis and follow-up studies of acute
myeloid leukemia (AML) is now widely recognized. However in contrast
to chronic myelogenous leukemia (CML), the cytogenetics of AML
is much more complex. More than 200 different structural and numerical
changes have been found to be recurrent chromosome aberration
in AML.
In this report, cytogenetic findings of 589 AML patients are presented.
Novel translocations, deletions and numerical abnormalities
were found besides of previously defined AML aberrations such as
t(15;17), t(16;16), t(8;21), del11q, monosomy 7, and trisomy 8. Two
complex, thirteen simple translocations, one inversion and three unbalance
changes t(2;19;10)(q21;q13;p11), t(15;17;21)(q24;q23;q21)
and t(1;11)(q32.1;q13.9), t(2;5)(q24.2;p13.3) t(2;21)(q11.2;q11.2)
t(3;5)(q21;q33), t(3;18)(p13;q23) t(3;18)(q21;q23) t(5;22)(p13:p11)
t(8;19) (q22;q13) t(9;17)(p11;p13), t(16;17)(p13;q21), t(7;17)(q11;p13)
t(8;18)(p23;q21.1), t(12;18)(p11;q11) inv (13)(p12q32) del(2)(q34),
del(2)(q37) dup(2)(q35;qter) respectively, were not reported before
as AML related translocations. Some of these breakpoints were previ-
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