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Blood, 118(26), 6760–6768
December, 2011

Impact of additional cytogenetic aberrations at diagnosis on prognosisof CML: long-term observation of 1151 patients from the randomizedCML Study IV.

Alice Fabarius, Armin Leitner, Andreas Hochhaus, Martin C Müller, Benjamin Hanfstein, Claudia Haferlach, Gudrun Göhring, Brigitte Schlegelberger, Martine Jotterand, Andreas Reiter, Susanne Jung-Munkwitz, Ulrike Proetel, Juliana Schwaab, Wolf-Karsten Hofmann, Jörg Schubert, Hermann Einsele, Anthony D Ho, Christiane Falge, Lothar Kanz, Andreas Neubauer, Michael Kneba, Frank Stegelmann, Michael Pfreundschuh, Cornelius F Waller, Karsten Spiekermann, Gabriela M Baerlocher, Michael Lauseker, Markus Pfirrmann, Joerg Hasford, Susanne Saussele, Rüdiger Hehlmann, für Klinische Krebsforschung (SAKK), Schweizerische Arbeitsg, the German CML Study Group,

The prognostic relevance of additional cytogenetic findings at diagnosis of chronic myeloid leukemia (CML) is unclear. The impact of additional cytogenetic findings at diagnosis on time to complete cytogenetic (CCR) and major molecular remission (MMR) and progression-free (PFS) and overall survival (OS) was analyzed using data from 1151 Philadelphia chromosome-positive (Ph(+)) CML patients randomized to the German CML Study IV. At diagnosis, 1003 of 1151 patients (87\%) had standard t(9;22)(q34;q11) only, 69 patients (6.0\%) had variant t(v;22), and 79 (6.9\%) additional cytogenetic aberrations (ACAs). Of these, 38 patients (3.3\%) lacked the Y chromosome (-Y) and 41 patients (3.6\%) had ACAs except -Y; 16 of these (1.4\%) were major route (second Philadelphia [Ph] chromosome, trisomy 8, isochromosome 17q, or trisomy 19) and 25 minor route (all other) ACAs. After a median observation time of 5.3 years for patients with t(9;22), t(v;22), -Y, minor- and major-route ACAs, the 5-year PFS was 90\%, 81\%, 88\%, 96\%, and 50\%, and the 5-year OS was 92\%, 87\%, 91\%, 96\%, and 53\%, respectively. In patients with major-route ACAs, the times to CCR and MMR were longer and PFS and OS were shorter (P

Am J Clin Pathol, 136(5), 712–720
November, 2011

Detection of genomic abnormalities in multiple myeloma: the applicationof FISH analysis in combination with various plasma cell enrichmenttechniques.

Luise Hartmann, Julie Sanford Biggerstaff, Douglas B. Chapman, Janice M. Scott, Krystal R. Johnson, Keely M. Ghirardelli, Wayne K. Fritschle, Dolores L. Martinez, Richard K. Bennington, Monica E. de Baca, Denise A. Wells, Michael R. Loken, Barbara K. Zehentner

Multiple myeloma (MM) is a hematopoietic neoplasm characterized by malignant plasma cells (PCs) that accumulate in the bone marrow. A number of different genomic abnormalities are associated with MM; however, detection of these by fluorescence in situ hybridization (FISH) can be limited by the percentage of PCs in the specimen. In this study, we tested 20 bone marrow specimens with known MM and a low concentration of monoclonal PCs for the presence of genomic abnormalities using FISH in combination with various PC enrichment techniques: magnetic cell sorting, targeted manual scoring, and automated image analysis. In addition, flow cytometric cell sorting of PCs in combination with FISH analysis was also tested for minimal residual disease applications. Different parameters were evaluated when assessing the detection efficiency of each approach. FISH results are highly dependent on the chosen enrichment method. We describe the evaluation of different techniques applicable for various laboratory settings and specimen parameters.

Leuk Res, 35(8), 1114–1116
August, 2011

Evolutionary sequence of cytogenetic aberrations during the oncogenesisof plasma cell disorders. Direct evidence at single cell level.

Zsófia Nagy, Béla Kajtár, Pál Jáksó, Mariann Dávid, Szabolcs Kosztolányi, Judit Hermesz, László Kereskai, László Pajor, Donát Alpár

Bone marrow specimens from 185 patients with plasma cell disorders (PCD) were investigated by fluorescence in situ hybridization (FISH) in order to determine the temporal sequence of cytogenetic aberrations. In 25 cases combined FISH analysis has also been performed at single cell level. Clonal evolution was observed in 16\% of cases. The ?13 was preceded by t(4;14)(p16;q32) and t(14;16)(q32;q23) translocations. Deletion of p53 gene was a secondary aberration compared to ?13 and t(11;14)(q13;q32) translocation. In 22\% of all cases with recurrent IGH translocation, this aberration was presented only in a subset of purified plasma cells questioning its initiating role.

Stem Cell Rev, 7(2), 471–477
June, 2011

An improved technique for chromosomal analysis of human ES and iPScells.

Daniela Moralli, Mohammed Yusuf, Mohammad A Mandegar, Suhail Khoja, Zoia L Monaco, Emanuela V Volpi

Prolonged in vitro culture of human embryonic stem (hES) cells can result in chromosomal abnormalities believed to confer a selective advantage. This potential occurrence has crucial implications for the appropriate use of hES cells for research and therapeutic purposes. In view of this, time-point karyotypic evaluation to assess genetic stability is recommended as a necessary control test to be carried out during extensive 'passaging'. Standard techniques currently used for the cytogenetic assessment of ES cells include G-banding and/or Fluorescence in situ Hybridization (FISH)-based protocols for karyotype analysis, including M-FISH and SKY. Critical for both banding and FISH techniques are the number and quality of metaphase spreads available for analysis at the microscope. Protocols for chromosome preparation from hES and human induced pluripotent stem (hiPS) cells published so far appear to differ considerably from one laboratory to another. Here we present an optimized technique, in which both the number and the quality of chromosome metaphase spreads were substantially improved when compared to current standard techniques for chromosome preparations. We believe our protocol represents a significant advancement in this line of work, and has the required attributes of simplicity and consistency to be widely accepted as a reference method for high quality, fast chromosomal analysis of human ES and iPS cells.

Cytometry A, 79(5), 375–382
May, 2011

Urovysion: Considerations on modifying current evaluation scheme,including immunophenotypic targeting and locally set, statisticallyderived diagnostic criteria.

Gabor Pajor, Laszlo Somogyi, Bela Melegh, Donat Alpar, Bela Kajtar, Laszlo Farkas, Maria Kneif, Daniel Bollmann, Laszlo Pajor, Norbert Sule

Urovysion multitarget fluorescence in situ hybridization (FISH) assay is a promising tool for detection of bladder cancer, however, there is still no consensus regarding abnormal signal pattern and cut-off level, and the recommended targeting carries limitations similar to urine cytology. Aim of this study was to explore diagnostic benefits of a recently introduced method featuring target specific genotyping, as well as to investigate the feasibility of locally and statistically determined cut-off, compared with conventional evaluation scheme. Histology, cytology, and comparative FISH approaches were performed on 42 patients with high clinical suspicion for urothelial carcinoma (UC). FISH parallels were (1) Urovysion-alone (according to manufacturer's instruction); (2) Targeted-Urovysion (cytokeratin7 immunophenotyping followed by Urovysion), both of which evaluated by both conventional and statistical evaluation scheme. For statistical evaluation cut-offs and sufficient sample size were determined on controls and ratio of positive cells was recorded, whereas conventional evaluation relied on manufacturer's recommendations. The specificity of cytology, Urovysion-alone in general and targeted-Urovysion in general appeared 86\%, 86\%, and 100\%, respectively. In the same comparison, overall sensitivity was 60\%, 80\%, and 93\%, respectively. In superficial cases sensitivity was 48\% for cytology, 72\% for Urovysion-alone and 91\% for targeted-Urovysion, while no prominent differences were seen in muscle invasive cases. The ratio of FISH positive cells was proportionate with both stage and grade, however, targeted genotyping could separate high grade/high stage cases more effectively. In conclusion, CK7 targeting raises diagnostic efficiency of Urovysion, and could be an ideal tool for identifying tumor cells in ambiguous cases or when other tumors are present. Statistical evaluation produces accuracy comparable with results of conventional evaluation, and with laboratories setting cut-offs individually but according harmonized protocol, it could aid method standardization. Furthermore, by providing additional quantitative information about tumor characteristics, is likely to have therapy relevant value in the future.

PLoS Genet, 7(4), e1002042
April, 2011

DNA damage, somatic aneuploidy, and malignant sarcoma susceptibilityin muscular dystrophies.

Wolfgang M Schmidt, Mohammed H Uddin, Sandra Dysek, Karin Moser-Thier, Christine Pirker, Harald Höger, Inge M Ambros, Peter F Ambros, Walter Berger, Reginald E Bittner

Albeit genetically highly heterogeneous, muscular dystrophies (MDs) share a convergent pathology leading to muscle wasting accompanied by proliferation of fibrous and fatty tissue, suggesting a common MD-pathomechanism. Here we show that mutations in muscular dystrophy genes (Dmd, Dysf, Capn3, Large) lead to the spontaneous formation of skeletal muscle-derived malignant tumors in mice, presenting as mixed rhabdomyo-, fibro-, and liposarcomas. Primary MD-gene defects and strain background strongly influence sarcoma incidence, latency, localization, and gender prevalence. Combined loss of dystrophin and dysferlin, as well as dystrophin and calpain-3, leads to accelerated tumor formation. Irrespective of the primary gene defects, all MD sarcomas share non-random genomic alterations including frequent losses of tumor suppressors (Cdkn2a, Nf1), amplification of oncogenes (Met, Jun), recurrent duplications of whole chromosomes 8 and 15, and DNA damage. Remarkably, these sarcoma-specific genetic lesions are already regularly present in skeletal muscles in aged MD mice even prior to sarcoma development. Accordingly, we show also that skeletal muscle from human muscular dystrophy patients is affected by gross genomic instability, represented by DNA double-strand breaks and age-related accumulation of aneusomies. These novel aspects of molecular pathologies common to muscular dystrophies and tumor biology will potentially influence the strategies to combat these diseases.

Blood, 117(15), e161–e170
April, 2011

Myelodysplasia and leukemia of Fanconi anemia are associated witha specific pattern of genomic abnormalities that includes crypticRUNX1/AML1 lesions.

Samuel Quentin, Wendy Cuccuini, Raphael Ceccaldi, Olivier Nibourel, Corinne Pondarre, Marie-Pierre Pag?s, Nadia Vasquez, Catherine Dubois d'Enghien, Jérôme Larghero, Peffault de Latour, Régis, Vanderson Rocha, Jean-Hugues Dalle, Pascale Schneider, Mauricette Michallet, Gérard Michel, André Baruchel, François Sigaux, Eliane Gluckman, Thierry Leblanc, Dominique Stoppa-Lyonnet, Claude Preudhomme, Gérard Socié, Jean Soulier

Fanconi anemia (FA) is a genetic condition associated with bone marrow (BM) failure, myelodysplasia (MDS), and acute myeloid leukemia (AML). We studied 57 FA patients with hypoplastic or aplastic anemia (n = 20), MDS (n = 18), AML (n = 11), or no BM abnormality (n = 8). BM samples were analyzed by karyotype, high-density DNA arrays with respect to paired fibroblasts, and by selected oncogene sequencing. A specific pattern of chromosomal abnormalities was found in MDS/AML, which included 1q+ (44.8\%), 3q+ (41.4\%), -7/7q (17.2\%), and 11q- (13.8\%). Moreover, cryptic RUNX1/AML1 lesions (translocations, deletions, or mutations) were observed for the first time in FA (20.7\%). Rare mutations of NRAS, FLT3-ITD, MLL-PTD, ERG amplification, and ZFP36L2-PRDM16 translocation, but no TP53, TET2, CBL, NPM1, and CEBP? mutations were found. Frequent homozygosity regions were related not to somatic copy-neutral loss of heterozygosity but to consanguinity, suggesting that homologous recombination is not a common progression mechanism in FA. Importantly, the RUNX1 and other chromosomal/genomic lesions were found at the MDS/AML stages, except for 1q+, which was found at all stages. These data have implications for staging and therapeutic managing in FA patients, and also to analyze the mechanisms of clonal evolution and oncogenesis in a background of genomic instability and BM failure.

DNA Repair (Amst), 10(3), 322–337
March, 2011

Validation of a fully automated COMET assay: 1.75 million singlecells measured over a 5 year period.

Albert Rosenberger, Ute Rössler, Sabine Hornhardt, Wiebke Sauter, Heike Bickeböller, H-Erich Wichmann, Maria Gomolka

The COMET assay is recognized as a rapid and sensitive method in quantifying radiation induced DNA damage. We investigated the distorting influence of endogenous, assay-inherent factors onto base (single cell level) and primary outcome measures (experimental/slide level), such as olive tail moment (OTM) and percentage DNA in the tail (\%tail-DNA). From 2003 to 2008, we performed the assay on lymphocytes isolated from the blood samples of 355 lung cancer patients, 170 controls, and 610 relatives, as well as one single reference individual, repeated 170 times. In total, the data from 10,016 single experiments containing around 1,750,000 cells have been included in this study. This is the first time that the endogenous variability of the COMET assay has been validated systematically on such a huge data set over a 5 year period. Assuming that the reference sample reflects assay specific white noise, we estimated a proportion of 7-95\% of the variability of the outcome measures due to assay variation (white noise) depending on parameter, exposure level, and study group. The proportion of white noise was largest for the initial radiation damage. The specific endogenous factors considered attribute to 14.8\% of the total variability in the primary outcome measurements of the OTM and 6.9\% of the \%tail-DNA. OTM turns out to be a sensitive parameter to detect variation, but is also more susceptible to disturbance caused by endogenous factors than \%tail-DNA. To reduce the experimental variability in COMET assays, we recommend a highly standardized operation protocol as well as inspecting and/or adjusting the primary outcome measures according to endogenous factors before calculating secondary outcome measures, e.g. DNA repair capacity (DRC) or testing statistical inference. A human reference (HR) sample is also useful to inspect homogeneity in the temporal progression of long lasting investigations, but not for calibrating primary outcome measurements.

J Biomed Biotechnol, 2011, 693691
2011

Chromosomal rearrangements in post-Chernobyl papillary thyroid carcinomas:evaluation by spectral karyotyping and automated interphase FISH.

Ludwig Hieber, Reinhard Huber, Verena Bauer, Quirin Schäffner, Herbert Braselmann, Geraldine Thomas, Tatjana Bogdanova, Horst Zitzelsberger

Structural genomic rearrangements are frequent findings in human cancers. Therefore, papillary thyroid carcinomas (PTCs) were investigated for chromosomal aberrations and rearrangements of the RET proto-oncogene. For this purpose, primary cultures from 23 PTC have been established and metaphase preparations were analysed by spectral karyotyping (SKY). In addition, interphase cell preparations of the same cases were investigated by fluorescence in situ hybridisation (FISH) for the presence of RET/PTC rearrangements using RET-specific DNA probes. SKY analysis of PTC revealed structural aberrations of chromosome 11 and several numerical aberrations with frequent loss of chromosomes 20, 21, and 22. FISH analysis for RET/PTC rearrangements showed prevalence of this rearrangement in 72\% (16 out of 22) of cases. However, only subpopulations of tumour cells exhibited this rearrangement indicating genetic heterogeneity. The comparison of visual and automated scoring of FISH signals revealed concordant results in 19 out of 22 cases (87\%) indicating reliable scoring results using the optimised scoring parameter for RET/PTC with the automated Metafer4 system. It can be concluded from this study that genomic rearrangements are frequent in PTC and therefore important events in thyroid carcinogenesis.

Mol Cytogenet, 4(1), 8
2011

A rare case of t(11;22) in a mantle cell lymphoma like B-cell neoplasiaresulting in a fusion of IGL and CCND1: case report.

Cristiano Krings Rocha, Inka Praulich, Iris Gehrke, Michael Hallek, Karl-Anton Kreuzer

ABSTRACT: The chromosomal translocation (11;14)(q13;q32) rearranging the locus for cyclin D1 (CCND1) to that of the immunoglobulin heavy chain (IGH) can be found in virtually all cases of mantle cell lymphoma (MCL), while other CCND1 translocations are extremely rare. As CCND1 overexpression and activation is a hallmark of MCL it is regarded as a central biological mechanism in the development and maintenance of this disease.Here we present a patient initially diagnosed with chronic lymphocytic leukemia (CLL) where chromosome banding analysis revealed, among other aberrations, a translocation (11;22)(q13;q11.2). We show by fluorescence in situ hybridization (FISH) analysis that on chromosome 22 the immunoglobulin light chain lambda (IGL) is involved in this cytogenetic aberration. Additionally, we demonstrate the resulting overexpression of CCND1 on the RNA and protein level, thereby consolidating the new diagnosis of a MCL-like B-cell neoplasia. Summing up, we described a rare case of t(11;22)(q13;q11.2) in a MCL-like neoplasia and showed that this aberration leads to an overexpression of CCND1 which is regarded as a key biological feature in MCL. This case underlines the importance of cytogenetic analyses especially in atypical cases of B cell lymphomas.

Mol Cytogenet, 4, 16
2011

Biclonal myelodysplastic syndrome involving six chromosomes and monoallelicloss of RB1 - A rare case.

Walid Al-Achkar, Abdulsamad Wafa, Elisabeth Klein, Abdulmunim Aljapawe

ABSTRACT:Myelodysplastic syndrome (MDS) represents a group of clonal hematological disorders characterized by progressive cytopenia, and reflects to defects in erythroid, myeloid and megakaryocytic maturation. MDS is more frequently observed in older aged patients with cytogenetic abnormalities like monosomy of chromosome(s) 5 and/or 7. In 50\% of de novo MDS cases, chromosomal aberrations are found and rearrangements involving the retinoblastoma (RB1) gene in 13q14 are found.Here, we are presenting a case report of a rare biclonal MDS with a karyotype of 45, XY,-4, der(6)t(4;6)(p15.1;p21.3), der(8)t(4;8)(q31.2;q22), t(13;16)(q21.3;p11.2)11/45, XY, der(7)t(7;13)(p22.2~22.3;q21.3),-13 9. The patient was diagnosed according to WHO classification as refractory anemia with excess of blasts (RAEB-II).Immunophenotyping was positive for CD11b, CD11c, CD10, CD13, CD15, CD16 and CD33.We report, a novel and cytogenetically rare case of a biclonal MDS with complex chromosomal aberrations and deletion of RB1-gene in both clones. These findings are associated with a poor prognosis as the patient died 3 months after diagnosis.

PLoS One, 6(12), e28368
2011

Characterization of Abcc4 gene amplification in stepwise-selectedmouse J774 macrophages resistant to the topoisomerase II inhibitorciprofloxacin.

Béatrice Marquez, Geneviève Ameye, Coralie M Vallet, Paul M Tulkens, Hélène A Poirel, Françoise Van Bambeke

Exposure of J774 mouse macrophages to stepwise increasing concentrations of ciprofloxacin, an antibiotic inhibiting bacterial topoisomerases, selects for resistant cells that overexpress the efflux transporter Abcc4 (Marquez et al. [2009] Antimicrob. Agents Chemother. 53: 2410-2416), encoded by the Abcc4 gene located on Chromosome 14qE4. In this study, we report the genomic alterations occurring along the selection process. Abcc4 expression progressively increased upon selection rounds, with exponential changes observed between cells exposed to 150 and 200 µM of ciprofloxacin, accompanied by a commensurate decrease in ciprofloxacin accumulation. Molecular cytogenetics experiments showed that this overexpression is linked to Abcc4 gene overrepresentation, grading from a partial trisomy of Chr 14 at the first step of selection (cells exposed to 100 µM ciprofloxacin), to low-level amplifications (around three copies) of Abcc4 locus on 1 or 2 Chr 14 (cells exposed to 150 µM ciprofloxacin), followed by high-level amplification of Abcc4 as homogeneous staining region (hsr), inserted on 3 different derivative Chromosomes (cells exposed to 200 µM ciprofloxacin). In revertant cells obtained after more than 60 passages of culture without drug, the Abcc4 hsr amplification was lost in approx. 70\% of the population. These data suggest that exposing cells to sufficient concentrations of an antibiotic with low affinity for eukaryotic topoisomerases can cause major genomic alterations that may lead to the overexpression of the transporter responsible for its efflux. Gene amplification appears therefore as a mechanism of resistance that can be triggered by non-anticancer agents but contribute to cross-resistance, and is partially and slowly reversible.

Diagn Pathol, 6, 76
2011

FISH as an effective diagnostic tool for the management of challengingmelanocytic lesions.

Mathew W. Moore, Robert Gasparini

The accuracy of melanoma diagnosis continues to challenge the pathology community, even today with sophisticated histopathologic techniques. Melanocytic lesions exhibit significant morphological heterogeneity. While the majority of biopsies can be classified as benign (nevus) or malignant (melanoma) using well-established histopathologic criteria, there exists a cohort for which the prediction of clinical behaviour and invasive or metastatic potential is difficult if not impossible to ascertain on the basis of morphological features alone. Multiple studies have shown that there is significant disagreement between pathologists and even expert dermatopathologists in the diagnosis of this subgroup of difficult melanocytic lesions.A four probe FISH assay was utilized to analyse a cohort of 500 samples including 157 nevus, 176 dysplastic nevus and 167 melanoma specimens.Review of the lesions determined the assay identified genetic abnormalities in a total of 83.8\% of melanomas, and 1.9\% of nevus without atypia, while genetic abnormalities were identified in 6.3\%, 6.7\%, and 10.3\% of nevus identified with mild, moderate and severe atypia, respectively.Based on this study, inheritable genetic damage/instability identified by FISH testing is a hallmark of a progressive malignant process, and a valuable diagnostic tool for the identification of high risk lesions.

Methods Mol Biol, 724, 91–103
2011

Automated Analysis of FISH-Stained HER2/neu Samples with Metafer.

Christian Schunck, Eiman Mohammad

The HER2/neu gene (also known as ERBB2) is located on chromosome 17 (q11.2-q12) and encodes a glycoprotein known to be a member of the epidermal growth factor receptor family. Clinically, the determination of its amplification status is of utmost importance, as 10-35\% of invasive human breast carcinomas come along with HER2/neu overexpression, and treatment has to be adjusted accordingly. Here a method to analyze HER2 FISH samples with digital microscopy, using the slide scanning -platform Metafer PV (MetaSystems, Altlussheim, Germany), is presented. Metafer PV is a system for the automation of HER2/neu FISH assay analysis of samples hybridized with the Abbott(™) PathVysion(®) probe kit.

Microscopy Research and Technique
2011

Automated signal pattern evaluation of a bladder cancer specific multiprobe�fish assay applying a user�trainable workstation

Pajor, Gabor, Alpar, Donat, Kajtar, Bela, Melegh, Bela, Somogyi, Laszlo, Kneif, Maria, Bollmann, Daniel, Pajor, Laszlo, Sule, Norbert

OBJECTIVE: Signal pattern enumeration of Urovysion Fluorescence in Situ Hybridization test is tedious and requires great experience. Our aim was to eliminate human interaction by automating the process, using an adoptable, automated image acquisition, and analysis system. METHODS: For extensive analytical analysis control, cell populations were used, while preliminary clinical study was performed on 21 patients with clinical suspicion for bladder cancer. All investigations were carried out using an automated user�trainable workstation (Metafer4�Metacyte). RESULTS: The system identified nuclei with a specificity and sensitivity of 92.7 and 96.6%, respectively, while signal detection accuracy was 81.1% on average. Both analytical and diagnostic accuracy of automated analysis was comparable to manual approach (94.8 and 71% vs. 97.9 and 76%, respectively), but classification accuracy increased with degree of polysomy, thus diagnostic sensitivity in low grade, low stage cases was poor. CONCLUSION: It is possible to automate signal enumeration of Urovysion using a user�trainable system, and achieve efficiency comparable to manual analysis. Previously introduced automated immunophenotypic targeting should further increase diagnostic sensitivity, while resulting in a comprehensively automated method. However, the problem of reduced detection accuracy in cases featured with low polysomy is likely to remain a great challenge of automated signal enumeration.

Methods Mol Biol, 730, 203–218
2011

The use of M-FISH and M-BAND to define chromosome abnormalities.

Ruth N. Mackinnon, Ilse Chudoba

Multicolour fluorescence in situ hybridisation (M-FISH) and multicolour banding (M-BAND) are advanced chromosome painting techniques combining multiple chromosome- or region-specific paints in one step. M-FISH identifies all chromosomes or chromosome arms at once, whereas M-BAND identifies the different regions of a single chromosome. The use of either or both can improve the accuracy of karyotyping and help identify cryptic chromosome rearrangements. These probes are prepared by pooling multiple chromosome- or chromosome region-specific DNA libraries, each labelled with a unique combination of fluorochromes. Commercial probes are available, avoiding the need for probe preparation. In the protocol described here, a commercial probe is used. Well-spread metaphases are prepared according to standard techniques, followed by alkaline denaturation and application of the denatured probe. After an incubation period, the slides are washed. A fluorescence microscope with filter sets specific to the fluorescent labels is used for analysis, together with specialised image analysis software. The software interprets the combination of fluorochromes to identify each chromosome and produce a false colour image specific for each chromosome or region. The single colour galleries - which show the hybridisation patterns of the individual fluorochromes - are useful to help interpret and confirm the false colour images produced by the software, including ambiguous signals.

BMC Biotechnol, 11, 121
2011

Combining M-FISH and Quantum Dot technology for fast chromosomalassignment of transgenic insertions.

Mohammed Yusuf, David L V Bauer, Daniel M Lipinski, Robert E MacLaren, Richard Wade-Martins, Kalim U Mir, Emanuela V Volpi

Physical mapping of transgenic insertions by Fluorescence in situ Hybridization (FISH) is a reliable and cost-effective technique. Chromosomal assignment is commonly achieved either by concurrent G-banding or by a multi-color FISH approach consisting of iteratively co-hybridizing the transgenic sequence of interest with one or more chromosome-specific probes at a time, until the location of the transgenic insertion is identified.Here we report a technical development for fast chromosomal assignment of transgenic insertions at the single cell level in mouse and rat models. This comprises a simplified 'single denaturation mixed hybridization' procedure that combines multi-color karyotyping by Multiplex FISH (M-FISH), for simultaneous and unambiguous identification of all chromosomes at once, and the use of a Quantum Dot (QD) conjugate for the transgene detection.Although the exploitation of the unique optical properties of QD nanocrystals, such as photo-stability and brightness, to improve FISH performance generally has been previously investigated, to our knowledge this is the first report of a purpose-designed molecular cytogenetic protocol in which the combined use of QDs and standard organic fluorophores is specifically tailored to assist gene transfer technology.

Pediatric Blood & Cancer, 6(6), 1239-1242
December, 2010

Sex chromosome changes after sex-mismatched allogeneic bone marrow transplantation can mislead the chimerism analysis

Donát Alpár, Gergely Nagy, Carsten Hohoff, Béla Kajtár, Katalin Bartyik, Judit Hermesz, Pál Jáksó, Hajnalka Andrikovics, László Kereskai, László Pajor

A 12-year-old male with pre-B-cell acute lymphoblastic leukemia with cryptic BCR/ABL rearrangement underwent sex-mismatched allogeneic bone marrow transplantation (allo-BMT). Contradictory results were provided by various chimerism analyses 3 months later. Y-chromosome-specific quantitative polymerase chain reaction and sex chromosome-specific interphase fluorescence in situ hybridization (i-FISH) showed complete donor chimerism. Analysis of autosomal short tandem repeats (A-STR), BCR/ABL i-FISH test, and X-STR haplotype indicated relapse. Metaphase-FISH and combined BCR/ABL and sex chromosome-specific i-FISH patterns revealed loss of the Y-chromosome and duplication of the X-chromosome in the host cells. Sex chromosome changes after allo-BMT can cause significant difficulties in chimerism analysis.

Cancer Genet Cytogenet, 203(2), 209–214
December, 2010

Clonal heterogeneity and chromosomal instability at disease presentationin high hyperdiploid acute lymphoblastic leukemia.

Anna Talamo, Yves Chalandon, Alfio Marazzi, Martine Jotterand

Although aneuploidy has many possible causes, it often results from underlying chromosomal instability (CIN) leading to an unstable karyotype with cell-to-cell variation and multiple subclones. To test for the presence of CIN in high hyperdiploid acute lymphoblastic leukemia (HeH ALL) at diagnosis, we investigated 20 patients (10 HeH ALL and 10 non-HeH ALL), using automated four-color interphase fluorescence in situ hybridization (I-FISH) with centromeric probes for chromosomes 4, 6, 10, and 17. In HeH ALL, the proportion of abnormal cells ranged from 36.3\% to 92.4\%, and a variety of aneuploid populations were identified. Compared with conventional cytogenetics, I-FISH revealed numerous additional clones, some of them very small. To investigate the nature and origin of this clonal heterogeneity, we determined average numerical CIN values for all four chromosomes together and for each chromosome and patient group. The CIN values in HeH ALL were relatively high (range, 22.2-44.7\%), compared with those in non-HeH ALL (3.2-6.4\%), thus accounting for the presence of numerical CIN in HeH ALL at diagnosis. We conclude that numerical CIN may be at the origin of the high level of clonal heterogeneity revealed by I-FISH in HeH ALL at presentation, which would corroborate the potential role of CIN in tumor pathogenesis.

Leuk Res, 34(8), 1002–1006
August, 2010

Recurrent involvement of heterochromatic regions in multiple myeloma-amulticolor FISH study.

Kathrin Lange, Dorothea Gadzicki, Brigitte Schlegelberger, Gudrun Göhring

Chromosome aberrations are important prognostic markers in multiple myeloma (MM), but their identification may be hampered by complexity of the karyotypes. Using multicolor fluorescence in situ hybridization (mFISH), we found cryptic aberrations in 7 of 10 patients with a complex karyotype. Moreover, in addition to typical aberrations involving 1q, 13q, 14q and 17p and structural aberrations in chromosomes 1, 6, 9 and 19, (iso)dicentric chromosomes and whole-arm translocations were detected. These chromosome aberrations were generated by breaks in heterochromatic regions indicating an increased breakage of these regions, which may predispose to the generation of chromosome aberrations in multiple myeloma.