Conventional Chromosome Banding Research Articles

Application of fluorescence in situ hybridization technique to verify the clonalities of non-clonal cytogenetic abnormalities identified in Myelodysplastic syndrome

To assess the value of fluorescence in situ hybridization (FISH) technique for the verification of the clonalities of non-clonal cytogenetic abnormalities (n-CCA) identified by conventional chromosome banding analysis (CBA) in patients with Myelodysplastic syndrome (MDS). Clinical data and results of karyotyping and FISH assays for 91 patients of MDS with n-CCA identified by CBA were retrospectively analyzed. In total 94 non-clonal +8, 5q-, -7/7q- or 20q- were detected by CBA, among which 43 (45.7%) were verified to be clonal abnormalities by FISH. The detection rates for +8, 5q-, -7/7q- and 20q- by FISH were 47.6% (30/63), 25% (2/8), 41.7% (5/12), 40% (2/5) and 66.7% (4/6), respectively, with the positive cells accounting for 4% to 90% of all counted cells, with a median value of 7%. The 91 patients were divided into three groups including ≥ 20, 10 ~< 20 and < 10 based on the numbers of metaphase cells in CBA, and the detection rates by FISH for the three groups were 43.7% (31/71), 33.3% (3/9) and 63.6% (7/11), respectively, which showed no statistically difference (P > 0.05). Continuous CBA and FISH surveys were conducted for 26 patients who received supportive treatment, and the results revealed that 91.7% (11/12) of FISH-verified positive abnormalities had persisted, whereas 92.9% (13/14) of the n-CCA verified as negative by FISH was transient. Nearly half of the CBA identified n-CCA have been verified as clonal aberrations by FISH, and the FISH detection rate showed no correlation with the number of metaphase cells. FISH test is strongly recommended for verifying the clonalities of n-CCA detected by CBA, and continuous cytogenetic survey of the patients with MDS is necessary.

Guiding the global evolution of cytogenetic testing for hematologic malignancies

AbstractCytogenetics has long represented a critical component in the clinical evaluation of hematologic malignancies. Chromosome banding studies provide a simultaneous snapshot of genome-wide copy number and structural variation, which have been shown to drive tumorigenesis, define diseases, and guide treatment. Technological innovations in sequencing have ushered in our present-day clinical genomics era. With recent publications highlighting novel sequencing technologies as alternatives to conventional cytogenetic approaches, we, an international consortium of laboratory geneticists, pathologists, and oncologists, describe herein the advantages and limitations of both conventional chromosome banding and novel sequencing technologies and share our considerations on crucial next steps to implement these novel technologies in the global clinical setting for a more accurate cytogenetic evaluation, which may provide improved diagnosis and treatment management. Considering the clinical, logistic, technical, and financial implications, we provide points to consider for the global evolution of cytogenetic testing.

Clinical utility of whole genome sequencing in hematological neoplasms.

7028 Background: Hematological neoplasms are often characterized by acute onset and rapid disease progression. Cytogenetics, FISH, SNP arrays, targeted DNA and RNA sequencing are performed to inform diagnosis, risk stratification and guide treatment decisions. Whole genome sequencing (WGS) offers the opportunity to comprehensively characterize all putative biomarkers in a single assay. However, a limitation in current WGS implementation is the requirement for a germline sample, as sources of control tissue are frequently contaminated with leukemic cells resulting in false negative calls. Methods: To evaluate the clinical utility and feasibility of WGS in the diagnostic work up of leukemias, we analyzed 57 B-cell acute lymphoblastic leukemia (B-ALL) from the UKALL14 trial (NCT01085617) with no informative biomarkers at diagnosis. WGS analysis was performed on the leukemic sample and a matching control sample (with minimal residual disease level of &lt;1%). Using this dataset, we trained the development of an unmatched (uWGS) analytical workflow (Isabl) for a tumor only WGS study. This workflow was validated across 20 hematologic neoplasms (12 B-ALL, 6 AML and 2 T-ALL). Results: Among the 57 cases, 5 failed QC owing to low tumor content (&lt;25%). Of the remaining 52, putative biomarkers of clinical relevance were identified by WGS in 69% (36/52). These included delineation of aberrant karyotypes where conventional chromosome banding failed (4/52), the detection of newly described fusion genes (such as IGH-DUX4 and EP300-ZNF384 in 21/52) and recurrent gene mutations (i.e. PAX5 P80R, ZEB2 H1038R in 11/52). uWGS workflow in our training dataset captured 86% of biomarkers identified in the matched analysis (3/3 ploidy, 21/22 fusion and 7/11 coding). Concordance between the matched and uWGS workflow for arm-level and focal copy number alterations (CNAs), structural variants (SVs) and annotated hotspot mutations were 94%, 84%, 83% and 100% respectively. Independent validation of the uWGS workflow across 20 myeloid and lymphoid neoplasms, recapitulated all clinically reported biomarkers (14/15 CNAs, 16/16 SVs) as well as captured two novel findings not previously detected in two B-ALL patients, to include a focal deletion in BTG1 and the fusion gene P2RY8-CRLF2, as well as a NOTCH1 translocation in T-ALL. Conclusions: Our findings demonstrate that comprehensive WGS allows for the detection of the same biomarkers as a range of clinical assays using a single test, as well as the opportunity to discover novel clinical and research findings to support future correlative research and biomarker development. Additionally, we developed and validated an uWGS workflow that allows WGS analysis of hematopoietic neoplasms at diagnosis, enabling detection and reporting of clinically relevant biomarkers.

Improved cytogenetic characterization and risk stratification of pediatric acute lymphoblastic leukemia using single nucleotide polymorphism array analysis: A single center experience of 296 cases.

Single nucleotide polymorphism array (SNP-A) analyses are increasingly being introduced in routine genetic diagnostics of acute lymphoblastic leukemia (ALL). Despite this, only few studies that have compared the diagnostic value of SNP-A with conventional chromosome banding have been published. We here report such a comparison of 296 ALL cases, the largest series to date. Only genomic imbalances >5 Mb and microdeletions targeting the BTG1, CDKN2A/B, EBF1, ERG, ETV6, IKZF1, PAX5, and RB1 genes and the pseudoautosomal region 1 (PAR1) were ascertained, in agreement with recent guidelines. Of 36 T-cell ALL cases, the karyotypes of 24 cases (67%) were revised by SNP-A analyses that either revealed additional imbalances >5 Mb or better characterized the changes found by G-banding. Of 260 B-cell precursor (BCP) ALL cases, SNP-A analyses identified additional copy number alterations, including the above-mentioned microdeletions, or better characterized the imbalances found by G-banding in 236 (91%) cases. Furthermore, the cytogenetic subtype classification of 41/260 (16%) BCP ALL cases was revised based on the SNP-A findings. Of the subtype revisions, 12/41 (29%) had clinical implications as regards risk stratifying cytogenetic groups or genotype-specific minimal residual disease stratification. We conclude that SNP-A analyses dramatically improve the cytogenetic characterization of both T-cell and BCP ALL and also provide important information pertinent to risk stratification of BCP ALL.

Use of Array Comparative Genomic Hybridization for the Diagnosis of DiGeorge Syndrome in Saudi Arabian Population

DiGeorge syndrome (DGS) is a genetic disorder known as a clinically variable syndrome with over 180 associated phenotypic features. It is caused by a common human deletion in the 22q11.2 chromosomal region and currently is affecting approximately 1 in 4,000 individuals. Despite the prevalence of inherited diseases mainly due to consanguineous marriages, the current diagnosis of DGS in Saudi Arabia is mainly based on conventional high-resolution chromosome banding (karyotyping) and FISH techniques. However, advanced genome-wide studies for detecting microdeletions or duplications across the whole genome are needed. The aim of this study is to implement and use aCGH technology in clinical diagnosis of the 22q11.2 deletion in Saudi Arabian DGS patients and to confirm its effectiveness compared to conventional FISH and chromosome banding techniques. Thirty suspected DGS patients were assessed for chromosome 22q11.2 deletion using high-resolution G-banding, FISH, and aCGH. The aCGH results were compared with those obtained by the other 2 cytogenetic techniques. G-banding detected the 22q11.2 deletion in only 1 patient in the cohort. Moreover, it detected additional chromosomal aberrations in 3 other patients. Using FISH, allowed for detection of the 22q11.2 deletion in 2 out of 30 patients. Interestingly, the use of aCGH technique showed deletions in the chromosome 22q11.2 region in 8 patients, indicating a 4-fold increase in diagnostic detection capacity compared to FISH. Our results show the effectiveness of aCGH to overcome the limitations of FISH and G-banding in terms of diagnostic yield and allow whole genome screening and detection of a larger number of deletions and/or duplications in Saudi Arabian DGS patients. Except for balanced translocations and inversions, our data demonstrate the suitability of aCGH in the diagnostics of submicroscopic deletion syndromes such as DGS and most chromosomal aberrations or complex abnormalities scattered throughout the human genome. Our results recommend the implementation of aCGH in clinical genomic testing in Saudi Arabia to improve the diagnostic capabilities of health services while maintaining the use of conventional cytogenetic techniques for subsequent validation or for specific and known aberrations whenever required.

CpG-ODN Stimulation in Population Screening Monoclonal B-Cell Lymphocytosis

Synthetic CpG-oligodeoxynucleotides (CpG-ODN) induce proliferation in normal and malignant lymphocytes B (LyB). This effect is widely exploited in CLL conventional chromosome banding analysis (CBA), which has become reliable only after the cultivation of CLL LyB using CpG-ODN stimulation in combination with IL-2. Monoclonal B-cell lymphocytosis (MBL) differs from CLL mainly in clone size. Only cytogenetic data on recurrent chromosomal aberrations analyzed by fluorescence in situ hybridization (FISH) are available for population screening MBL (sMBL). In sMBL the clone of malignant LyB is typically below 10/µL. We compared CpGODN stimulation in healthy donors and in individuals with sMBL. LyB and MBL LyB count were determined by flow cytometry in 15 samples from healthy subjects and 12 MBL cases. Mitotic indices were determined and CBA was done after cultivation of samples by CpG-ODN + IL2. In MBL samples, FISH analysis was performed on isolated LyB. MBL LyB clones in sMBL cases presented less than 1% of WBC and up to 33% of LyB. The MBL group was therefore compared to the group of healthy donors. Although normal and MBL group did not differ in WBC, overall LyB, and normal LyB count, a significantly higher mitotic index was observed in MBL samples (p = 0.0139). We were able to accomplish CBA in all samples which revealed a normal karyotype in all but one case. In this particular sMBL case FISH performed on isolated LyB showed 5% trisomy 12 which was later confirmed by CBA on CpG stimulated blood sample in 15% of metaphases. Our study, which was done on MBL cases obtained by population screening, confirmed that CpGODN preferentially induced proliferation in MBL LyB over normal LyB. Therefore, CBA can also be successfully accomplished in sMBL and can be used to additionally confirm clonality as well as to improve sensitivity of FISH analysis. Due to coexistence of comparable size of normal and malignant LyB, MBL can serve as a model for exvivo studying of LyB stimulation by CpG-ODN.

Cytogenetic place in managing myelodysplastic syndromes: an update by the Groupe francophone de cytogénétique hématologique (GFCH).

The myelodysplastic syndromes (MDS) are preleukemic diseases of elderly patients characterized by defective maturation of clonal hematopoietic progenitor cells resulting in peripheral blood cytopenias. Clonal chromosomal abnormalities are heterogeneous and can be detected in less than 50% of patients with de novo MDS and more frequently in secondary MDS (up to 80%). The karyotype plays an important role in the pathogenesis, diagnosis, and prognosis to evaluate the risk of leukemic transformation and, more recently, in treatment allocation. The gold standard for cytogenetic diagnosis in MDS is conventional chromosome banding analyses of bone marrow metaphases. The most frequent abnormalities are deletions and losses of chromosomes 5 (-5/5q-) and 7 (-7/7q-) and various isolated or combined abnormalities. Fluorescent in situ hybridization and array comparative genomic hybridization can reveal cryptic genetic abnormalities but are not recommended in routine diagnosis. New techniques including next generation sequencing revealed somatic driver mutations especially those affecting genes involved in RNA splicing or those harboring important prognostic value (TP53, ASXL1…) with potential applications in clinical practice in the future.

Using chromosomal data in the phylogenetic and molecular dating framework: karyotype evolution and diversification in Nierembergia (Solanaceae) influenced by historical changes in sea level.

Karyotype data within a phylogenetic framework and molecular dating were used to examine chromosome evolution in Nierembergia and to infer how geological or climatic processes have influenced in the diversification of this solanaceous genus native to South America and Mexico. Despite the numerous studies comparing karyotype features across species, including the use of molecular phylogenies, to date relatively few studies have used formal comparative methods to elucidate chromosomal evolution, especially to reconstruct the whole ancestral karyotypes. Here, we mapped on the Nierembergia phylogeny one complete set of chromosomal data obtained by conventional staining, AgNOR-, C- and fluorescent chromosome banding, and fluorescent insitu hybridisation. In addition, we used a Bayesian molecular relaxed clock to estimate divergence times between species. Nierembergia showed two major divergent clades: a mountainous species group with symmetrical karyotypes, large chromosomes, only one nucleolar organising region (NOR) and without centromeric heterochromatin, and a lowland species group with asymmetrical karyotypes, small chromosomes, two chromosomes pairs with NORs and centromeric heterochromatin bands. Molecular dating on the DNA phylogeny revealed that both groups diverged during Late Miocene, when Atlantic marine ingressions, called the 'Paranense Sea', probably forced the ancestors of these species to find refuge in unflooded areas for about 2Myr. This split agrees with an increased asymmetry and heterochromatin amount, and decrease in karyotype length and chromosome size. Thus, when the two Nierembergia ancestral lineages were isolated, major divergences occurred in chromosomal evolution, and then each lineage underwent speciation separately, with relatively minor changes in chromosomal characteristics.

Comprehensive Genetic Characterization of Pediatric T-Cell Acute Lymphoblastic Leukemia

A comprehensive genetic characterization comprising conventional chromosome banding, fluorescence in situ hybridization (FISH), and single nucleotide polymorphism (SNP) array analyses as well as large-scale sequencing of 75 genes were performed on a consecutive series of 47 pediatric T-cell acute lymphoblastic leukemia (T-ALL) patients. An abnormal karyotype was identified in 46% of the cases. Recurrent cytogenetic aberrations comprised T-cell receptor (TCR) translocations and deletions of 6q and 9p. FISH analyses of TCR rearrangements were positive in 26% of the investigated cases. The vast majority (37/39; 95%) of cases analyzed by SNP arrays displayed aberrations, with a median of 3 changes (range 0-11) per case. The genes recurrently deleted were CDKN2A, CDKN2B, LEF1, PTEN, RBI, and STIL. One case displayed chromothripsis involving 6q. No case had a whole chromosome uniparental isodisomy (wUPID); in fact, only one T-ALL of 123 informative cases in the literature has had a wUPID. However, segmental UPIDs (sUPIDs) were seen in 44% of the present cases, with most being sUPID9p. CDKN2A was homozygously deleted in all cases with sUPID9p, with a heterozygous deletion occurring prior to the sUPID9p in all instances. There was no evidence for chromosomal instability when comparing diagnostic and relapse samples. Among the genes sequenced, 14 were mutated in 28 cases. The genes targeted are involved in signaling transduction, epigenetic regulation, and transcription. In some cases, NOTCH1 mutations were seen in minor subclones and lost at relapse, showing that such mutations also can be secondary events. These findings support a multistep leukemogenic process. DisclosuresNo relevant conflicts of interest to declare.

Cytogenetic and molecular genetic study of fetal supernumerary marker chromosomes and derivative chromosomes

Objective To investigate the prenatal diagnosis and phenotypic assessment strategies for fetal supernumerary marker chromosomes and derivative chromosomes. Methods Five cases of fetal supernumerary marker chromosomes and one case of fetal derivative chromosomes were diagnosed in the First Affiliated Hospital of Sun Yat-Sen University from March 12, 2010 to November 9, 2012 by conventional chromosome banding, fluorescence in situ hybridization （FISH） and spectral karyotyping （SKY）. These cases were retrospectively reviewed. Combined with the results of ultrasonography, abnormal phenotypes and pregnancy outcomes were evaluated in these cases. Results All of the five supernumerary marker chromosomes were de novo, in which two were mosaic and the remaining three cases were non-mosaic. Of these five cases, two were type 47, XX＋mar and ultrasound indicated abnormal phenotypes. FISH and SKY confirmed that they were＆amp;nbsp;derived from chromosome 4 and 22, respectively. The other three cases were marker chromosome with Turner syndrome karyotype （abnormal phenotypes were not found by ultrasound）, in which two cases were derived from chromosome Y （by FISH） and one case was identified as ring chromosome X （by FISH and SKY）. One de novo derivative chromosome was verified as a product of reciprocal translocation between chromosome 2 and 6 （by FISH and SKY）. Induced abortion was performed in all cases between 25 and 32 gestational weeks. Conclusions By combining conventional chromosome banding, FISH and SKY, the origin and content of supernumerary marker chromosomes and derivative chromosomes can be identified. On this basis, clinical phenotype evaluation and genetic counseling may be offered with the ultrasonographic result. Key words: Chromosome aberrations; Prenatal diagnosis; Genetic markers; Chromosome banding; In situ hybridization,fluorescence; Spectral karyotyping

NOR- bearing as a plesiomorphic characteristic in Mimus saturninus (Passeriformes Mimidae)

The order Passeriformes is the largest group of species karyotyped among birds, however little is known about the cytogenetic of the Mimidae family, registering only karyology basic data (giemsa staining). The aim of this study was to analyze the chromosomal complement from the species Mimus saturninus by conventional staining and differential chromosome banding. Diploid number and chromosome morphology were determined, as well as the distribution pattern of constitutive heterochromatin (CBG-banding), GTG-banding andAgNOR staining (NORs). The Chalk-browed Mockingbird has 2n=80. The first and fourth pairs are submetacentric and the second, third and fifth are acrocentric. The remaining chromosomes pairs of the complement have telocentric morphology. The Z chromosome is submetacentric and the W is metacentric. CBG-banding showed positive staining in the pericentromeric region of most macrochromosomes and microchromosomes and also at Z chromosome, differently from W chromosome which appeared totally heterochromatic. The GTG-banding was similar to Gallus gallus and in other species which have already been GTG-banded. The NORs were identified in a pair of microchromosomes characterized by presenting a remarkable secondary constriction. This can be considered as a plesiomorphic characteristic for M. saturninus once baseline groups (Paleognathae) also showed a pair of microchromosomes bearing NORs.

Clonal evolution in chronic lymphocytic leukemia detected by fluorescence in situ hybridization and conventional cytogenetics after stimulation with CpG oligonucleotides and interleukin-2: A prospective analysis

Chronic lymphocytic leukemia (CLL) patients may acquire new chromosome abnormalities during the course of their disease. Clonal evolution (CE) has been detected by conventional chromosome banding (CBA), several groups also confirmed CE with fluorescence in situ hybridization (FISH). At present, there are minimal prospective data on CE frequency determined using a combination of both methods. Therefore, the aim of our study was to prospectively assess CE frequency using a combination of FISH and CBA after stimulation with CpG oligonucleotides and interleukin-2. Between 2008 and 2012, we enrolled 140 patients with previously untreated CLL in a prospective trial evaluating CE using FISH and CBA after stimulation. Patients provided baseline and regular follow-up peripheral blood samples for testing. There was a median of 3 cytogenetic examinations (using both methods) per patient. CE was detected in 15.7% (22/140) of patients using FISH, in 28.6% (40/140) using CBA, and in 34.3% (48/140) of patients by combining both methods. Poor-prognosis CE (new deletion 17p, new deletion 11q or new complex karyotype) was detected in 15% (21/140) of patients and was significantly associated with previous CLL treatment (p=0.013). CBA provides more complex information about cytogenetic abnormalities in CLL patients than FISH and confirms that many patients can acquire new abnormalities during the course of their disease in a relatively short time period.

Molecular cytogenetic monitoring from CD34+ peripheral blood cells in myelodysplastic syndromes: First results from a prospective multicenter German diagnostic study

The gold standard of cytogenetic analysis in myelodysplastic syndromes (MDS) is conventional chromosome banding (CCB) analysis of bone marrow (BM) metaphases. Most aberrations can also be detected by fluorescence-in situ-hybridization (FISH). For this prospective multicenter German diagnostic study (www.clinicaltrials.gov: #NCT01355913) 360 patients, as yet, were followed up to 3 years by sequential FISH analyses of immunomagnetically enriched CD34+ peripheral blood (PB) cells using comprehensive FISH probe panels, resulting in a total number of 19,516 FISH analyses. We demonstrate that CD34+ PB FISH correlates significantly with CCB analysis and represents a feasible method for a reliable non-invasive cytogenetic monitoring from PB.

Biological and Clinical Features of Patients with Chronic Lymphocytic Leukemia Bearing Trisomy 12

AbstractAbstract ▪3907▪This icon denotes a clinically relevant abstractCytogenetic abnormalities are among the most important predictors of clinical course and response to therapy in patients (pts) with chronic lymphocytic leukemia (CLL). Conventional chromosome banding (CBA) and fluorescence in situ hybridization (FISH) analyses detect abnormalities in 40–50% and 80% of pts, respectively. Trisomy 12 (+12), observed in ∼20% of CLL pts by FISH, is associated with atypical morphology and immunophenotype, and a more aggressive clinical course. We, therefore, review the clinical characteristics and outcome of 312 CLL pts with +12 evaluated at our center between 1988 and 2011.FISH analysis for common abnormalities associated with CLL was performed on interphase nuclei obtained from cultured bone marrow cells using a multi-color probe panel designed to detect deletions of 11q22.3 (ATM), 13q14.3 (D13S319), 13q34 (LAMP1), 17p13.1 (TP53) and trisomy 12 (12p11.1-q11) (Abbott Molecular, Abbott Park, IL). Survival curves were calculated using Kaplan-Meier estimates and compared using the log-rank test. Differences were considered significant for p < 0.05.Patient characteristics at diagnosis are presented in Table 1. Of 215 pts assessed by both CBA and FISH, 105 were positive for +12 by both analyses and 110 were positive only by FISH. By CBA (112 pts, including 7 assessed only by CBA), +12 was the sole abnormality in 52 pts (47%); +12 was associated with +19 in 17 pts (16%), with del(14q) in 9 pts (8%), with +18 in 8 pts (7%), with +8 in 3 pts (3%), with del(13q) in 3 pts (3%), with t(14;19)(q32;q13) in 3 pts (3%) and with other abnormalities in 17 pts (13%). By FISH (287 pts), +12 was the sole abnormality in 225 pts (78%) and was associated with del(13q) in 62 pts (22%). The median number of interphase nuclei positive for +12 by FISH was 47% (range, 5–93%). One-hundred-eighty-seven pts (60%) needed treatment, with a median Time-To-Treatment (TTT) of 46 months (range, 35–56). The TTT was significantly shorter in pts with Rai stage III-IV disease, splenomegaly, lymphadenopathy, B2m > 4 mg/L, CD38+, ZAP70+, +12 detected by both CBA and FISH, and +12 associated with del(14q) or t(14;19). All 187 pts with progressive disease received treatment: 105 with an FCR-based regimen, 28 with rituximab(R)-based therapy (R+ GM-CSF or R+ methylprednisolone), and 28 with investigational drugs (Lenalidomide, R+ lenalidomide, GS101, or Ibrutinib). Overall response rate was 98%, 89% and 96%, respectively, whereas complete remission rate was 87%, 11% and 36%, respectively. Fifty-five pts failed first-line treatment; their median Failure-Free Survival (FFS) was 27 months (range, 0–87). The FFS was significantly longer in pts who received FCR-based regimens (p<0.001)(Fig 1). The median overall survival (OS) has not been reached, and only 33 pts have died. The OS was significantly shorter in pts older than 65 years, with ALC > 30,000, and with a median +12 positivity in >30% of interphase nuclei by FISH. A trend toward longer OS was observed for pts with +12 associated with +19 (p=0.07). Richter’s Syndrome (RS) and second malignancies (SM) were the leading causes of death (5 and 13 of 33 deaths, respectively). RS was reported in 12 pts (4%), after a median time of 36 months from diagnosis. SM was reported in 31 pts (10%), after a median time of 30 months from diagnosis. At the time of diagnosis of SM, 13 patients had received a therapy for CLL and 18 were untreated.In conclusion, pts with CLL and +12 have unique laboratory and clinical features. A high proportion develops progressive disease and requires treatment. Among available therapies, FCR-based regimens are associated with a longer FFS. A high rate of SM is observed in pts with +12, including in pts who have not received prior treatment [Display omitted] [Display omitted] Disclosures:Wierda:Abbott Laboratories: Research Funding. O'Brien:Avila: Research Funding; Bayer: Consultancy; Bristol-Myers Squibb: Research Funding; Gilead Sciences: Consultancy, Research Funding; Celgene: Consultancy; Cephalon: Consultancy; CII Global Research Foundation: Membership on an entity's Board of Directors or advisory committees; Genentech BioOncology: Research Funding; Genzyme: Consultancy; GlaxoSmithKline: Consultancy; MorphoSys: Consultancy; Novartis: Consultancy; Pharmacyclics: Membership on an entity's Board of Directors or advisory committees, Research Funding; Pfizer: Consultancy; Seattle Genetics, Inc.: Consultancy; Sigma Tau Pharmaceuticals: Consultancy; Talon: Research Funding; The Medal Group: Speakers Bureau.

Equivalence of BCR-ABL Transcript Levels

AbstractAbstract 2495 Introduction:Response to therapy in patients with chronic myeloid leukemia (CML) is monitored by both cytogenetic assessment of bone marrow metaphases and quantitative reverse transcriptase polymerase chain reaction (RT-PCR) of peripheral blood samples. Although standardization of BCR-ABL quantification according to the international scale (IS) provides results comparable between different laboratories, current treatment recommendations are still predominantly based on cytogenetic analyses. The aim of this work was to determine a BCR-ABL expression level according to the IS (BCR-ABLIS) which corresponds to complete cytogenetic remission (CCyR). Patients:1,329 paired cytogenetic and molecular assessments of 557 chronic phase CML patients on imatinib-based therapies from the German CML study IV, all during follow-up, have been considered. Median number of samples per individual was 3 (range 1–24). Only molecular evaluations derived from peripheral blood and from patients expressing b2a2 and/or b3a2 BCR-ABL transcripts were considered. Participating laboratories provided results standardized according to the international scale. For cytogenetic analyses at least 20 metaphases, evaluated by conventional chromosome banding analysis, were required. Paired molecular and cytogenetic analyses were performed within an interval of <3 days. Methods:Data was split randomly at the rate of 2:1 into learning and validation sample. 10,000 subsamples that contained no more than one observation per patient were repeatedly drawn randomly from the original learning sample, according to the bootstrap method Using these subsamples, the BCR-ABLIS expression level providing the best discrimination between CCyR and no CCyR was determined choosing the smallest p-value of the exact Fisher test. Only cut-off levels with p-values which were significant after adjustment for multiple testing were considered.To confirm these results, again 10,000 subsamples were randomly drawn from the original validation sample. For the cut-off points discovered in the learning sample, sensitivity and specificity for predicting a CCyR from the molecular data and the p-values from the Fisher test were calculated within each of these subsamples. Results:1329 cytogenetic analyses using a median of 25 metaphases (range, 20–30) of which 75% were in CCyR were compared with 1329 molecular data with a median BCR-ABLIS expression level of 0.055% (range, 0–237%). In the learning sample the most frequently found BCR-ABLIS value was 0.35%, but all values between 0.2% and 1.1% were similarly well-suited for separating between patients in CCyR and not in CCyR. Based on this range, two potential cut-off levels were chosen for validation, 0.35% and 1%. While the first one represents a value, where one would rather expect to underestimate the number of CCyRs, the latter represents a value, where one would rather expect to overestimate the number of CCyRs. For the level of 0.35% the p-value was below 0.05 for 67.2% of the 10,000 subsamples, the median p-value was 0.017. With a median value of 88.4%, CCyR cases were correctly identified while cases that were not in CCyR were correctly assessed with a median rate of 71.4%. For the 1% BCR-ABLIS level, the p-value was below 0.05 for 72.0% of the 10,000 subsamples with a median p-value of 0.011. At a median value of 96.0%, CCyR cases were correctly identified while cases that were not in CCyR were correctly assessed with a median rate of 60.0%. When restricting on BCR-ABLIS values between 0.1 and 10.0%, the median concordance rate was 76%. Conclusions:Compared to molecular analyses, cytogenetic assessment is imprecise and limited with regard to sensitivity. Thus, it is not surprising to find a range of molecular data equivalent to CCyR but not a one-to-one cut-off point. However, for practical reasons it seems desirable to have such a cut-off point. Since lack of CCyR is considered a failure criterion according to the ELN treatment recommendations, it is suggested to keep the proportion of patients small that are considered erroneously not to be in CCyR. Additionally, a considerable amount of patients in major molecular remission or even better is present in the sample, so there might be a slight bias towards lower cut-off values. Thus, BCR-ABLIS expression of <1% is considered to be equivalent to CCyR in chronic phase CML patients treated with imatinib with a median concordance rate of 89%. Disclosures:Haferlach:MLL Munich Leukemia Laboratory: Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Equity Ownership. Hochhaus:Novartis, BMS, MSD, Ariad, Pfizer: Consultancy Other, Honoraria, Research Funding. Müller:Novartis: Honoraria, Membership on an entity’s Board of Directors or advisory committees, Research Funding; Bristol-Myers Squibb: Honoraria, Membership on an entity’s Board of Directors or advisory committees, Research Funding.

Multiplex ligation dependent probe amplification (MLPA) for rapid distinction between unique sequence positive and negative marker chromosomes in prenatal diagnosis.

BackgroundSmall supernumerary marker chromosomes (sSMC) are extra structurally abnormal chromosomes that cannot be unambiguously identified with conventional chromosome banding techniques. These marker chromosomes may cause an abnormal phenotype or be harmless depending on different factors such as genetic content, chromosomal origin and level of mosaicism. When a sSMC is found during prenatal diagnosis, the main question is whether the sSMC contains euchromatin since in most cases this will lead to phenotypic abnormalities. We present the use of Multiplex Ligation Dependent probe Amplification (MLPA) for rapid distinction between non-euchromatic and euchromatic sSMC.Results29 well-defined sSMC found during prenatal diagnosis were retrospectively investigated with MLPA with the SALSA MLPA centromere kits P181 and P182 as well as with the SALSA MLPA telomere kits P036B and P070 (MRC Holland BV, Amsterdam, The Netherlands). All unique-sequence positive sSMC were correctly identified with MLPA, whereas the unique-sequence negative sSMC had normal MLPA results.ConclusionsAlthough different techniques exist for identification of sSMC, we show that MLPA is a valuable adjunctive tool for rapidly distinguishing between unique-sequence positive and negative sSMC. In case of positive MLPA results, genetic microarray analysis or, if not available, targeted FISH can be applied for further identification and determination of the exact breakpoints, which is important for prediction of the fetal phenotype. In case of a negative MLPA result, which means that the sSMC most probably does not contain genes, the parents can already be reassured and parental karyotyping can be initiated to assess the heritability. In the mean time, FISH techniques are needed for determination of the chromosomal origin.

Detection of Karyotype Evolution From Peripheral Blood by Sequential FISH Analyses of Circulating CD34+ Cells In MDS Patients: Results of the Ongoing German Multicenter Prospective Diagnostic Study

AbstractAbstract 2937 Introduction:Chromosomal aberrations in myelodysplastic syndromes (MDS) play a major role in diagnostics, pathogenesis, prognosis, and, more recently, in treatment allocations. The acquisition of clonal abnormalities in pts with initially normal karyotype, the expansion of an aberrant cell clone with a given anomaly or the occurrence of new abnormalities are called karyotype evolution (KE). A model of stepwise cytogenetic changes is proposed, but only a few systematic studies had focused on this phenomenon as yet. Chromosomal anomalies can be detected by conventional chromosome banding analyses of bone marrow (bm) metaphases and most of them are provable by Fluorescence in Situ Hybridization (FISH) of circulating CD34+ cells from peripheral blood (pb). Aims:To closely follow chromosomal aberrations from pb, to assess karyotype evolution and rare anomalies and to correlate the molecular-cytogenetic results with pb blood counts, bm morphology and treatment modalities. For this purpose, we initiated a German multicenter prospective, non-interventional diagnostic study in October 2008. Methods:Sequential FISH analyses were performed on immunomagnetically enriched circulating CD34+ cells from pb as follows: a “super-panel” (D7/CEP7, EGR1, CEP8, CEP XY, D20, p53, IGH/BCL2, TEL/AML1, RB1, MLL, 1p36/1q25, CSF1R) was used for initial screening, every 12 months during follow-up and in every case of suspected progression. A “standard-panel” (EGR1, D7/CEP7, CEP8, p53, D20, CEP X/Y, TEL/AML1) was performed for analyses at short intervals every 2 months in the 1st year and every 3 months during the 2nd year. Results were also correlated with those of conventional banding and FISH analyses performed on bm samples, which typically were collected every 6 months. Results:As yet, 205 pts have been included in the study. Concerning median age, gender distribution, and MDS subtypes (according to WHO and IPSS) the study cohort was representative for the disease. Up to date, chromosomal aberrations were detectable in 126 pts. (62%) by FISH from pb. Most of them had 1 or 2 anomalies, but there were even pts with 4 or more aberrations. The most common aberrations- as known from other studies based on bm analyses- were del(5q) (64%), aberrations of chromosome 7 (del(7q)/-7) (25%), allelic loss of p53 (12%), +8 (11%), del(20q) (10%) and aberrations of chromosome 21 (del(21q)/-21/+21) (7%). Interestingly, a 12p-deletion was detectable as often as a trisomy 8 (11%), and in most cases as part of complex aberrations. A loss of p53 was significantly associated with aberrations of chromosome 7: 67% of pts with aberrations of chromosome 7 showed an allelic loss of p53 at the same time. In 4 cases, a coexistence of del(7q) and -7 in the same clone was observed.Within a median observation time of 7 months (2-21), a KE was detectable from pb by FISH in 17 pts (13%) out of 135 with at least 2 sequential analyses. In most cases del(7q)/-7 developed as a new anomaly, and was followed in frequency by aberrations of chromosome 21. Conclusions:FISH analyses of enriched circulating CD34+ cells are a feasible, less-invasive method to detect chromosomal aberrations in MDS pts and to follow the clone size from peripheral blood. By that method we are able to observe karyotype evolution as a step wise process in detail and to follow even rare abnormalities to learn more about their clinical and prognostic impact. Disclosures:No relevant conflicts of interest to declare.

FISH analysis of circulating CD34+ cells as a new tool for genetic monitoring in MDS: Verification of the method and application to 27 MDS patients

In myelodysplastic syndromes (MDS) chromosomal anomalies can be identified in 50–80% of patients. They have a diagnostic and prognostic impact and are increasingly considered for therapeutic decisions. Cytomorphology and cytogenetic analyses of bone marrow (bm) cells define the goldstandard to diagnose MDS patients and to document treatment response. We present a novel method using peripheral blood (pb) for frequent cytogenetic monitoring: after immunomagnetic cell separation circulating CD34+ cells were analysed by fluorescence in situ hybridization (FISH). We compared FISH analyses of enriched and non-enriched pb and bm cells with conventional chromosome banding analyses of bm metaphases: analysing circulating CD34+ cells by FISH is a sensitive, reliable method to measure the abnormal cell clones in pb. This method is practicable, non-invasive, representative for the clonal situation in the bm, and has a predictive value. Its feasibility was proven in a cohort of 27 MDS patients.

Genome Wide SNP Analysis Reveals Frequent Cryptic Clonal Chromosomal Aberrations Including Uniparental Disomy (UPD) in Waldenstrom's Macroglobulinemia.

Abstract 3932Poster Board III-868 BackgroundWaldenstrom's macroglobulinemia (WM) is a rare lymphoproliferative disorder characterized by bone marrow (BM) infiltration of lymphoplasmacytic cells that secrete monoclonal IgM antibody. Approximately 50% of patients (pts) with WM exhibit a normal karyotype using either conventional chromosome banding analysis (CBA) or FISH approach. However, CBA is a low resolution method and FISH only target previously described abnormalities. Comparative genomic hybridization (CGH) array delineated the minimal deleted region on 6q deletion, the most frequent aberration in WM, and pointed out the role of NFKB pathway key regulators genes. However, tumour suppressor gene or oncogene involved in WM physiopathology is not known, to date. Partial uniparental disomy (UPD) induced by copy neutral loss of heterozygosity (LOH) are important mechanisms for tumour suppressor gene inactivation or oncogene activation in cancer. Recently, Single Nucleotide Polymorphism (SNP) based arrays had been described as a powerful high resolution method allowing both the detection of LOH and copy number alteration (CNA) analysis in the same experiment, a major advantage over CGH array. Our aim was to identify new CNA and LOH involved in WM pathogenesis using SNP arrays analysis. Material and Methods. BM samples of 12 pts with WM (7 males, mean age: 67 years, 7 symptomatic pts) were analysed. DNA was extracted following CD19 B cells selection. Genome-Wide Human SNP Array 6.0 (Affymetrix chips) was used to detect both LOH and CNA. In 6 pts, paired samples (tumor / normal T lymphocytes) were used as an intra-individual reference to identify germline polymorphisms. In the 6 left pts, CN polymorphisms were excluded using copy-number variants database (http://projects.tcag.ca/variation) and the reference genotyping data from the HapMap project. Size, position and location of genes were identified with UCSC Genome Browser HG18 assembly, LOH and CNA using genotyping console 3.02 software (Affymetrix) and Partek genomic suite. FISH analysis was performed to detect deletion 6q; 13q14, 11q22, TP53, trisomy 4 and 12 chromosomal aberrations using Vysis probes. ResultsSNP array detected 35 CNA (23 gains, 12 losses) in 9/12 pts, with a mean of 2.9 abnormalities per patient (range 0 to 10). 91% of CNA were observed in symptomatic pts. 50% of CNA were < 5 mb in size, the lower limit of detection by CBA. 15 cryptic aberrations were identified among the somatic CNA spread over 7 pts. These 11 gains and 4 losses are identified by *. Deletions were observed on chromosomal segments 1p36*, 3p21.*, 6q16-q27 (2pts), 8p21*, 8p23-q24, 9p21*, 11q22 (2pts), 16p13*, 19p13*. One cryptic homozygous deletion in 13q14 was identified. Gains were observed on chromosomal segments 3p26, 4p16-q35 (3pts), 4q24*, 5p15 (2pts)*, 5p14, 7p22, 12p13-q24, 16p13*, 17q11*, 18p11-q23, 19p13-q13, Xq21* (5pts), Xq22*, Xq25*, Xp22-q28, Xq27-q28*(2pts).We also identified 42 LOH in 9/12 pts (mean of 3.5 per genome, range 0 to 7) dispersed on 17/23 chromosomes. The LOH observed in the absence of CNA loss are consistent with UPD in 35 cases (83%). 59% of LOH were observed in symptomatic pts. The interstitial or telomeric UPD regions varied in size, from 0.4 to 154mb. Two recurrent regions were identified on chromosome 4 (1.2mb involving genes DCLK2 and LRBA) and 13 (0.8mb involving genes KPNA3, ARL11 and SETDB2), probably subsequent to mitotic recombination. No UPD was observed on chromosome 6q.SNP arrays detected all FISH and CBA findings, except in one pt with subclonal deletion of TP53. Of the 5 pts with normal CBA or FISH, SNP array detected a CNA and 4 UPD in one patient and 7 UPD in an other patient. The remaining 3 cases (25%) had no detected CNA or LOH.Overall, SNP array detected a total of 77 genetic aberrations (CNA + LOH) (6.4 per genome, range 0 -16) in this cohort allowing the selection of 976 relevant genes (159 implicated in cellular growth and proliferation, 165 in cancer, 69 in cell cycle). ConclusionNew cryptic clonal chromosomal lesions were detected using high resolution SNP array in this study. Several abnormalities were recurrent. We described a high frequency of UPD in WM, that might contribute to the inactivation of tumour suppressor genes by mutations or epigenetic alterations and subsequently to the regulation of tumor progression in WM. Further confirmation of the role of these candidate genes is underway. Disclosures:Leleu:Celgene: Research Funding; Janssen Cilag: Research Funding; Chugai: Research Funding.

Genome-wide profiling of DNA copy number abnormalities in adult acute myeloid leukemia (AML) using high density single nucleotide polymorphism array

7023 Background: Acute myeloid leukemia (AML) is a heterogeneous disease with various chromosomal aberrations. The karyotype at diagnosis provides important prognostic information that influences therapy and outcome of this disease. However, using conventional chromosome banding techniques alone, karyotype abnormalities are detected in only half of all AML cases. We performed a genome-wide, single-nucleotide polymorphism (SNP) analysis in order (i) to identify novel genomic regions of interest in normal karyotype AML; (ii) novel candidate regions and disease-related genes, in patients with complex karyotypes. Methods: 20 AML patients were analyzed until now. Cases included FAB-M0, M1, M2, M4, M5, miscellaneous cytogenetic abnormalities and normal karyotype. 250 ng of genomic DNA were processed on 500K SNP array according to protocols provided by the manufacturer. Copy number state was calculated with respect to a set of 48 Hapmap normal individuals and a set of samples obtained from acute leukaemia cases in remission using Partek Genomics Suite. Results: An enormous spectrum of different genetic lesions (gains/losses) involving complete chromosome arms (del 16q, i(13q10), del 3p, del 7p, monosomy 9) or submicroscopic genomic intervals were identified in a substantial proportion of cases without differences in the frequency of losses or gains. The most frequent genomic gains affected: 9p12 (ZNF658B, FOXD4L2), 10q11.2 (PPYR1), 5q31-q33 (CDX1) and 8p23.2 (CSMD1). The most frequent deletions were identified in regions lacking annotated genes. Other recurring genetic lesions were uncommon. Marked differences in the combination of copy number anomalies were identified across the different genetic subtypes of AML. Some lesions affected regions with a single gene, such as: ETAA1, FIGN, STK32B, PRAGMIN, PCM1, GLIS3, MRGPRX1, SESN3, BCL2L14. Conclusions: Different genetic anomalies were identified by using an SNP-based chip array. Genetic abnormalities are associated with disease subtype. Supported by: European LeukemiaNet, AIL, AIRC, FIRB 2006, Fondazione del Monte di Bologna e Ravenna, PIO project 2007, Strategico di Ateneo. No significant financial relationships to disclose.