High-Resolution Genomic Arrays Facilitate Detection of Novel Cryptic Chromosomal Lesions in MDS.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 370-370
Author(s):  
Christine L. O’Keefe ◽  
Ramon Tiu ◽  
Lukasz Gondek ◽  
Aaron Viny ◽  
Karl Theil ◽  
...  
Keyword(s):  
High Resolution ◽  
Chromosomal Abnormalities ◽  
Bone Marrow Cells ◽  
Genomic Analysis ◽  
Normal Karyotype ◽  
Chromosome 7 ◽  
Comparative Genomic ◽  
Stem Loop ◽  
Monosomy 7 ◽  
Normal Cytogenetics

Abstract The evolution of abnormal hematopoietic clones characterized by acquired chromosomal abnormalities is the central event in the pathogenesis of MDS. Defective chromosomes have significant clinical implications in the management of MDS and suggest the presence of an inherent chromosomal instability. As karyotypic lesions are not found in all MDS patients, it is possible that in some the dysplastic clone may evolve without a chromosomal defect or, more likely, the resolution of routine metaphase cytogenetics is not sufficient to detect smaller lesions; in many instances lack of growth precludes the analysis. Array-based comparative genomic hybridization (A-CGH) allows for a high-resolution genomic scan that circumvents some of the limitations associated with the use of conventional cytogenetics. We hypothesized that high-resolution genomic analysis of genetic gains and losses by A-CGH may detect cryptic lesions, particularly in patients with negative/non-informative cytogenetics that may be of clinical/scientific significance. We examined bone marrow cells from 39 MDS patients (18 RA/RARS, 11 RAEB-t, 6 CMML and 4 secondary AML) and 11 controls using a 2632 BAC microarray and CGH. Dye swapping on duplicate arrays assured reproducibility of the CGH results, confirmed globally by a high resolution 50K SNP microarray in 4 patients and by microsatellite analysis in others. By traditional cytogenetics 19 patients had chromosomal lesions, 18 were normal and 2 tests non-informative. When A-CGH was applied, a normal karyotype was found in only 15% of patients in comparison to 46% by metaphase cytogenetics. Of note is that both cases with uninformative cytogenetics showed an abnormal CGH result and in several patients (N=11) with an abnormal karyotype additional lesions were found. Karyotypic results were confirmed in 7 cases; discordant analysis may be due to a lower proportion of dysplastic cells in marrow. Irrespective of the genomic area affected, when we studied the raw number of lesions more advanced forms of MDS (RAEB-t/AML) were evenly distributed between patients subdivided on sheer number of lesions (0, 1–17, >17). Many hotspots of genomic instability shared between patients were identified. For example, 1p26.3, 10q26 and 4p16 lesions were found in 2 or more patients. Interestingly, these regions contain genes of potential pathologic significance, including tubulin gamma complex associated protein 2 (TUBGCR2) and histone stem-loop binding protein (SLBP). Cryptic lesions on chromosome 7 (e.g. 7p21, 7q31) were identified in 5 patients with normal cytogenetics. These patients suffered from severe cytopenias, consistent with the prognosis of monosomy 7 and highlighting a consensus defect on chromosome 7. Certain chromosomes were rarely or never affected, implying that a more targeted array might be designed for clinical use. A-CGH Cytogenetics Unsuccessful Normal Abnormal Unsuccessful (N=2) 0 0 2 Normal (N=18) 0 3 15 Abnormal (n=19) 0 3 16 In summary, our study highlights the superior level of resolution of A-CGH as compared to metaphase analysis in the diagnosis of MDS. A prospective analysis is underway to determine the prognostic value of CGH-detected lesions and their pathophysiologic significance.

Distinct clinical outcomes for cytogenetic abnormalities evolving from aplastic anemia

Blood ◽  
2002 ◽  
Vol 99 (9) ◽  
pp. 3129-3135 ◽  
Author(s):  
Jaroslaw P. Maciejewski ◽  
Antonio Risitano ◽  
Elaine M. Sloand ◽  
Olga Nunez ◽  
Neal S. Young
Keyword(s):  
Aplastic Anemia ◽  
Chromosomal Abnormalities ◽  
Bone Marrow Cells ◽  
Chromosome 7 ◽  
Trisomy 8 ◽  
Monosomy 7 ◽  
Cytogenetic Abnormalities ◽  
Constant Rate ◽  
Structural Abnormalities ◽  
Actuarial Risk

Abstract A serious complication of aplastic anemia (AA) is its evolution to clonal hematologic diseases such as myelodysplasia (MDS) and leukemia, which is usually associated with the appearance of a cytogenetic abnormality in bone marrow cells. We present here an analysis of a cohort of 30 patients with otherwise typical AA in whom clonal karyotypic evolution was observed during frequent periodic marrow examinations. The actuarial risk for this complication has been estimated in other studies at around 15% at 5 years. Conversion from normal to abnormal karyotype occurred at a constant rate after initial diagnosis, with about 50% of cases developing within the first 30 months. Transient chromosomal abnormalities were infrequent. Clinically, AA patients with clonal cytogenetic patterns were heterogenous; a variety of karyotypic defects with numerical and structural abnormalities of chromosome 7 accounted for 40% of all cases followed by trisomy 8, structural and numerical abnormalities of chromosome 13, deletion of Y chromosome, and complex cytogenetic abnormalities. Unlike in primary MDS, aberrancies of chromosome 5 and 20 were infrequent. The clinical course depended on the specific abnormal cytogenetic pattern. Most deaths related to leukemic transformation occurred in patients with abnormalities of chromosome 7 or complex cytogenetic alterations or both. Evolution of chromosome 7 abnormalities was seen most often in refractory patients who had failed to respond to therapy. In contrast, trisomy 8 developed in patients with good hematologic responses who often required chronic immunosuppression with cyclosporine A (CsA), and survival was excellent. Although AA patients with monosomy 7 showed a similar prognosis to those with primary MDS, trisomy 8 in AA appears to have a more favorable prognosis than in MDS.

scholarly journals Discovery and comparative genomic analysis of elk circovirus (ElkCV), a novel circovirus species and the first reported from a cervid host

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mathew Fisher ◽  
Thomas M. R. Harrison ◽  
Michelle Nebroski ◽  
Peter Kruczkiewicz ◽  
Jamie L. Rothenburger ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Analysis ◽  
Rocky Mountain ◽  
International Committee ◽  
Comparative Genomic Analysis ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Stem Loop ◽  
Genome Wide ◽  
Replication Region

Abstract The complete genome sequence of a novel circovirus (elk circovirus (ElkCV) Banff/2019) was determined via high throughput sequencing of liver tissue from a euthanized Rocky Mountain elk (Cervus canadensis nelsoni) from Alberta, Canada. The genome is circular and 1,787 nucleotides long, with two major ORFs encoding predicted proteins. Comparative genomic analysis to 4,164 publicly available complete and near complete circovirus genomes showed that ElkCV shares approximately 65% pairwise genome-wide nucleotide identity with the most closely related circovirus species, porcine circoviruses (PCV) 1 and 2 and bat-associated circovirus (BatACV) 11. ElkCV features a stem-loop within the origin of replication region characteristic of circoviruses. However, it differs from those found in PCV1, PCV2 and BatACV11 since it has a longer stem and contains hexamer repeats that overlap the stem in opposing orientations. Interestingly, stem-loop structures of similar length featuring repeats in a similar position and orientation are also seen in some avian circoviruses. Based on the demarcation threshold established by the International Committee on Taxonomy of Viruses (ICTV) for members of Circoviridae (80% pairwise genome-wide nucleotide identity), ElkCV represents a novel species and is the first complete circovirus genome reported from a cervid host.

scholarly journals Prognostic implications of morphology and karyotype in primary myelodysplastic syndromes

Blood ◽  
1986 ◽  
Vol 67 (6) ◽  
pp. 1765-1772 ◽  
Author(s):  
RH Jacobs ◽  
MA Cornbleet ◽  
JW Vardiman ◽  
RA Larson ◽  
MM Le Beau ◽  
...  
Keyword(s):  
Median Survival ◽  
Myelodysplastic Syndromes ◽  
Chromosomal Abnormalities ◽  
Bone Marrow Cells ◽  
Normal Karyotype ◽  
Refractory Anemia ◽  
Survival Times ◽  
Trisomy 8 ◽  
Leukemic Transformation ◽  
Abnormal Karyotype

Abstract Forty-nine patients with primary myelodysplastic syndromes (MDS) were subclassified according to French-American-British (FAB) Cooperative Group criteria. Eight patients had acquired idiopathic sideroblastic anemia (AISA), ten had chronic myelomonocytic leukemia (CMMoL), 14 had refractory anemia (RA), nine had refractory anemia with excess blasts (RAEB), and five had refractory anemia with excess blasts in transformation (RAEB-T); three patients could not be subclassified. The actuarial median survival for patients with AISA or with RA had not been reached at 60 months of follow-up. The median survival times for patients with CMMoL, RAEB, and RAEB-T were 25, 21, and 16 months, respectively. The percentages of patients with each subtype who developed ANLL were none in AISA, 20% in CMMoL, 7% in RA, 56% in RAEB, and 40% in RAEB-T. Patients with CMMoL had a poor prognosis independent of transformation to acute nonlymphocytic leukemia (ANLL), whereas patients with RAEB and RAEB-T had a high incidence of transformation and short survival times. Clonal chromosomal abnormalities were present in bone marrow cells from 19 patients at the time of diagnosis, and two others developed an abnormal karyotype at the time of leukemic transformation. The most frequent abnormalities, including initial and evolutionary changes, were trisomy 8 (9 patients), deletion of 5q (4 patients), and deletion of 20q (4 patients). The median survival times were 32 months for patients with an abnormal karyotype, and 48 months for those with a normal karyotype (P = 0.2). Specific chromosomal abnormalities were not associated with particular histologic subtypes; however, a high percentage of patients with RAEB and RAEB-T had an abnormal clone (89% and 80%, respectively). The percentages of patients with clonal abnormalities were 13% for AISA, 20% for CMMoL, and 29% for RA. The MDS transformed to ANLL in 42% of patients with an abnormal karyotype, compared to 10% of those with an initially normal karyotype (P less than .01). Among patients with RA, RAEB, and RAEB-T, the risk of leukemic transformation was confined to those with an abnormal karyotype (P less than .01). Thus, in the present study, morphology and karyotype combined were the best indicators of outcome in patients with MDS.

Chromosomal Abnormalities in MDS Are Linked to Dysregulation of CDC20 and CEP55 Genes

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 36-37
Author(s):  
Mayara Magna de Lima Melo ◽  
Daniela de Paula Borges ◽  
Antônio Wesley Araújo Dos Santos ◽  
Gabrielle Melo Cavalcante ◽  
Leticia Rodrigues Sampaio ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Chromosomal Instability ◽  
Spindle Assembly Checkpoint ◽  
Chromosomal Abnormalities ◽  
Bone Marrow Cells ◽  
Conflicts Of Interest ◽  
Normal Karyotype ◽  
Mitotic Arrest ◽  
Complex Karyotype ◽  
Increased Risk

Myelodysplastic syndrome (MDS) is a clonal hematopoietic disorder characterized by cytopenias and an increased risk of progression to acute myeloid leukemia (AML). Its pathogenesis is strictly linked to chromosomal instability, which in turn provides a valuable prognostic marker. Malignant cells develop alternative routes to escape mitosis checkpoints, overcoming the mitotic arrest imposed by Spindle Assembly Checkpoint (SAC), a process dependent on CDC20 inactivation. Abnormal levels of CDC20 can inhibit mitotic arrest, promoting premature exit from mitosis. Overexpression of CEP55 also facilitates the mitotic exit, resulting in polyploidy (an event called Mitotic Slippage). Since chromosomal abnormalities are one of the most important prognostic factors for patients with MDS, this study aimed to analyze the possible link between chromosomal abnormalities and CDC20 and CEP55 mRNA expression in MDS. We evaluated the bone marrow cells from 45 patients diagnosed as MDS according to 2016 WHO-classification (1 MDS-SLD, 15 MDS-RS-MLD, 5 MDS-MLD, 1 t-MDS, and 23 MDS-EB) and 5 bone marrow of healthy controls. Conventional Karyotyping was performed by G-banding of 20 metaphases whenever possible. TaqMan expression assays for CDC20 (Hs00426680_mH) and CEP55 (Hs01070181_m1) were performed in duplicate and the expression ratios were calculated using the 2−ΔCq method. Normality was evaluated by Shapiro-Wilk test. Outliers were removed. The Student's t-test or one-way ANOVA with Tukey/Games Howell post-hoc test was used to analyze the influence of relative expression regarding variables. Patients with MDS showed increased expression of CDC20 and CEP55 compared to healthy individuals (p<0.0001 and p<0.0001). Regarding karyotype, there was the overexpression of CDC20 and CEP55 in patients with altered karyotype and aneuploid karyotype when compared to patients with normal karyotype (p <0.0001 and p =0.001; p = 0.013 and p = 0.022, respectively) (Figure 1A-D). CDC20 and CEP55 have fundamental functions in controlling the progression of metaphase to anaphase and both, when upregulated, induce chromosomal instability. Additionally, patients with del(7q) and complex karyotype showed hyperexpression of CEP55 when compared with patients with normal karyotype (p = 0.005 and p = 0.019) (Figure 1E-F), while patients with deletion (5q) had an increased expression of CDC20 when compared with patients with normal karyotype (p <0.0001). Our group previously demonstrate that high CDC20 protein expression is associated with complex karyotype in MDS patients. Thus, we hypothesized that the deregulation of CDC20 and CEP55 expression induces chromosomal changes, each one in its way. Both can cause disturbances in crucial phases of mitosis (anaphase and cytokinesis, respectively). Finally, we detected a strong correlation between CDC20 and CEP55 (r = 0.646; p <0.0001), suggesting both genes may play a synergistic role during chromosomal abnormalities in MDS, creating possible new targets to be evaluated in MDS. Our data suggest CDC20 and CEP55 as possible new therapeutic targets in MDS. There is a need for further studies, validations and urgent in-depth investigations in cell lines/primary samples or murine models. Disclosures No relevant conflicts of interest to declare.

High-Resolution Genomic Scan for Cryptic Chromosomal Lesions in MDS and AML.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3427-3427
Author(s):  
Christine L. O’Keefe ◽  
Evan Howe ◽  
Matt E. Kalaycio ◽  
Mikkael Sekeres ◽  
Anjali Advani ◽  
...  
Keyword(s):  
Copy Number ◽  
Chromosomal Abnormalities ◽  
Normal Karyotype ◽  
Hematologic Malignancies ◽  
Comparative Genomic ◽  
Telomeric Region ◽  
Fluorescent Intensity ◽  
Novel Technologies ◽  
Healthy Elderly ◽  
Chromosomal Changes

Abstract Cytogenetic analysis is of eminent importance for the diagnosis and prognosis of hematologic malignancies. Due to limitations of traditional karyotyping, novel technologies which improve resolution and sensitivity are under development. In array-based comparative genomic hybridization (A-CGH), differentially labeled test and reference DNA samples are hybridized to genomic microarrays. Differences in sequence copy number between the samples are reflected in a shift of the fluorescent intensity. The resolution of A-CGH is limited solely by the number of clones; it is theoretically possible to achieve linear coverage of the chromosomes. The principle of the CGH techniques allows for detection of unbalanced chromosomal changes of the whole genome. These types of genomic aberrations are most common in MDS, but may exist and further subclassify malignancies with defined balanced translocations. In MDS, depending on the study, 40–60% of patients have a normal or non-informative karyotype by traditional methods. It is likely that this number may be reduced if the resolution and sensitivity level is increased. Additionally, diagnosis of patients with known chromosomal abnormalities can be further refined. We first applied A-CGH to the analysis of normal marrow (N=8) to establish whether it will detect chromosomal defects that may acquired and are compatible with normal hematopoiesis. Moreover, defects may be present in healthy elderly. We utilized arrays of up to 2621 clones with a maxium coverage of 1Mb (Vysis, Spectral Genomics). The results were verified by a dye-swap protocol on two arrays per sample. Four controls showed a normal array profile or only changes in clones previously identified as having a polymorphic copy number within the human genome. The remaining controls had changes including a loss of material on 6p (N=1), loss of 6p and 8q material (N=1) and a gain of 4p and loss of 9p sequences (N=1). These changes may reflect unidentified polymorphisms. In contrast, one control had gains of multiple contiguous clones on chromosomes 9, 15 and 22. We also studied the marrow of patients with advanced MDS (N=43) using A-CGH and traditional cytogenetics. The cohort included patients with known singular lesions (N=7) and complex karyotypes (N=1). The remaining patients had either normal or non-informative cytogenetics. For a del 5q patient and a trisomy 21 patient, A-CGH verified the karyotype without identifying further lesions, in a second del 5q patient was a gain of material on 19p, and a monosomy X patient had a gain of 1p36 by CGH. In 3 cases with partially clonal defects, A-CGH did not detect the abnormality. A normal genomic composition was confirmed in a patient with noninformative (N=1) and normal (N=1) karyotypes. Losses of material on 2q and 3q and gains of material on 22q and the 11p telomeric region were identified in a patient with normal cytogenetics, while another "normal" had gains on 2p, 14q and 21q. Additionally, one normal karyotype had loss of chromosome 16 material and one had loss of 6p sequences. This pilot study demonstrates the utility of A-CGH analysis to study chromosomal aberrations in MDS. A-CGH allows for the detection of cytogenetically undetected abnormalities. Analysis of a large number of samples may allow for the detection of consensus defects or global genomic instability with clinical implications.

Genetic and Epigenetic Silencing of Mesoderm Specific Transcript (MEST) In Acute Myelogenous Leukemia.

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3639-3639
Author(s):  
Anna R Poetsch ◽  
Rainer Claus ◽  
Lars Bullinger ◽  
Tania Witte ◽  
Michael Lübbert ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Tumor Suppressor ◽  
Cpg Island ◽  
Normal Karyotype ◽  
Epigenetic Silencing ◽  
Myelogenous Leukemia ◽  
Chromosome 7 ◽  
Special Importance ◽  
Monosomy 7 ◽  
Chromosomal Changes

Abstract Abstract 3639 About 10 % of patients with either myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML) present either with deletions on the long arm of chromosome 7 or monosomy 7. These chromosomal aberrations are associated with a poor prognosis. Following biallelic inactivation as proposed by Knudsen, a “second hit” of the remaining allele might be required for loss of gene function. Epigenetic silencing might display such a hit in particular since no additional genetic hits could be identified so far. The role of epigenetic regulation might be of special importance in patients with -7/7q-, since several studies have shown that patients harbouring a chromosome 7 abberrations do more benefit from a therapy with demethylating agents as compared to patients with other chromosomal changes. To address the issue of epigenetic silencing in these AML cases we utilized DNA methylation profiling to identify the potential tumor suppressor genes on chromosome 7. We used MBD2 based enrichment of methylated DNA from 4 AML patient samples with monosomy 7 and from 23 patient samples with with other chromosomal changes including normal karyotype AML. For validation we analyzed regional DNA methylation using quantitative MassArray technology on DNA from 115 del(7q) AML or monosomy 7 patients as well as normal karyotype patients (n=20) and CD34 + cells from healthy individuals (n=5). We could identify the gene MEST to be silenced by hypermethylation (> 30 %) of a CpG island on the remaining allele in 20% of the patients with -7/7q- and 40% of patients with normal karyotype. Thus, preferentially in patients that do not have a deletion already. MEST is an imprinted gene located on 7q32.2. However, silencing is correlated with hypermethylation of a CpG island located at an alternative promoter of MEST, independent of the methylation status of the imprinting control region. In two patient samples with monosomy 7 and hypermethylation of MEST (> 80%), DNA methylation was erased after 5-Aza-2′-deoxycytidine (DAC) treatment to less than 10 %. In concordance, also AML cell lines with hypermethylation of the MEST locus loose methylation after sublethal DAC treatment which leads to a reexpression of the gene. Thus, we hypothesize that MEST functions as a tumor suppressor in AML and is genetically as well as epigenetically silenced AML. Reactivation of MEST by demethylating treatment may contribute to the mechanism by which demethylating drugs display their therapeutic potential in leukemia. Disclosures: No relevant conflicts of interest to declare.

scholarly journals High resolution genomic analysis of 18q− using oligo-microarray comparative genomic hybridization (aCGH)

2009 ◽  
Vol 149A (7) ◽  
pp. 1431-1437 ◽  
Author(s):  
Patricia L. Heard ◽  
Erika M. Carter ◽  
AnaLisa C. Crandall ◽  
Courtney Sebold ◽  
Daniel E. Hale ◽  
...  
Keyword(s):  
High Resolution ◽  
Comparative Genomic Hybridization ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Oligo Microarray ◽  
Microarray Comparative Genomic Hybridization

Identification of targetable cellular subsets within melanoma tumors

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. 9082-9082
Author(s):  
A. Sekulic ◽  
A. Miller ◽  
M. Barrett ◽  
S. Ejadi ◽  
A. Mengos ◽  
...  
Keyword(s):  
High Resolution ◽  
Dna Content ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Cancer Tissue ◽  
Cancer Therapies ◽  
Fresh Frozen ◽  
The Individual ◽  
Personalized Cancer ◽  
Molecular Aberrations

9082 Background: Human tumors, including melanoma, are complex mixtures of individual, molecularly distinct subpopulations, or clones of cancer cells. Effective cancer therapy will likely require targeting of all tumor subsets within a given cancer. Understanding the tumor complexity and the ability to identify points of therapeutic vulnerability within the individual tumor subsets will be essential for development of effective personalized cancer therapies. Methods: We have developed an approach that combines identification of individual tumor subsets using a multiparameter nuclear flow cytometry coupled with a high-resolution genomic analysis using the array-based comparative genomic hybridization (aCGH). Melanoma nuclei were isolated from tumor tissues and subjected to flow cytomery using melanocyte-specific antibodies (to separate melanoma cells from stroma) and DNA content, to separate individual tumor subpopulations. DNA extracted from isolated nuclear subpopulations was extracted and analyzed by aCGH. This approach was adopted for both fresh-frozen and paraffin-embedded clinical specimens. Results: We initially demonstrate the feasibility of the outlined approach by successful separation of melanoma from stromal nuclei and separation of individual melanoma nuclear subpopulations by DNA content. aCGH analysis of the DNA derived from isolated tumor subpopulations allowed successful identification of potentially targetable molecular aberrations in individual subsets of tumor cells. Notably, such aberrations were often not detected in unsorted, bulk tumors analyzed by the same high-resolution aCGH approach. Conclusions: We demonstrate a feasible approach to in-depth molecular analysis of tumor subpopulations within a clinical cancer tissue. This approach allows identification of potentially targetable molecular aberrations within individual tumor subsets, thus opening a possibility for a broad tumor targeting through design of individually-tailored therapeutic approaches. No significant financial relationships to disclose.

Disclosure of Copy Number Alterations in AML with Normal Karyotype Using Matrix-Based Comparative Genomic Hybridization.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 759-759
Author(s):  
Frank G. Rucker ◽  
Lars Bullinger ◽  
Hans A. Kestler ◽  
Peter Lichter ◽  
Konstanze Dohner ◽  
...  
Keyword(s):  
Molecular Markers ◽  
High Resolution ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Normal Karyotype ◽  
Comparative Genomic ◽  
Copy Number Alterations ◽  
Genomic Hybridization ◽  
Genomic Imbalances ◽  
Genome Wide

Abstract Clonal chromosome abnormalities represent one of the most important prognostic factors in adult acute myeloid leukemia (AML), and cytogenetic data are used for risk-adapted treatment strategies. By conventional cytogenetic analysis, approximately 50% of patients lack clonal chromosome aberrations, and normal cytogenetics are associated with an intermediate clinical outcome. This clinically heterogeneous group seems to be in part characterized by molecular markers, such as MLL, FLT3, CEBPA, and NPM1 mutations. In order to identify novel candidate regions of genomic imbalances, we applied comparative genomic hybridization to microarrays (matrix-CGH). Using this high-resolution genome-wide screening approach we analyzed 49 normal karyotype AML cases characterized for the most common clinically relevant molecular markers (MLL-PTD n=13, FLT3-ITD n=7, FLT3-ITD/NPM1+ n=4, MLL-PTD/FLT3-ITD n=3, CEBPA+ n=12, CEBPA+/FLT3-ITD n=1; CEBPA+/NPM1+ n=1; no molecular markers n=8) with a microarray platform consisting of 2799 different BAC or PAC clones. A set of 1500 of these clones covers the whole human genome with a physical distance of approximately 2 Mb. The remaining 1299 clones either contiguously span genomic regions known to be frequently involved in hematologic malignancies (e.g., 1p, 2p, 3q, 7q, 9p, 11q, 12q, 13q, 17p, 18q) (n=600) or contain oncogenes or tumor suppressor genes (n=699). In addition to known copy number polymorphisms in 5q11, 7q22, 7q35, 14q32, and 15q11, the CLuster Along Chromosomes method (CLAC; http://www-stat.stanford.edu/~wp57/CGH-Miner) disclosed copy number alterations (CNAs) in terms of gains in 1p, 11q, 12q, and 17p. CNAs in terms of losses were identified in 9p, 11q, 12p, 12q, and 13q. Two-class supervised analyses using the significance analysis of microarrays (SAM) method identified for the MLL-PTD cases a gain of a single clone harboring the MLL gene. While the significance of these findings, which are currently validated using fluorescence in-situ hybridization (FISH), still remains to be determined, our preliminary results already demonstrate the power and reliablity of this microarray-based technique allowing genome-wide screens of genomic imbalances as the MLL aberration was detected in all cases known to have a MLL-PTD. Furthermore, ongoing correlation of high-resolution genomic profiling with global gene expression studies will help to disclose pathways underlying normal karyotype AML, thereby leading to new insights of leukemogenesis.

Chromosomal Instability: A Probable Unfavorable Prognostic Factor For Patients Of Myeloidysplastic Syndromes

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 5243-5243
Author(s):  
Yajuan Xiao ◽  
Yuanlu Huang ◽  
Na Xu ◽  
Rong Lin ◽  
Xuan Zhou ◽  
...  
Keyword(s):  
Chromosomal Instability ◽  
Chromosomal Abnormalities ◽  
Conflicts Of Interest ◽  
Normal Karyotype ◽  
Chromosome 7 ◽  
Complex Karyotype ◽  
Karyotypic Analysis ◽  
Hematopoetic Stem Cell ◽  
Significant Difference

Abstract Objective Myelodysplastic syndromes (MDS) are a group of heterogeneous hematopoetic stem cell clonal disorders with a high frequency of karyotypic abnormalities (40-60%). Among karyotypic abnormalities, abnormal chromosome numbers (aneuploidy) occurs frequently. In aneuploidy, chromosomal instability (CIN) is defined as persistent mis-segregation of whole chromosomes and is caused by defects during mitosis with an odd number of chromosomes. CIN is associated with tumor heterogenesis, multidrug resistance and aggressiveness in solid tumor. Hence, we performed a one-center study on MDS patients to uncover the role of CIN in MDS clinical development. Method A total of 104 cases , 62 male and 42 female, aged from 15 years to 89 years, were tested by fluorescent in situ hybridization (FISH) and karyotypic analysis before any therapeutic intervention. According to the cytogenetic analysis of those two technology they were separated into 5 groups including: CIN, normal karyotype, complex karyotype excluding CIN, deletion chromosome 7 abnormality and other chromosomal abnormalities. All cases were followed up for a median of 19.5 months. Results Karyotyping and FISH identified 70 (67.3%) patients with abnormal karyotypes containing 32 cases of CIN, 9 cases of deletion chromosome 7 abnormality and 5 cases of complex karyotype excluding CIN. The median survival for CIN group was 13 months (incredible interval:6-20 months) compared with 23 months (incredible interval :20-27 months) in all cases, 44months in normal karyotype, 23 months in deletion chromosome 7 abnormality and 13 months in complex karyotype excluding CIN group (P=0.001 for log rank method). In CIN group, 11 cases transformed into acute leukemia with a incidence of 34% with no significant difference with total cases. And the length of time for leukemia transformation shows no significant difference between CIN group and total cases. Conclusion Chromosomal instability in MDS patients of the study revealed worst prognosis compared with other groups. This may suggest that chromosomal instability in MDS chromosomal abnormality confer a significant independent adverse impact on patients survival. However this effect might have no relation to leukemia transformation. Disclosures: No relevant conflicts of interest to declare.

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