Band 14q32 Research Articles

Identification of a submicroscopic 3.2 Mb chromosomal 16q12.2‐13 deletion in a child with short stature, mild developmental delay, and craniofacial anomalies, by high‐density oligonucleotide array‐a recognizable syndrome

Interstitial deletion of 16q has emerged into a recognizable pattern of congenital malformation. We report on a 9-year-old boy with short stature, psychomotor retardation, high forehead, broad flat nasal bridge, hypertelorism, cup-shaped ears, short neck, and a normal karyotype. Using high-density oligonucleotide array chip (Affymetrix 6.0) to perform parental and proband samples concurrently on three chips and interpreted as a trio set, a de novo 3.2 Mb deletion from bands q12.2 to q13 on chromosome 16 (from 52.08 to 55.3 Mb) of paternal origin was identified. The deletion was confirmed by quantitative genomic PCR and the break points were defined by junction PCR. Our study demonstrated the power of high-density oligonucleotide array chip in identifying novel submicroscopic deletions that were not detectable using G-banding cytogenetic technology. Furthermore, our result narrowed down the critical region for craniofacial features in interstitial 16q11.2-q13 deletion syndrome. In patients who have high forehead, broad flat nasal bridge, hypertelorism, cup-shaped ears, short neck and short stature, high-density array should be included in initial work up.

Cytogenetic and molecular characterization of double inversion 3 associated with a cryptic BCR-ABL1 rearrangement and additional genetic changes

Rearrangements of chromosome 3 involving bands 3q21 and 3q26 have been reported in about 2% of patients with acute myeloid leukemia, and rarely in myelodysplastic syndrome or chronic myelogenous leukemia (CML). To date, only six cases of inversion of both homologues have been reported. Loss of normal chromosome 3 and duplication of the inverted chromosome have been proposed as the most likely mechanism, but have not been shown experimentally. We present a 36-year-old male with an initial diagnosis of CML and resistance to imatinib mesylate. Chromosome analysis showed an inversion within the long arm of both homologues of chromosome 3 and an interstitial deletion within the long arm of one chromosome 7. The rearrangement of EVI1 locus on both homologues of chromosome 3 was confirmed by fluorescence in situ hybridization (FISH). Additional FISH studies showed a cryptic insertion of ABL1 into the BCR region, and subsequent duplication of the derivative chromosome 22. The single-nucleotide polymorphism array showed copy-neutral loss of heterozygosity on chromosomes 3 and 22, suggesting that a somatic repair mechanism is involved in the evolution of these genetic alterations. This case illustrates the complexity of genetic aberrations in neoplastic cells, and the value of array technology, used in concert with conventional cytogenetic methods, for a better understanding of the pathogenesis.

The refinement of the critical region for the 2q31.2q32.3 deletion syndrome indicates candidate genes for mental retardation and speech impairment

Current literature provides more than 30 patients with interstitial deletions in chromosome 2q31q33. Only a few of them were studied using high-resolution methods. Among these, two patients had presented with a particular consistence of some clinical features associated to a deletion between bands q31.2 and q32.3 of chromosome 2. This clinical pattern, labeled as "2q31.2q32.3 syndrome," consists of multiple dysmorphisms, developmental delay, mental retardation and behavioural disturbances. We report an adult female patient with a 4.4 Mb deletion in the 2q31.2q32.3 region, showing facial dysmorphisms, mental retardation and absence of speech. The region overlaps with the deletion found in the two cases previously reported. The critical region points to a few genes, namely NEUROD1, ZNF804A, PDE1A, and ITGA4, which are good candidates to explain the cognitive and behavioural phenotype, as well as the severe speech impairment associated with the 2q31.2q32.3 deletion.

Incidence and susceptibility to therapy-related myeloid neoplasms

Therapy-related myeloid neoplasms (t-MN) include acute myeloid leukemias and myelodysplastic syndromes arising in patients who have been treated with chemotherapy, radiation therapy, immunosuppressive agents or after documented exposure to environmental carcinogen. t-MN are defined according to the primary treatment and the corresponding genetic and molecular lesions. Chromosome(s) 7 and/or 5 monosomies or deletions are typical of alkylating agent-induced AML, while balanced translocations involving chromosome bands 11q23 and 21q22 are associated to preceeding therapy with DNA-topoisomerase II inhibitors. Antimetabolites, and in particular the immunosuppressive agents azathioprine and fludarabine, have also been recently associated to t-MN. Leukemias developing after benzene exposure are similar to t-MN and are characterized by chromosomal aberrations, which have been also observed among otherwise healthy benzene-exposed workers. Individual predisposing factors, including polymorphisms of detoxification and DNA-repair enzymes have been identified. Two genetic variants in key metabolizing enzymes, myeloperoxidase and NAD(P)H:quinone oxidoreductase, have been shown to influence susceptibility to benzene hematotoxicity. Combination of polymorphisms impairing detoxification and DNA repair may significantly increase therapy-related myeloid neoplasm risk. Among hematological malignancies, long-term survivors of Hodgkin's lymphoma are exposed to an increased t-MN risk, particularly when receiving MOPP-based and escalated-BEACOPP regimens, and when alkylators are combined to radiotherapy. Patients with lymphoma are at highest risk if total body irradiation followed by autologous stem cell transplantation is used as rescue or consolidation. The addition of granulocyte-colony stimulating factor (G-CSF) and radiotherapy plays a significant role in t-MN following treatment of childhood acute lymphoblastic leukemia. In solid tumors, treatment for breast cancer and germ-cell tumors has been associated with a 1–5% lifetime risk of t-MN.

Therapy-Related Chronic Myeloid Leukemia and Myelodysplastic Syndrome with -7, t(9;22), and 5q-, t(9;22).

Abstract 4726 IntroductionTherapy-related hematologic diseases are known to include acute myelocytic leukemia (AML) and myelodysplastic syndromes (MDS), but reports of therapy-related chronic myeloid leukemia (CML) are rare. Philadelphia chromosome-positive (Ph+) CML has been described in patients who were previously exposed to alkylating agents or topoisomerase II inhibitors. Below, we present a patient with Ph+ CML and MDS with both monosomy 7 (-7) and deletion of the long arm of chromosome 5 (5q-) following chemotherapy and radiation for pleomorphic liposarcoma. CaseAn 80 year old African American man was diagnosed with pleomorphic liposarcoma involving his right thigh fourteen years ago. He received six cycles of peri-operative chemotherapy with cyclophosphamide, doxorubicin and dacarbazine, and adjuvant radiation therapy. Six years later, he received seven cycles of dacarbazine, ifosfamide/mesna and etoposide peri-operatively for a recurrence in the abdomen. Twelve years later, he received sixteen cycles of gemcitabine and docetaxel for another intra-abdominal recurrence, with disease progression. He then received a study drug, ANG (1-7) for a year, with disease progression. This was treated with radiation therapy to the abdominal site, completed three months ago. On routine follow up, he was doing well and had an unremarkable physical examination. A CT scan of his abdomen revealed stable disease. He was noted to have a WBC count of 30,000/microliter with 61% segmented neutrophils, 5% band neutrophils, 6% metamyelocytes, 4% myelocytes, 2% basophils, 1% eosinophils, 14% monocytes and 7% lymphocytes. Hemoglobin was 12.6 grams/deciliter and platelets 129,000/microliter. A bone marrow biopsy showed marked granulocyte hyperplasia with large paratrabecular aggregates of immature myeloid precursors. Megakaryocytes were increased in number with dysplastic features including small, hyperchromatic and hypolobated forms. There was frequent clustering. There were no dysplastic features in the erythroid cell line. Background hematopoiesis was decreased. There was no increase in blasts. 11 cells were karyotyped with a band resolution of 450, revealing 2 cell lines. One was an abnormal clonal male cell line with t(9;22) and monosomy 7. The other, had t(9;22) and deletion of the long arm of chromosome 5. Peripheral blood RT-PCR for BCR-ABL gene rearrangement quantitation showed a ratio of 1.607 of fusion transcript to control. A diagnosis of therapy-related CML in chronic phase and MDS was thus made. His IPSS score is intermediate-1. He is currently on imatinib mesylate, which he is tolerating well. After 2 weeks of therapy, his WBC count was 7,800/microliter with a normal differential count, hemoglobin 10.7 grams/deciliter and platelets 86,000/microliter. DiscussionThe presence of -7 and t(9;22) in one cell line, and 5q- and t(9;22) in the other implies that the t(9;22) may have been an earlier event. Abnormalities in chromosome 5 and 7 are typically associated with therapy-related MDS and AML following exposure to alkylating agents, and carry a poor prognosis. The abnormalities involving chromosomes 5 and 7 affecting the cells carrying the t(9;22) overwhelmingly support a diagnosis of therapy-related CML. Topoisomerase II inhibitors have been associated with therapy-related AML with balanced translocations involving the chromosome bands 11q23 and 21q22. The t(9;22) could have arisen as a result of mitotic, non-homologous chromosomal recombination of topoisomerase II-induced double-strand breaks of DNA. In this case, CML is the presenting diagnosis of therapy-related malignant hematologic disease. This patient was initiated on treatment for CML, but close follow up will be maintained regarding his MDS. ConclusionTherapy-related CML should be considered in patients who have had chemotherapy and/or radiation. It may present prior to the onset of other more fatal therapy-related hematologic disorders, and therefore has implications on treatment and long term follow up. Disclosures:Powell:Novartis Pharmaceuticals: Research Funding.

Correlation between losses ofIGHor its segments and deletions of 13q14 in t(11;14) (q13;q32) multiple myeloma

Multiple myeloma (MM) is a malignancy of the plasma cells (PCs) characterized by a wide variety of genetic and chromosomal abnormalities. In recent years, major attention was drawn to the significance of chromosomal aberrations involving chromosome arm 13q and the IGH region on chromosome band 14q32 as a prognostic indicator in MM. In this study we applied a combined cell morphology and FISH method for the analysis of coexistence of t(11;14)(q13;q32) with deletions of the long arm of chromosome 13 (Delta13) in PCs from 51 MM patients using several probes for the 13q14, 11q13, and IGH regions. We found 15 different variants of the t(11;14) that are the consequence of different 11q13 breakpoints and various deletions of Variable (del IGH Var) or Constant (del IGH Const) IGH segments and also duplications and losses of the IGH gene on the normal nontranslocated chromosome 14 as well as IGH/Cyclin D1 (CCND1) fusion on der(14) and CCND1/IGH fusions on der(11). A strong association between Delta13 and specific variants of t(11;14) was found: variants with deletion of the IGH gene or its segments were found only in MM cases with deleted chromosome 13, while the common translocation t(11;14) was found only in the MM cases with normal chromosome arm 13q. In contrast, we did not find any association between Delta13 and deletions of the IGH gene or its segments in the MM patients with t(4;14)(p16;q32).

Acute myeloid leukaemia with associated eosinophilia: justification for FIP1L1‐PDGFRA screening in cases lacking the CBFB‐MYH11 fusion gene

Acute myeloid leukaemia with associated eosinophilia: justification for <i>FIP1L1‐PDGFRA</i> screening in cases lacking the <i>CBFB‐MYH11</i> fusion gene

BCL2 and BCL3 are recurrent translocation partners of the IGH locus

Chromosomal translocations affecting the immunoglobulin heavy chain ( IGH) locus in chromosomal band 14q32 are the most frequent cytogenetic changes in B-cell lymphomas. We studied the presence of IGH translocations in a consecutively ascertained series of 94 classical Hodgkin lymphomas (cHL) by combined immunofluorescence for CD30 and interphase cytogenetics (FICTION technique). The Hodgkin and Reed–Sternberg cells of a total of 11 of 87 evaluable cases (13%) showed signal patterns indicative of IGH translocations. To identify the translocation partners, these cases were further studied with probes for the MYC, BCL2, BCL6, BCL3, REL/BCL11A, JAK2/PDCD1LG2 (alias PDL2) C14orf43, and C2TA loci. The IGH translocation partner could be identified in four cHL and involved BCL2 and BCL3 in two cases each. Immunohistochemistry in cases with suitable material revealed that tumor cells of the two cHL with IGH/BCL2 fusion and the cHL with IGH/BCL3 fusion expressed the BCL2 and BCL3 protein, respectively. These data indicate that BCL2 or BCL3 are recurrent translocation partners of the IGH locus in cHL; however, most of the translocation partners of IGH translocations in cHL remain to be identified.

Rearrangements of chromosome 9 in different hematological neoplasias

The frequencies of chromosome 9 abnormalities in children with hematological neoplasia have constituted: 25/112 in acute lymphoblastic leukemia (ALL), 10/83--in acute myeloid leukemia (AML), 3/20--in refractory anemia (RA). The frequency of deletions was higher than of translocations in ALL. Deletions were found as sole abnormalities as in complexity karyotypes. More often the rearrangements affected bands 9q34 and 9q22. Translocation t (9;22)(q34; q11) occured in 7.1% cases ALL. In AML the translocations were detected with greater frequency than deletions. The long arm bands 9q22 and 9q34 were more often involved in structural rearrangements. Deletions, translocations and duplications were registered in MDS. Comparison with clinical features showed no correlation with age and the main hematological indexes including the amount of blast cells in initial period. Multidrug resistance and disease progression during chemotherapy were noted in t (9;22).

Rearrangement and allelic imbalance on chromosome 5 leads to homozygous deletions in the CDKN2A/2B tumor suppressor gene region in rat endometrial cancer

The inbred BDII rat is a valuable experimental model for the genetic analysis of hormone-dependent endometrial adenocarcinoma (EAC). One common aberration detected previously by comparative genomic hybridization in rat EAC is loss affecting mostly the middle part of rat chromosome 5 (RNO5). First, we applied an RNO5-specific painting probe and four region-specific gene probes onto tumor cell metaphases from 21 EACs, and found that rearrangements involving RNO5 were common. The copy numbers of loci situated on RNO5 were found to be reduced, particularly for the CDKN2A/2B locus. Second, polymerase chain reaction analysis was performed with 22 genes and markers and homozygous deletions of the CDKN2A exon 1β and CDKN2B genes were detected in 13 EACs (62%) and of CDKN2A exon 1α in 12 EACs (57%) Third, the occurrence of allelic imbalance in RNO5 was analyzed using 39 microsatellite markers covering the entire chromosome and frequent loss of heterozygosity was detected. Even more intriguing was the repeated finding of allele switching in a narrow region of 7 Mb across the CDKN2A/2B locus. We conclude that genetic events affecting the middle part of RNO5 (including bands 5q31∼q33 and the CDKN2A locus) contribute to the development of EAC in rat, with the CDKN2A locus having a primary role.

Is There an Entity of Chemically Induced BCR-ABL–Positive Chronic Myelogenous Leukemia?

Advances in the therapy of malignancy have been accompanied by an increased frequency of cases of secondary acute myelogenous leukemia and related clonal cytopenias and oligoblastic (subacute) myelogenous leukemia (myelodysplastic syndromes). The acute myelogenous leukemia incidence can be increased by high-dose acute ionizing radiation exposure, alkylating agents, topoisomerase II inhibitors, possibly other DNA-damaging therapeutic agents, heavy, prolonged cigarette smoking, and high dose-time exposure to benzene, the latter less frequently seen in industrialized countries with worksite regulations. Acute myelogenous leukemia and myelodysplastic syndromes may result from innumerable primary types of chromosome damage. In the case of chronic myelogenous leukemia, a specific break in chromosome bands 9q34 and 22q11 must occur to result in the causal fusion oncogene (BCR-ABL). A review of 11 studies of the chromosomal abnormalities found in presumptive cases of cytotoxic therapy-induced leukemia and of 40 studies of the subtypes of leukemia that occur following cytotoxic therapy for other cancers has not provided evidence of an increased risk for chemically induced BCR-ABL-positive chronic myelogenous leukemia. Studies of the effects of alkylating agents, topoisomerase inhibitors, and benzene on chromosomes of hematopoietic cells in vitro, coupled with the aforementioned epidemiological studies of secondary leukemia after cytotoxic therapy or of persons exposed to high dose-time concentrations of benzene in the workplace, do not indicate a relationship among chemical exposure, injury to chromosome bands 9q34 and 22q11, and an increased risk for BCR-ABL-positive chronic myelogenous leukemia.

Delineation of a critical region on chromosome 18 for the del(18)(q12.2q21.1) syndrome

Deletions involving the long arm of chromosome 18 have been reported in many patients. Most of these deletions are localized in the distal half of the long arm (18q21.1 --> qter) and are detectable by standard cytogenetic analysis. However, smaller interstitial deletions leading to a recognizable phenotype and residing in the region around chromosome band 18q12.3 (bands q12-q21) are less common. Here we report on an interstitial deletion of less than 1.8 Mb within chromosomal band 18q12.3. The phenotypic features of the propositus correspond well with those observed in patients with larger cytogenetically detectable deletions encompassing chromosome band 18q12.3. The deletion enabled us to define a critical region for the following features of the del(18)(q12.2q21.1) syndrome: hypotonia, expressive language delay, short stature, and behavioral problems.

Cytogenetic studies in non-Hodgkin lymphomas--results from surgical biopsies.

Cytogenetic analysis using Giemsa banding technique was successful in 30 of the 49 adult patients with nonHodgkin lymphomas investigated. The results are correlated with previous findings in 48 non‐Hodgkin lymphoma patients studied by means of fine needle aspiration in our laboratory. As 8 patients were included in both series, the total number successfully investigated was 70. The success rate with both sampling techniques was equivalent, and both methods also seemed to give qualitatively similar information about chromosome pattern. However, cells with a normal diploid karyotype were more frequent in the surgical biopsies. In the total material, normal karyotypes only were found in 10 patients. In two patients the aberrations were too complex to allow evaluation. The chromosome variation among the remaining 58 cases was distinctly nonrandom. Chromosomes 3, 7, 12, and 18 were preferentially gained, whereas chromosomes 1, 6, and 14 were most often involved in structural rearrangements. A 14q+ marker chromosome was the single most frequent abnormality; originating through t(14; 18) (q32; q21) in 10 of 23 cases. The second most common structural aberration was a deletion of the long arm of chromosome 6 with breakpoints at bands q15 and q21 (12 cases). At least one of the two most common numerical and/or structural changes, +7, +12, 14q+, and 6q‐, were present in 39 of the 58 patients with aberrations (67%). Longitudinal studies demonstrated karyotypic evolution during the course of the disease in five of six patients. Simultaneous samples from different tumor sites were studied in 10 patients. The findings in 9 cases suggested a monoclonal origin; in one case totally unrelated karyotypes were found in two different lymph nodes at third relapse, suggesting a multifocal origin. (Less)

Chromosome 1p and 11q Deletions and Outcome in Neuroblastoma—A Critical Review

Neuroblastoma is an embryonic neoplasm of the sympathetic nervous system that accounts for approximately 15 percent of all pediatric cancer fatalities. Genomic change in neuroblastoma has been shown to correlate with both behavior and outcome. More specifically, amplification of the MYCN oncogene occurs in about 20% of neuroblastoma patients and has been shown to provide important prognostic information. This correlation has typically led to a multidisciplinary approach in the treatment of this condition, including preventive screening, dose-intensive chemotherapy, stem-cell transplantation, targeted therapies (radiation, monoclonal antibodies, prodifferentiation agents), and monitoring of minimal disease. However, although MYCN has been associated with high-risk tumors, more than 60% of patients with aggressive disease do not exhibit this mutation, suggesting that other genetic mechanisms are involved in the pathophysiology of neuroblastoma. Consequently, the development of additional genetic markers could be useful not only in further understanding the molecular biology underlying these tumors, but also defining more effective therapy and aiding prognosis in this patient population. To this end, Attiyeh and colleagues published the results of their study investigating the effects of loss of heterozygosity (LOH) at chromosomes 1p and 11q on relapse and survival in neuroblastoma (1). LOH at chromosome arms 1p and 11q are noted frequently in neuroblastoma, and previous studies have suggested an association with high-risk features. Furthermore, 11q23 LOH is rarely observed in association with MYCN amplification. Given this fact, Attiyeh and colleagues hypothesized that 11q23 LOH could be a useful prognostic marker. In this study 915 samples of neuroblastoma were screened for LOH at chromosome bands 1p36 and 11q23, and associations with event-free and overall survival were performed. Results were as follows: patients in whom tumors showed 1p36 LOH had three-year event-free and overall survival rates of 47% and 64% respectively, as compared with 77% and 85%, respectively, in those patients who did not have 1p36 LOH. Similarly, unbalanced 11q LOH (unb11q LOH) was strongly associated with both decreased event-free and decreased overall survival. Analysis of the subgroup of cases without MYCN amplification showed that both 1p36 LOH and unb11q LOH were highly associated with decreases in both event-free and overall survival. More specifically, patients with unb11q LOH had three-year event-free and overall survival rates of 50% and 66%, respectively, as compared with 74% (P < 0.001) and 83% (P < 0.001) in those that did. Finally, in a multivariate analysis, unb11q LOH was found to be independently associated with decreased event-free survival. Based on these findings, the authors conclude that 1p36 and unb11q LOH are risk factors that should be incorporated into clinical trials of neuroblastoma. This study highlights the growing importance of genetic markers for use in stratification of tumor behavior. A number of markers including, MYCN amplification, HER2/neu over-expression, chromosome 17 gain, Trk expression, and CD44 genetic aberrations have proven useful, and the ability to detect risk factors at the time of diagnosis and tailor therapy accordingly could make the treatment of cancer both more effective and less toxic. Of greatest concern in neuroblastoma is the rare patient who despite a favorable clinical profile and no MYCN amplification progresses to high-risk disease. This study, although somewhat limited by the small numbers within subgroups, demonstrates that 1p36 LOH and unb11q LOH are strongly associated with outcome in patients with neuroblastoma. It is the hope of the authors’ that recognition and appreciation of these additional genetic markers will allow clinicians to more effectively tailor currently used prognostic schemes and treatment regimens.

T(6;14)(p22;q32): a new recurrent IGH@ translocation involving ID4 in B-cell precursor acute lymphoblastic leukemia (BCP-ALL)

Translocations involving the immunoglobulin heavy chain locus (IGH@) at chromosome band 14q32 are common in mature B-cell neoplasms, but are rare in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Here, we report the translocation, t(6;14)(p22;q32), involving IGH@ as a novel recurrent translocation in 13 BCP-ALL patients. Fluorescence in situ hybridization and long-distance inverse polymerase chain reaction (PCR) identified ID4 as the partner gene. Breakpoints were scattered over a 19kb region centromeric of ID4. Quantitative real-time PCR showed up-regulation of ID4 mRNA. All patients had deletions of CDKN2A and PAX5 located on the short arm of chromosome 9, frequently as a result of an isochromosome, i(9)(q10) (9/13, 69%). This study defines a new subgroup of BCP-ALL characterized by ID4 over-expression and CDKN2A and PAX5 deletions. Preliminary survival data suggest that this subgroup may be associated with a good response to therapy.

Therapy-related leukemia and myelodysplasia: susceptibility and incidence

Therapy-related myelodysplastic syndrome/acute myeloid leukemia (t-MDS/AML) is an increasingly recognized treatment complication in patients treated with radiotherapy or chemotherapy for previous hematologic malignancies or solid tumors. Distinct clinical entities have been described according to the primary treatment, corresponding to defined genetic lesions. Chromosome 7 and/or 5 losses or deletions are typical of alkylating agent-induced AML, while development of t-AML with balanced translocations involving chromosome bands 11q23 and 21q22 has been related to previous therapy with drugs targeting DNA-topoisomerase II. In addition, antimetabolites, and in particular the immunosuppressant azathioprine, have been shown to induce defective DNA-mismatch repair. This could promote survival of misrepaired cells giving rise to the leukemic clone. Individual predisposing factors, including polymorphisms in detoxification and DNA repair enzymes have been identified. Their combination may significantly increase the risk of t-MDS/AML. Among patients with hematologic malignancies, long-term survivors of Hodgkin's lymphoma are exposed to an increased risk of t-MDS/AML, particularly when receiving MOPP-based, and escalated BEACOPP regimens, and when alkylators are combined with radiotherapy. Patients with Hodgkin's and non-Hodgkin's lymphoma are at highest risk when total body irradiation followed by autologous stem cell transplantation is used as rescue or consolidation therapy. The addition of granulocyte-colony-stimulating factor and radiotherapy plays a significant role in t-AML following treatment of children with acute lymphoblastic leukemia. In non-hematologic malignancies, treatment for breast cancer and germ-cell tumors has been associated with a 1-5% lifetime risk of both lymphoid as well as myeloid leukemia. In all cases the risk of t-MDS/AML drops sharply by 10 years after treatment.

Neuroblastomas have distinct genomic DNA profiles that predict clinical phenotype and regional gene expression

Neuroblastoma is a heterogeneous neoplasm that has served as a paradigm for the clinical utility of somatically acquired genomic aberrations. DNA copy number alterations (CNA) are currently used to predict prognosis, including MYCN amplification and deletions at chromosome bands 1p36 and 11q23. We predicted that genome-wide assessment of DNA aberrations in neuroblastoma tumors would provide a more precise estimation of clinical phenotype, and could be used to predict outcome. We measured CNAs in a representative set of 82 diagnostic tumors on a customized high-resolution BAC array-based CGH platform supplemented with additional clones across 1p36, 2p24, 3p21-22, 11q14-24, and 16p12-13, and integrated these data with RNA expression data. We used an unbiased statistical method to define a set of minimal common regions (MCRs) of aberration. Unsupervised hierarchical clustering identified four distinct genomic subclasses. First, a subset of tumors with a clinically benign phenotype showed predominantly whole chromosome gains and losses. Second, tumors with MYCN amplification had a unique genomic signature of 1p deletion and 17q gain, but few other rearrangements. Third, tumors with an aggressive clinical phenotype without MYCN amplification, showed multiple structural rearrangements. Most notable were deletions of 3p, 4p, and 11q and gain of 1q, 2p, 12q, and 17q. Lastly, there was a subset of tumors with an aggressive clinical phenotype and no detectable DNA CNAs. The genomic subsets were highly correlated with patient outcome, and individual MCRs remained prognostic in a multivariable model. DNA signature patterns embed important prognostic information in diagnostic neuroblastoma samples, and can identify candidate cancer-related genes.

Natural history of patients with myelodysplastic syndromes (MDS) with interstitial deletions of chromosome 5q detected on G-banded karyotyping

7077 Background: MDS includes a heterogenous group of hematopoietic stem cell malignancies characterized by ineffective hematopoiesis and recurring clonal cytogenetic abnormalities with poorly understood functional consequences. Interstitial deletion of chromosome 5 including band q31 is of special interest currently because of the striking effectiveness of lenalidomide therapy in patients with this lesion. Methods: We reviewed the clinical and pathological features of 175 consecutive patients with 5q31 deletions whose final diagnosis was MDS from 1996 to 2006. Patients not meeting the definition of a clonal chromosomal anomaly (i.e., only 1 abnormal metaphase) and those with &gt;20% marrow blasts (now defined as AML) were excluded. Results: The median age at diagnosis was 73 years old (range 8–91). The 5 most common MDS subtypes (WHO classification) were RAEB2 (38 cases), 5q- syndrome (33 cases), MDS NOS (26 cases), RCMD (22 cases), and RAEB1 (20 cases). Chromosomal breakpoints encountered most frequently were q13q33 (86 cases), q15q33 (38 cases), and q22q33 (14 cases). The 5q deletion was present as a sole cytogenetic anomaly in 31%, was present along with one other anomaly in 10%, and was part of complex karyotype in 59%. Median time to death from confirmation of diagnosis at our institution was only 7.2 months (range 1 month –1.8 years). Survival was greatest in those diagnosed with 5q- syndrome, but the median survival time of 1.8 years (p=0.001) was lower than reported in other series. Survival was also superior in women (7.9 months, versus 6.6 months for men, p=0.05) and those with non-complex cytogenetics (1.44 versus 0.41 years, p&lt;0.001). Poorer survival was noted in those with prior chemotherapy (median 6.6 months versus 7.6 months, p=0.01). Differences in breakpoint (p=0.55) and number of metaphases involved with the 5q abnormality (p=0.08) did not have a statistically significant impact on survival. Conclusion: Classic 5q- syndrome as defined by the WHO represents only a minority of MDS patients with interstitial 5q deletions. Although the short survival in our series compared with previous reports may be due in part to referral bias, it is also possible that deletions of chromosome 5q are less benign than previously suspected. No significant financial relationships to disclose.

Assessment of the clinical and molecular impact of different cytogenetic subgroups in a series of 272 lipomas with abnormal karyotype

Conventional lipomas harbor karyotypic changes that could be subdivided into four, usually mutually exclusive, categories: rearrangement, in particular through translocations, of chromosome bands 12q13-15, resulting in deregulation of the HMGA2 gene, loss of material from or rearrangement of chromosome 13, supernumerary ring or giant marker chromosomes, and aberrations of chromosome band 6p21. In the present study, 272 conventional lipomas, two-thirds of them deep-seated, with acquired clonal chromosome changes were assessed with regard to karyotypic and clinical features. A nonrandom distribution of breakpoints and imbalances could be confirmed, with 83% of the cases harboring one or more of the previously known cytogenetic hallmarks. Correlation with clinical features revealed that lipomas with rings/giant markers were larger, occurred in older patients, were more often deep-seated, and seemed to have an increased tendency to recur locally, compared with tumors with other chromosome aberrations. The possible involvement of the HMGA2 gene in cases that did not show any of the characteristic cytogenetic changes was further evaluated by locus-specific metaphase fluorescence in situ hybridization (FISH) and RT-PCR, revealing infrequent cryptic disruption of the gene but abundant expression of full length or truncated transcripts. By FISH, we could also show that breakpoints in bands 10q22-23 do not affect the MYST4 gene, whereas breakpoints in 6p21 or 8q11-12 occasionally target the HMGA1 or PLAG1 genes, respectively, also in conventional lipomas.

Changes in the Pattern of Cytogenetic Aberrations with Advancing Age in Acute Myeloid (Non-APL) Leukemia: A Southwest Oncology Study (S9007).

It is well known that, with advancing age, diseases and clinical procedures are associated with increased morbidity and mortality. This increasing vulnerability in the elderly with acute myeloid leukemia has been documented in a previous report of a study of a group of patients enrolled in five Southwest Oncology Group (SWOG) studies (Appelbaum, et al., Blood, 2006 May 1;107(9):3481-6). The authors of that study observed that the frequency of unfavorable risk cytogenetics was significantly elevated in patients over the age of 75. In this study we have examined the nature of cytogenetic changes over the entire adult life span in greater detail. We included the same patient population noted above plus additional AML patients with eligible cytogenetics data registered on a cytogenetics ancillary study SWOG 8750/9007, including a recent treatment study with subjects over the age of 70 years (S0432). A total of 1069 patients from 10 SWOG therapeutic clinical trials of previously untreated AML were included in this analysis. The abnormalities detected in this study are consistent with the emergence of increased genomic instability in the malignant clone. We observed an increasing frequency of complex karyotypes in the older subjects. For each 10 years increase in age there was a 16% increase (95% confidence interval 14%–19%) in the average number or abnormalities per individual, which was statistically significant (Poisson regression model, P<0.0001). The frequency of homogeneously staining regions and double minutes, cytogenetic evidence of gene amplification, progressively increased in patients in the fifth to the eighth decade (logistic regression model P<0.016). A similar increase was observed in the frequency of isochromosome formation. The breakpoints in the structural aberrations tended to cluster in specific regions of the karyotype. This clustering was more pronounced in the karyotypes from the older patients with significant increases most evident in bands 7q22 and 12p13 (logistic regression model P = 0.0073). For patients less than 60 years of age, 4% have a loss of chromosome 17 or 18 compared to 13% of patients 60 years or older (logistic regression model P = 0.0001). The total number of identifiable chromosomes lost and gained also significantly increased with age (Poisson regression model P values < 0.0001 and = 0.001, respectively). An increase in the frequency of marker chromosome formation with age correlated with the total chromosome loss (Spearman rank correlation P = 0.0001). These results suggest that the numerical changes that occur with advancing age can be accounted for by both mitotic instability and the degradation of identifiable chromosomes into marker chromosomes. These findings are consistent with the notion that the increased severity of acute myeloid leukemia in elderly patients is, in addition to the increased vulnerability associated with aging phenotype, also due to a pathogenetic progression that is distinct from that present in most younger leukemic patients.