Oguz Altungoz

DNA copy number changes detected by comparative genomic hybridization and their association with clinicopathologic parameters in breast tumors

The purpose of this study was to use comparative genomic hybridization (CGH) to screen breast tumors for copy number changes: 22 ductal, 9 lobular, 7 mixed, 2 micropapillary carcinomas, and 2 ductal carcinoma in situ were studied and various regional genomic imbalances were detected. The majority of the aberrations identified in this study were in line with previous CGH findings. The most frequent DNA sequence copy number changes were 1q, 8q, and 20q gains. The frequency of 16q losses was significantly higher in lobular carcinomas. The nodal involvement was 10 times higher in cases showing losses of 13q than in cases having normal peak profile at this region. Estrogen receptor positivity was significantly higher in cases displaying 20q gains and 16q losses. Unambiguous high-level DNA amplifications have also been detected. These mapped to 4q31, 6q21 approximately q22, 8q21 approximately q24, 8p11.2 approximately p12, 11q13, 15q24 approximately qter, 20q13.1 approximately qter, and 20q12 approximately qter chromosomal locations. Our results highlight several chromosomal regions that may be important in the molecular genetics of distinct clinicopathologic breast cancer subgroups.

Cytogenetic findings‐in 19 malignant bone tumors

Background. The majority of karyotypes observed in osteosarcomas (OS) and chondrosarcomas (CS) are complex, Specific chromosomal abnormalities have not yet been characterized in either tumor except for a ring chromosome in parosteal OS. The purpose of this study was to determine recurrent chromosomal abnormalities and establish a possible correlation between the cytogenetic changes and the pathologic findings.

Translocation (6;10)(p21;q22) in Uterine Leiomyomas

A translocation between chromosomes 6 and 10 was observed in two uterine leiomyomas. Translocation (6;10) may be important in the pathogenesis of a subgroup of uterine leiomyomas.

Cytogenetic findings in 21 malignant melanomas

Cytogenetic analysis was performed on 21 tumor samples of malignant melanoma to identify the presence of consistent chromosome abnormalities. Four cases had a normal karyotype, and 17 were cytogenetically abnormal. Numerical chromosome alterations were observed in 15 tumors: 12 were hyperdiploid and three were hypodiploid. The most frequent losses consisted of chromosomes 5, 9, 17 and Y. The structural abnormalities were usually complex, consisting mainly of nonreciprocal translocations and deletions affecting 1p, 1q, 3p, and 9p. This study adds further data to previously reported melanoma cases, confirming that chromosomes 1, 3, 6, and 9 are nonrandomly affected.

Coexistence of chronic neutrophilic leukemia with light chain myeloma

A 60-year-old woman who presented with weakness, night sweats, bone pain, easy bruising and weight loss was found to have ecchymoses and hepatosplenomegaly. Blood counts showed persistent neutrophilia of mature cell type with Döhle bodies and toxic granulation. Coexistence of chronic neutrophilic leukemia and multiple myeloma of kappa light chain type was documented by bone marrow examination and immunofixation.

Copy number status and mutation analyses of anaplastic lymphoma kinase (ALK) gene in 90 sporadic neuroblastoma tumors.

Somatic and germline mutations of the anaplastic lymphoma kinase (ALK) gene were recently described in neuroblastoma (NB). In this study, we investigated the association of ALK copy number alterations with copy number status 2p24.1 amplicon harboring DEAD box polypeptide 1 (DDX1), MYCN and neuroblastoma-amplified (NAG) genes in 90 primary tumors of sporadic NB cases by multiplex ligation-dependent probe amplification (MLPA). We also performed mutation analysis of ALK gene by directly sequencing the exons 20-28 which cover the region that encodes juxtamembrane and kinase domains. A total of 39 (43.3%) NB cases revealed copy numbers alterations of ALK gene. There was highly significant association of ALK copy number gains with gains of one or more of the genes at 2p24.1 (DDX1, MYCN or NAG) in MYCN unamplified tumors (P<0.000). In addition, 15 of 17 MYCN amplified cases (88.2%) had aberrant ALK status. Solitary gain of ALK with normal copy number status of all other genes was observed only in one case. DNA sequencing of exons 20-28 of ALK revealed two different nucleotide changes in three cases leading to amino acid substitutions of F1245V and R1275Q in tyrosine kinase domain. In conclusion, the frequency of ALK mutations in NB is low and solitary copy number change of it is rarely observed.

Deletion 6q in three cases of mixed type liposarcoma in addition to t(12;16)(q13;p11)

We report the cytogenetic findings in three mixed liposarcoma following short-term cultures. During the course of cytogenetic investigation of various types of liposarcomas, we observed an interstitial deletion of the long arm of chromosome 6 together with the translocation (12;16)(q13;p11) in three tumors. Translocation (12;16) is associated with myxoid and mixed (myxoid/round cell) liposarcomas, although deletion of chromosome 6 has been observed in only a few of these tumors. Our findings suggest that del(6), as an additional change in myxoid liposarcoma, is probably related to tumor progression.

Association of MYCN amplification and 1p deletion in neuroblastomas with high tumor vascularity.

The biologic behavior of neuroblastoma (NB) is extremely variable; therefore, the clinical behavior may be reliably predicted based on the analysis of a panel of prognostic parameters. High vascular density has been correlated with aggressive tumor progression in many types of cancers. The goal of this study was to correlate the tumor vascularity in NB with status of MYCN and the short arm of chromosome 1 (1p) to address the association between angiogenesis and genetic markers of prognostic significance. The study population consisted of 33 patients with histologically proven diagnosis of primary NB and no history of previous chemotherapy. Histologic quantitation of tumor angiogenesis was performed using 3 different methods: microvessel density, vascular grading, and Chalkley counting. MYCN amplification and 1p deletion were determined by using fluorescence in situ hybridization technique. The differentiation and mitosis-karyorrhexis index of tumor cells were also assessed using the Shimada System. MYCN amplification was present in 12 cases (36.3%), and 1p deletion in 16 (48.5%). Both genetic changes significantly correlated with increased tumor vascularity. In addition, tumor vascularity was significantly increased in tumors with high mitosis-karyorrhexis index or of undifferentiated histology. We conclude that angiogenesis shows close association with histologic and genetic prognosticators in NB. Our data support the validity of recent applications of antiangiogenic agents which interfere or block NB progression.

Rapid identification of Helicobacter pylori and assessment of clarithromycin susceptibility from clinical specimens using FISH

Helicobacter pylori remains one of the most common bacterial infections worldwide. Clarithromycin resistance is the most important cause of H. pylori eradication failures. Effective antibiotic therapies in H. pylori infection must be rapidly adapted to local resistance patterns. We investigated the prevalence of clarithromycin resistance due to mutations in positions 2142 and 2143 of 23SrRNA gene of H. pylori by fluorescence in situ hybridisation (FISH), and compared with culture and antimicrobial susceptibility testing in 234 adult patients with dyspepsia who were enrolled. Antrum and corpus biopsy specimens were obtained for rapid urease test, histopathology and culture. Epsilometer test was used to assess clarithromycin susceptibility. H. pylori presence and clarithromycin susceptibility were determined by FISH in paraffin‐embedded biopsy specimens. We found that 164 (70.1%) patients were positive for H. pylori based on clinical criteria, 114 (69.5% CI 62.5–76.6%) were culture positive, and 137 (83.5% CI 77.8–89.2%) were FISH positive. Thus the sensitivity of FISH was significantly superior to that of culture. However specificity was not significantly different (91.4 versus 100.0%, respectively). The resistance rate to clarithromycin for both antrum and corpus was detected in H. pylori‐positive patients; 20.2% by FISH and 28.0% by E‐test.The concordance between E‐test and FISH was only 89.5% due to the presence of point mutations different from A2143G, A2142G or A2142C. We conclude that FISH is significantly more sensitive than culture and the E‐test for the detection of H. pylori and for rapid determinination of claritromycin susceptibility. The superior hybridisation efficiency of FISH is becoming an emerging molecular tool as a reliable, rapid and sensitive method for the detection and visualisation of H. pylori, especially when the management of H. pylori eradication therapy is necessary. This is particularly important for the treatment of patients with H. pylori eradication failure.

The Detection of Genetic Parameters for Prognostic Stratification of Neuroblastoma Using Multiplex Ligation-Dependent Probe Amplification Technique.

BACKGROUND Neuroblastoma (NB) is a neoplasm of the sympathetic nervous system and the most frequent extra cranial solid tumor of early childhood. These tumors display a wide range of clinical behavior and are characterized by complex chromosomal changes, some of which are associated with distinct clinical phenotypes. We investigated the contribution of genetic variables to staging and histology by logistic regression analyses. METHODS We used multiplex ligation-dependent probe amplification (MLPA) to detect segmental genomic imbalances and gene copy number changes in 202 primary NBs. RESULTS Cases with NB were categorized into four distinct groups based on the genomic changes. Group 1 (48 cases, 23.7%) contained tumors with a 1p deletion and/or MYCN gene amplification (MNA). Group 2 included 46 cases (22.8%) with 3p and/or 11q deletions without 1p deletion and MYCN gene amplification. Tumors harboring at least two commonly observed deletions with or without MNA were classified as Group 3 (25 cases, 12.4%). Tumors with chromosomal imbalance other than MYCN gene amplification and 1p, 3p, and 11q deletions were in Group 4 (83 cases, 41.1%). MYCN gene amplification and 17q gain were significant predisposing factors for unfavorable histology. Significant correlations were detected between 1p deletion and MYCN gene amplification; 3p and 11q deletions; and 11q deletion and 17q gain. CONCLUSION MLPA can be used effectively to simultaneously detect multiple genomic imbalances and these changes can be utilized to classify neuroblastomas by prognostic subtypes. The genetic changes detected in NB in this study and their associations with clinical characteristics are in line with previously published reports.