Tehran University Medical Journal

---

Background: Nonlethal genetic damage is the basis for carcinogenesis. As various gene aberrations accumulate, malignant tumors are formed, regardless of whether the genetic damage is subtle or large enough to be distinguished in a karyotype. The study of chromosomal changes in tumor cells is important in the identification of oncogenes and tumor suppressor genes by molecular cloning of genes in the vicinity of chromosomal aberrations. Furthermore, some specific aberrations can be of great diagnostic and prognostic value. Comparative genomic hybridization (CGH) is used to screen the entire genome for the detection and/or location chromosomal copy number changes.

Methods: In this study, frozen sections of 20 primary breast tumors diagnosed as invasive ductal carcinoma from the Cancer Institute of Imam Khomeini Hospital, Tehran, Iran, were studied by CGH to detect chromosomal aberrations. We compared histopathological and immunohistochemical findings.

Results: Hybridization in four of the cases was not optimal for CGH analysis and they were excluded from the study. DNA copy number changes were detected in 12 (75%) of the remaining 16 cases. Twenty-one instances of chromosomal aberrations were detected in total, including: +1q, +17q, +8q, +20q, -13q, -11q, -22q, -1p, -16q, -8p. The most frequent were +1q, +17q, +8q, -13q, similar to other studies. In three cases, we detected -13q, which is associated with axillary lymph node metastasis and was reported in one previous study. The mean numbers of chromosomal aberrations per tumor in metastatic and nonmetastatic tumors was 1.5 and 1, respectively. No other association between detected chromosomal aberrations and histopathological and immunohistochemical findings were seen.

Conclusion: Since intermediately to widely invasive carcinomas are more likely to have chromosomal aberrations, CGH can be a valuable prognostic tool. Furthermore, CGH can be used to detect targeting molecules within novel amplifications which holds the potential for a new therapeutic approach for intractable cancer.

---

Normal 0 false false false EN-US X-NONE AR-SA MicrosoftInternetExplorer4 Since the recognition of true number of human chromosomes in 1956, many techniques have been developed to detect chromosomal aberrations. A number of those, such as karyotyping and fluorescence in situ hybridization (FISH), are valuable tools in both research and diagnostics. But these techniques have defects that limit their application. One of the important limitations is resolution resolution limitations make it impossible to detect small aberrations. The other major defect is the disability to analyze whole genome. In 1997 Solinas-Toldo introduced a new technique that could cover other techniques' defects. This new technique called microarray-based comparative genomic hybridization (array CGH). Array CGH, with the powerful resolution of FISH and also the ability of whole genome analysis in single experiment accelerated the genetic research. Array CGH has resulted in to a great progress in oncology and genetic disorders research. In addition, this technique has the ability to be used in diagnostics too. This review article, witch include the data of recent published papers and our experiences, gives an overview of the array CGH and compare it with the other molecular cytogenetic techniques. Its application in oncology and genetic disorder is also discussed.

---

In situ hybridization (ISH) is a method that uses labeled complementary single strand DNA or RNA to localize specific DNA or RNA sequences in an intact cell or in a fixed tissue section. The main steps of ISH consist of: probe selection, tissue or sample preparation, pre-hybridization treatment, hybridization and washing, detection and control procedure. Probe selection is one of the important aspects of successful hybridization. ISH sensitivity and specificity can be influenced by: probe construct, efficiency of labeling, percentage of GC, probe length and signal detection systems. Different methods such as nick translation, random priming, end tailing and T4 DNA polymerase replacement are used for probe generation. Both radioactive and non-radioactive labels can be used in order to probe labeling. Nucleic acid maintenance in samples, prevention of morphological changes of samples and probe penetration into tissue section are the main aims of sample preparation step. Then, a small amount of solution containing probe, is added on slides containing tissue sections for hybridization process, then slides are incubated overnight. Next day, washes are carried out to remove the probes which are not bound to target DNA or RNA. Finally, in order to be sure that the observed labeling is specific to the target sequence, using several control procedures is very important. Various techniques based on ISH consist of: Fluorescence in situ hybridization (FISH), chromogenic in situ hybridization (CISH), genomic in situ hybridization (GISH), comparative genomic hybridization (CGH), spectral karyotyping (SKY) and multiplex fluorescence in situ hybridization (MFISH). One of the most common techniques of ISH is fluorescence in situ hybridization. FISH can be used to: 1) detect small deletions and duplications that are not visible using microscope analysis, 2) detect how many chromosomes of a certain type are present in each cell and 3) confirm rearrangements that are suspected after microscope analysis. In this technique different fluorescent labels are attached to the probes. In this review article ISH, its different types, their application, advantages and disadvantages have been considered.