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.

After the birth of the “cytogenetics” in 1956 and its application in medicine in 1959 as valuable tool for the diagnosis of congenital diseases caused by chromosomal abnormalities, its limitations persuades the investigators to discover and employ “banding” techniques. This method could overcome many pre-existing problems and limitations but was not diagnostic especially when tissue culture was not possible due to tissue necrosis or in microdeletions. Fortunately, Fluorescent In Situ HYBRIDIZATION (FISH) could prevail over many of the aforementioned limitations but it could not evaluate necrosed tissues since it required a specific probe for each disease. Array COMPARATIVE GENOMIC HYBRIDIZATION (a(CGH)) is a new technique which enables us to study both necrosed and viable tissues. Another advantage of this method is the ability to study the whole genome and assess any decrease or increase in the chromosome material. This technique is currently regarded as the best and most efficient. Since stillbirths and viable or necrosed curettage specimens comprise most of the referred specimens to Kariminejad & Najmabadi Pathology and Genetic Center and evaluation of the specimens with a special focus on chromosomal aberrations are required by clinicians, we have equipped our center with technical equipment and experienced cytogenetic technicians. In the end, two cases whose definite diagnoses were made using FISH and Array (CGH) are presented.

Introduction: Array COMPARATIVE GENOMIC HYBRIDIZATION ((CGH)) has been developed that allows a more detailed examination of the genome when compared with a standard chromosome analysis. Array COMPARATIVE GENOMIC HYBRIDIZATION ((CGH)) is a new and exciting diagnostic tool represents a major technological step forward in cytogenetic testing and addresses many of the limitations of current cytogenetic methods. Conventional chromosome analysis, FISH and QF-PCR rapidly detect common chromosomal abnormalities but do not provide a genome wide screen for unexpected imbalances In contrast, array (CGH) analysis simultaneously evaluates regions across the entire genome and allows for detection of unbalanced structural and numerical chromosome abnormalities of less than one hundred kb.Materials and Methods: Fifteen fetuses ongoing pregnancies and fifteen pathogen children were studied by array (CGH) on targeted BAC-arrays and oligoarray.Results: all Fifteen fetuses and children were successfully by array-(CGH) identified and comprised with conventional karyotyping.In the 9/15 foetus ware healthy In the 5 case were found trisomy 21, 18 and 13 in 1 case unbalanced translocation 7p; 9p that were also subjected to conventional karyotyping. All fifteen pathogen Children were identified all chromosomal abnormality and microdeletions like in 1p36.33, and 22q.11 chromosomal region that were not found by conventional karyotyping which were confirmed by FISH.Conclusion: This study demonstrates the feasibility of prenatal genetic diagnosis using BAC-array (CGH) analysis for direct analysis of amniocytes without culturing cells and Amplification. This new method replaces conventional cytogenetics, FISH and in many cases to Multiplex-PCR for Mutation less than 100 kb in the great majority of prenatal and postnatal diagnosis cases. Furthermore, the direct analysis allows for rapid array (CGH) results and shorter reporting time.

Chromosome microarray is being suggested and replacing karyotype as first tier diagnostic test for individuals with unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), or multiple congenital anomalies (MCA). Chromosome microarray gives a diagnostic yield of 15-20% for genetic testing of individuals with DD/ID, ASD or MCA compared to 3% in karyotype (excluding Down syndrome and other recognizable chromosomal syndromes). We present the results of chromosome microarray performed on 110 individuals with DD/ID, ASD or MCA. From the 110 cases, 23 cases (20.9%) showed copy number variations, of which 13 were deletions, 5 were duplication and 5 were duplication and deletion. The limitations of chromosome microarray are for detection of balanced translocation and low-level mosaicism, but these chromosomal abnormalities are rare causes of abnormal phenotypes in this category of patients.

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.

Objective: Array COMPARATIVE GENOMIC HYBRIDIZATION (Array-(CGH)) has been used in diagnostic laboratories for the evaluation of individuals with intellectual disability/developmental delay, autism spectrum disorders, multiple congenital anomalies/dysmorphic features, prenatal diagnosis, and products of conception. Clinically available whole-genome a(CGH) can detect unbalanced chromosomal rearrangements/abnormalities with coverage of about one probe per 6 kb to one probe per 70 kb. Materials and Methods: We report the a(CGH) results of 142 patients referred to Sarem Cytogenetic laboratory, Sarem Women's Hospital for cytogenetic analysis between 2017 and 2020. They comprised 60 prenatal cases using amniotic fluid, 52 cases of products of conception, and 30 peripheral blood samples for postnatal cases. Chromosome analysis and a(CGH) were done for most of the referred samples. Results: Four out of fifty-two aborted fetuses had pathogenic a(CGH) results including,two male fetuses with gain of whole chromosome 21 (compatible with trisomy 21), one male fetus with a gain of whole chromosome 9 (compatible with trisomy 9), and one female fetus with a pathogenic gain of 78. 2 Mb on 13q13. 3q34 and loss of 612 Kb on 20p13p13 which overlap with 175 and 7 OMIM genes, respectively. The later aborted fetus's karyotype result is 46, XX, der(20)t(13, 20)(q13, p13) which is originated from the father. Also, five out of sixty prenatal amnion fluid's analysis demonstrated pathogenic chromosomal abnormalities. Ten out of thirty postnatal peripheral blood samples showed abnormal chromosomal a(CGH) results. Conclusion: The results of this report emphasize the importance of the combination of classic karyotyping with a(CGH) in better management of the patients.