RAN-aCGH is an R GUI tool for the analysis and visualization of array comparative genomic hybridization (array-CGH) experiments. The tool consists of data-loading, preprocessing for missing data, several methods for statistical identification of DNA copy number aberration, and visualization of the copy number change. RAN-aCGH requires a single input format, provides various visualizations, and allows the addition of a new statistical method, all in a user-friendly graphic user interface (GUI).
Comparative Genomic Hybridization ; DNA

No abstract available.
Comparative Genomic Hybridization ; DNA

No abstract available.
Chromosome Aberrations ; Comparative Genomic Hybridization*

Next-generation sequencing (NGS) and array-based comparative genomic hybridization (array CGH) have enabled us to perform high-throughput mutation screening and genome-wide copy number analysis, respectively. These methods can be used for molecular diagnosis of pediatric endocrine disorders. NGS has determined the frequency and phenotypic variation of mutations in several disease-associated genes. Furthermore, whole exome analysis using NGS has successfully identified several novel causative genes for endocrine disorders. Array CGH is currently used as the standard procedure for molecular cytogenetic analysis. Array CGH can detect various submicroscopic genomic rearrangements involving exons or enhancers of disease-associated genes. This review introduces some examples of the use of NGS and array CGH for the molecular diagnosis of pediatric endocrine disorders.
Comparative Genomic Hybridization* ; Cytogenetic Analysis ; Diagnosis* ; Exome ; Exons ; Mass Screening

BACKGROUND: The most consistent chromosomal abnormality in ependymomas, is loss of 22q (17-75%) and gain of 1q (0-50%). However, significance of this abnormality is uncertain. METHODS: Genomic imbalances in 27 Korean ependymomas, including 21 low grade ependymomas, 4 anaplastic and 2 myxopapillary ependymomas, were analyzed by degenerate oligonucleotide primed-PCR-comparative genomic hybridization. RESULTS: Common gains were found in 17 (63%), 20q (59%), 9q34 (41%), 15q24-qter (33%), 11q13 (30%), 12q23 (26%), 7q23-qter (26%), 16q23-qter (30%), 19 (26%), and 1q32-qter (22%). DNA amplification was identified in 12 tumors (44%). Chromosomal loss was a less common occurrence in our study, but was found in 13q (26%), 6q (19%), and 3 (11%). CONCLUSION: The recurrent gains or losses of the chromosomal regions which were identified in this study provide candidate regions that may be involved in the development and progression of ependymomas.
Chromosome Aberrations ; Comparative Genomic Hybridization ; DNA ; Ependymoma* ; Nucleic Acid Hybridization* ; Polymerase Chain Reaction

Deletions of 14q including band 14q32.33 are uncommon. Patients with terminal deletions of chromosome 14 usually share a number of clinical features. By molecular techniques (array comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH), we identified a young girl with 0.3 Mb terminal 14q32.33 deletion. Review of the nine cases with pure terminal 14q32.3 deletions described to date documented that our observation is the smallest terminal 14q deletion ever reported. The phenotype of our patient is much less severe than the phenotypes of the patients reported previously. We report our experience in examining the clinical, behavioral, and cognitive findings in a 5-year-old girl studied with chromosomal microarray hybridization and reviewed previously reported patients with 14q32 deletions.
Chimera ; Chromosomes, Human, Pair 14 ; Comparative Genomic Hybridization ; Fluorescence ; Humans ; In Situ Hybridization ; Phenotype ; Preschool Child ; Seizures

Degenerate oligonucleotide primed PCR is an useful technique to amplify whole genome and its the applications for fluorescent in situ hybridization and comparative genomic hybridization (CGH) were reported. For the CGH, topoisomerase and sequenase were recommended to use for the better hybridization. But adding the enzymes to PCR reaction per every cycle is labor-intensive and can easily contaminate PCR reaction. This study was carried out to prove the possibility of application of DOP-PCR to CGH without use of sequenase. Several combinations of CGH e.g., DOP-PCR amplified normal DNA vs. DOP-PCR amplified normal DNA, DOP-PCR amplified normal DNA vs. non-DOP normal DNA, DOP-PCR amplified normal DNA vs. DOP-PCR amplified MCF-600 cell line DNA, and non-DOP normal DNA vs. non-DOP MCF-600 DNA were performed. In addition, randomly selected microsatellite loci were tested to know whether DOP-PCR covers whole genome amplification. Apparently the DOP-PCR provides enough amount and size of DNA for CGH application and covers whole genome amplification. These results suggest that DOP-PCR can be used for CGH and genotyping.
Cell Line ; Comparative Genomic Hybridization* ; DNA ; Genome ; In Situ Hybridization, Fluorescence ; Microsatellite Repeats ; Polymerase Chain Reaction*

OBJECTIVE: To determine the origin of a mosaicism small supernumerary marker chromosome (sSMC) by cytogenetic and molecular analysis. METHODS: Karyotype analysis, fluorescence in situ hybridization (FISH) and SNP-array were carried out. RESULTS: The karyotype of the patient was mos47,XX,+mar[45]/48,XX,+2mar[3]/46,XX[52]; the SNP-array result was arr[hg19]15q11.1q11.2 (20 161 372-24 314 675)×3, and the repeat fragment was about 4.15 Mb. FISH showed that approximately 50% of the cells have contained a sSMC with double D15Z1 probe site segments derived from abnormal idic(15). This sSMC did not contain SNRPN and PML probe fragments of Prader-Willi syndrome/Angelman syndrome. CONCLUSION When the patient's karyotype and phenotype are inconsistent, cytogenetic and molecular biology technologies should be combined to clarify the karyotype and gene location, so as to provide more accurate genetic consultation for the follow-up treatments.
Chromosome Disorders ; Chromosomes, Human, Pair 15 ; Comparative Genomic Hybridization ; Humans ; In Situ Hybridization, Fluorescence ; Karyotype ; Mosaicism

BACKGROUND AND OBJECTIVES: Cancer of the thyroid is the sixth common cancer in Korea, and fourth common among the Korean women, in particular. Aming the prevalent carcinomas of thyroid, the papillary thyroid carcinoma is the most frequent type. Genomic instability is the characteristic of nearly all tumors as well as thyroid cancers. However, despite the high frequency of papillary thyroid carcinomas, their chromosomal alterations are poorly characterized in Korea. Comparative genomic hybridization (CGH) is a new fluorescence in situ hybridization (FISH) technique to identify genomic imbalances in cancers. In this study, CGH was carried out with the aim of analyzing non-random chromosomal aberrations involved in papillary thyroid carcinomas. MATERIALS AND METHOD: CGH was carried out. Biotin-labeled tumor DNA and digoxigenin-labeled normal DNA were co-hybridized to normal metaphase cells. Then, the ratio of fluorescence was analyzed by an image analyzer. In array-CGH, Cy3 labeled tumor DNA and Cy5 labeled normal DNA were hybridized to microarray template, and then image analysis was performed by microarray image analyzer. RESULTS: Gains of 22q13, 6p24, 7p13, 7q21, 7q31, 8q24, 17q24 and 19p13.3 were found frequently. CONCLUSION: Non-random aberrations which were disclosed in this study might be candidate regions for the abnormal genes involved in papillary thyroid cancer.
Carcinoma, Papillary* ; Chromosome Aberrations* ; Comparative Genomic Hybridization* ; DNA ; Female ; Fluorescence ; Genomic Instability ; Humans ; Hybridization, Genetic ; In Situ Hybridization ; Korea ; Metaphase ; Thyroid Gland* ; Thyroid Neoplasms

BACKGROUND: The aim of the present study was to identify chromosomal loci that contribute to the pathogenesis of aortic dissection (AD) in a Korean population using array comparative genomic hybridization (CGH) and to confirm the results using real-time polymerase chain reaction (PCR). MATERIALS AND METHODS: Eighteen patients with ADs were enrolled in this study. Genomic DNA was extracted from individual blood samples, and array CGH analyses were performed. Four corresponding genes with obvious genomic changes were analyzed using real-time PCR in order to assess the level of genomic imbalance identified by array CGH. RESULTS: Genomic gains were most frequently detected at 8q24.3 (56%), followed by regions 7q35, 11q12.2, and 15q25.2 (50%). Genomic losses were most frequently observed at 4q35.2 (56%). Real-time PCR confirmed the results of the array CGH studies of the COL6A2, DGCR14, PCSK6, and SDHA genes. CONCLUSION: This is the first study to identify candidate regions by array CGH in patients with ADs. The identification of genes that may predispose an individual to AD may lead to a better understanding of the mechanism of AD formation. Further multicenter studies comparing cohorts of patients of different ethnicities are warranted.
Aorta ; Cohort Studies ; Comparative Genomic Hybridization ; DNA ; Humans ; Polymerase Chain Reaction ; Real-Time Polymerase Chain Reaction