Advances in identification methods of alien genomic components in plants / 生物工程学报

Plants with alien genomic components (alien chromosomes / chromosomal fragments / genes) are important materials for genomic research and crop improvement. To date, four strategies based on trait observation, chromosome analysis, specific proteins, and DNA sequences have been developed for the identification of alien genomic components. Among them, DNA sequence-based molecular markers are mainly used to identify alien genomic components. This review summarized several molecular markers for identification of alien genomic components in wheat, cabbage and other important crops. We also compared the characteristics of nine common molecular markers, such as simple sequence repeat (SSR), insertion-deletion (InDel) and single nucleotide polymorphism (SNP). In general, the accuracy of using a combination of different identification methods is higher than using a single identification method. We analyzed the application of different combination of identification methods, and provided the best combination for wheat, brassica and other crops. High-throughput detection can be easily achieved by using the new generation molecular markers such as InDel and SNP, which can be used to determine the precise localization of alien introgression genes. To increase the identification efficiency, other new identification methods, such as microarray comparative genomic hybridization (array-CGH) and suppression subtractive hybridization (SSH), may also be included.

Microdeleción 16p11. 2: primeros casos reportados en Argentina / 16p11. 2 Microdeletion: first report in Argentina

La microdeleción 16p11.2 se relaciona, habitualmente, con discapacidad intelectual y trastornos del espectro autista. El rango fenotípico incluye un espectro que se extiende desde discapacidad intelectual con o sin autismo, alteraciones del aprendizaje y del lenguaje hasta fenotipos normales. El diagnóstico de la microdeleción se realiza mediante estudios genómicos capaces de identificar variación en número de copias, como la hibridación genómica comparativa en microarreglos, conocida como arrayCGH. Sin embargo, la predicción del fenotipo de un individuo basada únicamente en la localización de dicha deleción sigue siendo un desafío, ya que la existencia de un gran número de variantes en el genoma dificulta la interpretación de posibles efectos funcionales de los genes que contribuyen a dicha región. Se describen dos casos clínicos de pacientes con microdeleción heterocigota en 16p11.2 y se destacan los hallazgos fenotípicos y conductuales que dificultaron la estrategia diagnóstica. También se discuten las implicancias del diagnóstico para el asesoramiento genético familiar.

The 16p11.2 recurrent microdeletion phenotype is characterized by developmental delay, intellectual disability, and/or autism spectrum disorder. This microdeletion is associated with variable clinical outcome, the phenotypical spectrum ranges from intellectual disability and/or multiple congenital anomalies, autism, learning and speech problems, to a normal phenotype. Genomic testing that determines copy number of sequences, such as chromosomal microarray, is used to identify this microdeletion. However, the prediction of the individual phenotype of a patient based only on the location of such deletion remains a challenge, regarding the existence of many genomic variants that might hinder the interpretation of possible functional effects between most of the contributing genes to that region. We describe the clinical findings in two subjects with heterozygous microdeletions at 16p11.2, highlighting the phenotypic and behavioural findings that conditioned the diagnostic strategy. We also discuss the implications of diagnosis, in practical counselling situations.

GAB2 Amplification in Squamous Cell Lung Cancer of Non-Smokers

Lung squamous cell cancer (SCC) is typically found in smokers and has a very low incidence in non-smokers, indicating differences in the tumor biology of lung SCC in smokers and non-smokers. However, the specific mutations that drive tumor growth in non-smokers have not been identified. To identify mutations in lung SCC of non-smokers, we performed a genetic analysis using arrays comparative genomic hybridization (ArrayCGH). We analyzed 19 patients with lung SCC who underwent surgical treatment between April 2005 and April 2015. Clinical characteristics were reviewed, and DNA was extracted from fresh frozen lung cancer specimens. All of copy number alterations from ArrayCGH were validated using The Cancer Genome Atlas (TCGA) copy number variation (CNV) data of lung SCC. We examined the frequency of copy number changes according to the smoking status (non-smoker [n = 8] or smoker [n = 11]). We identified 16 significantly altered regions from ArrayCGH data, three gain and four loss regions overlapped with the TCGA lung squamous cell carcinoma (LUSC) patients. Within these overlapped significant regions, we detected 15 genes that have been reported in the Cancer Gene census. We also found that the proto-oncogene GAB2 (11q14.1) was significantly amplified in non-smokers patients and vice versa in both ArrayCGH and TCGA data. Immunohistochemical analyses showed that GAB2 protein was relatively upregulated in non-smoker than smoker tissues (37.5% vs. 9.0%, P = 0.007). GAB2 amplification may have an important role in the development of lung SCC in non-smokers. GAB2 may represent a potential biomarker for lung SCC in non-smokers.

Microarray-based comparative genomic hybridization analysis in neonates with congenital anomalies: detection of chromosomal imbalances / Hibridização genômica comparativa baseada em microarranjos em neonatos com anomalias congênitas: detecção de desequilíbrios cromossômicos

OBJECTIVE: To identify chromosomal imbalances by whole-genome microarray-based comparative genomic hybridization (array-CGH) in DNA samples of neonates with congenital anomalies of unknown cause from a birth defects monitoring program at a public maternity hospital. METHODS: A blind genomic analysis was performed retrospectively in 35 stored DNA samples of neonates born between July of 2011 and December of 2012. All potential DNA copy number variations detected (CNVs) were matched with those reported in public genomic databases, and their clinical significance was evaluated. RESULTS: Out of a total of 35 samples tested, 13 genomic imbalances were detected in 12/35 cases (34.3%). In 4/35 cases (11.4%), chromosomal imbalances could be defined as pathogenic; in 5/35 (14.3%) cases, DNA CNVs of uncertain clinical significance were identified; and in 4/35 cases (11.4%), normal variants were detected. Among the four cases with results considered causally related to the clinical findings, two of the four (50%) showed causative alterations already associated with well-defined microdeletion syndromes. In two of the four samples (50%), the chromosomal imbalances found, although predicted as pathogenic, had not been previously associated with recognized clinical entities. CONCLUSIONS: Array-CGH analysis allowed for a higher rate of detection of chromosomal anomalies, and this determination is especially valuable in neonates with congenital anomalies of unknown etiology, or in cases in which karyotype results cannot be obtained. Moreover, although the interpretation of the results must be refined, this method is a robust and precise tool that can be used in the first-line investigation of congenital anomalies, and should be considered for prospective/retrospective analyses of DNA samples by birth defect monitoring programs. .

OBJETIVO: Identificar desequilíbrios cromossômicos por meio da hibridização genômica comparativa baseada em microarranjos (CGH-array) em amostras de DNA de neonatos com anomalias congênitas de causa desconhecida de um programa de monitoramento de defeitos congênitos em uma maternidade pública. MÉTODOS: Uma análise genômica cega foi realizada retrospectivamente em 35 amostras armazenadas de DNA de neonatos nascidos entre julho de 2011 e dezembro de 2012. Todas as possíveis variações no número de cópias (CNVs) de DNA foram comparadas com as relatadas em bases de dados genômicos públicas, e sua relevância clínica foi avaliada. RESULTADOS: De um total de 35 amostras testadas, foram detectados 13 desequilíbrios genômicos em 12/35 casos (34,3%). Em 4/35 casos (11,4%), os desequilíbrios cromossômicos poderiam ser definidos como patogênicos; em 5/35 (14,3%) deles foram identificadas CNVs de DNA de relevância clínica incerta; e, em 4/35 (11,4%), foram detectadas variações normais. Dentre os quatro casos com resultados considerados relacionados causalmente aos achados clínicos, 2/4 (50%) apresentaram alterações causais já relacionadas a síndromes de microdeleção bem definidas. Em 2/4 amostras (50%), os desequilíbrios cromossômicos encontrados, embora preditivos como patogênicos, não estavam relacionados anteriormente a entidades clínicas reconhecidas. CONCLUSÕES: A análise de CGH-array permitiu maior taxa de detecção de anomalias cromossômicas, e essa determinação é valiosa principalmente em neonatos com anomalias congênitas de etiologia desconhecida ou em casos em que os resultados do cariótipo não podem ser obtidos. Além disso, embora a interpretação dos resultados deva ser refinada, esse método é uma ferramenta robusta e precisa que pode ser usada na investigação de primeira linha de anomalias congênitas e deve ser considerada em análises futuras/retrospectivas de amostras de DNA por programas de monitoramento de defeitos congênitos. .

Ribosomal protein mutations in Korean patients with Diamond-Blackfan anemia

Diamond-Blackfan anemia (DBA) is a congenital bone marrow failure syndrome characterized by hypoproliferative anemia, associated physical malformations and a predisposition to cancer. DBA has been associated with mutations and deletions in the large and small ribosomal protein genes, and genetic aberrations have been detected in approximately50-60% of patients. In this study, nine Korean DBA patients were screened for mutations in eight known DBA genes (RPS19, RPS24, RPS17, RPS10, RPS26, RPL35A, RPL5 and RPL11) using the direct sequencing method. Mutations in RPS19, RPS26 and RPS17 were detected in four, two and one patient, respectively. Among the mutations detected in RPS19, two mutations were novel (c.26T>A, c.357-2A>G). For the mutation-negative cases, array-CGH analysis was performed to identify copy-number variations, and no deletions involving the known DBA gene regions were identified. The relative mRNA expression of RPS19 estimated using real-time quantitative PCR analysis revealed two- to fourfold reductions in RPS19 mRNA expression in three patients with RPS19 mutations, and p53 protein expression analysis by immunohistochemistry showed variable but significant nuclear staining in the DBA patients. In conclusion, heterozygous mutations in the known DBA genes RPS19, RPS26 and RPS17 were detected in seven out of nine Korean DBA patients. Among these patients, RPS19 was the most frequently mutated gene. In addition, decreased RPS19 mRNA expression and p53 overexpression were observed in the Korean DBA patients, which supports the hypothesis that haploinsufficiency and p53 hyperactivation represent a central pathway underlying the pathogenesis of DBA.

Molecular cytogenetic evaluation of chromosomal microdeletions: the experience of a public hospital in Southern Brazil

Introduction: During the past few decades, the number of diseases identified to be caused by chromosomal microdeletions has increased quickly, bringing a new and crucial role for cytogenetics on the diagnosis of these conditions. The purpose of this study was to identify and characterize chromosomal microdeletions associated with malformation syndromes and intellectual disability. Methods: We retrospectively evaluated a consecutive series of samples from a cohort of 598 subjects with clinical symptoms of a microdeletion syndrome, including the deletion of chromosomes 4p16.3, 5p15.2, 5q35, 7q11.23, 8q24.12, 15q11.2, 16p13.3, 17p13.3, 17p11.2,2, and 22q11.2, as investigated by fluorescence in situ hybridization (FISH). Array-based comparative genomic hybridization (array-CGH) was performed on 25 samples with microdeletions. Results: A total of 598 samples were evaluated from patients whose clinical phenotypes were most indicative of 22q11.2 deletion syndrome (29.10%), Prader-Willi syndrome (23.41%), Angelman syndrome (16.89%), and Williams-Beuren syndrome (14.72%). In 142 of the samples (23.75%), a chromosomal imbalance associated with phenotypic abnormalities was found. The deletion of 7q11.23 was the most frequent (8.03%), followed by del22q11.2 (5.68%) and del15q11.2 (5%). Conclusion: Our study reinforces the idea that the effort to improve the capacity to perform molecular cytogenetic investigations associated with a qualified clinical evaluation is crucial for the detection and precise characterization of submicroscopic chromosome deletions, bringing benefits to patients, relatives, and genetic counselors. It also contributes to the continuing education of cytogeneticists and to the knowledge of chromosomal rearrangements associated with genomic disorders.

Genome-Wide Analysis of DNA Copy Number Changes in Liver Steatosis.

Aims: Liver steatosis is the most common benign form of non-alcoholic fatty liver disease. It might be a risk factor for hepatocellular carcinoma, either (i) by causing fibrosis, which highly predisposes to hepatoma, or (ii) by being an early precursor of carcinoma, although it is usually considered not to be pre-neoplastic. We investigated the genomic profile of liver samples from patients with fatty liver disease. Study Design & Methodology: Copy number variation was investigated by array-CGH, using the Human Genome 244K catalogue array (Agilent Technologies), and changes validated by quantitative polymerase chain reaction analysis. Results: The analysis of liver biopsies from 17 patients, 10 of whom had histological diagnosis of non-alcoholic fatty liver disease, showed differences in the type of variants in patients with steatosis compared to those without steatosis at several chromosome bands, including 3q29, 6p2, 11q11 and 22q11. Conclusion: The genomic copy number changes we have demonstrated suggest that genomic structural variations may be associated with the pathogenesis or the evolution of steatosis.

De la observación microscópica de los cromosomas en el cariotipo a los array-CGH en el diagnóstico prenatal / From microscopic chromosome observation in karyotyping to array-CGH in prenatal diagnosis

Introducción: el cariotipo ha sido la prueba de oro para el análisis cromosómico en el diagnóstico prenatal en los últimos cuarenta años; sin embargo, a partir del 2011 se publican múltiples artículos y los primeros meta-análisis que muestran posibles ventajas de los array-CGH (del inglés array-comparative genomic hibridization) sobre el cariotipo en el diagnóstico prenatal. Objetivo: hacer una reflexión acerca del uso de array-CGH en el diagnóstico prenatal y mostrar algunas de las potenciales ventajas y desventajas de esta prueba molecular con relación al cariotipo, así como su aplicación por obstetras, perinatólogos y especialistas en medicina materno-fetal. Conclusión: los a-CGH son una nueva alternativa en el análisis cromosómico en el diagnóstico prenatal en fetos con anomalías anatómicas; pueden usarse en todos los casos en que se justifique una intervención invasiva en el diagnóstico prenatal de alteraciones cromosómicas, y es probable que los array-CGH reemplacen al cariotipo en el diagnóstico prenatal en esta década.

Introduction: Karyotyping has been the gold standard for chromosomal analysis in prenatal diagnosis over the past 40 years. However, many articles and the first meta-analysis on the potential advantages of array-CGH (array comparative genomic hybridization) compared to karyotyping in prenatal diagnosis began to appear in 2011. Objective: The objective of this article is to examine the use of array-CGH in prenatal diagnosis, and to show certain potential advantages and disadvantages of this molecular test over karyotyping, as well as its application by obstetricians, perinatologists and specialists in maternal-fetal medicine. Conclusion: Array-CGH is a new option for chromosomal analysis in prenatal diagnosis of fetuses with anatomical abnormalities; it maybe used in all instances where an invasive intervention is warranted in the prenatal diagnosis of chromosomal abnormalities, and it may eventually replace karyotyping in prenatal diagnosis before this decade is out.

Diagnóstico citogenético de pacientes com retardo mental idiopático / Cytogenetic diagnosis of patients with idiopathic mental retardation

O retardo mental é uma condição presente em 2 por cento a 3 por cento da população e mais da metade dos casos ainda são considerados idiopáticos. Sua etiologia é heterogênea e as anomalias cromossômicas têm importante contribuição. A aplicação de técnicas de citogenética clássica e de citogenética molecular tem permitido o diagnóstico preciso em muitos casos, proporcionando melhor acompanhamento clínico e aconselhamento genético. Este trabalho tem como objetivo informar sobre os principais exames atualmente disponíveis para a investigação de rearranjos cromossômicos em pacientes com retardo mental idiopático, incluindo cariótipo com bandeamento G, hibridação in situ fluorescente (FISH), cariotipagem espectral (SKY), amplificação de múltiplas sondas dependente de ligação (MLPA) e hibridação genômica comparativa em array (array-CGH).

Mental retardation is a condition that affects 2 percent-3 percent of the population and more than half of the cases are still deemed idiopathic. Its etiology is heterogeneous and chromosome abnormalities play a significant role. The application of classical cytogenetic and molecular cytogenetic techniques has enabled accurate diagnosis in several cases, which allows better clinical monitoring and genetic counseling. This paper aims at informing about the major tests currently available to investigate chromosome abnormalities in patients with idiopathic mental retardation, including GTG-banded karyotyping, fluorescence in situ hybridization (FISH), spectral karyotyping (SKY), multiplex ligation-dependent probe amplification (MLPA) and array-comparative genomic hybridization (array-CGH).

Amplification of the UQCRFS1 Gene in Gastric Cancers

PURPOSE: The specific aim of this study is to unravel a DNA copy number alterations, and to search for novel genes that are associated with the development of Korean gastric cancer. MATERIALS AND METHODS: We investigated a DNA copy number changes in 23 gastric adenocarcinomas by array-comparative genomic hybridization and quantitative real-time polymerase chain reaction analyses. Besides, the expression of UQCRFS1, which shows amplification in array-CGH, was examined in 186 gastric cancer tissues by an immunohistochemistry, and in 9 gastric cancer cell lines, as well as 24 gastric cancer tissues by immunoblotting. RESULTS: We found common gains at 48 different loci, and a common loss at 19 different loci. Amplification of UQCRFS1 gene at 19q12 was found in 5 (21.7%) of the 23 gastric cancers in an array-comparative genomic hybridization and DNA copy number were increased in 5 (20.0%) out of the 25 gastric cancer in quantitative real-time polymerase chain reaction. In immunohistochemistry, the overexpression of the protein was detected in 105 (56.5%) out of the 186 gastric cancer tissues. Statistically, there was no significant relationship between the overexpression of UQCRFS1 and clinicopathologic parameters (P>0.05). In parallel, the overexpression of UQCRFS1 protein was confirmed in 6 (66.7%) of the 9 gastric cancer cell lines, and 12 (50.0%) of the 24 gastric cancer tissues by immunoblotting. CONCLUSIONS: These results suggest that the overexpression of UQCRFS1 gene may contribute to the development and/or progression of gastric cancer, and further supported that mitochondrial change may serve as a potential cancer biomarker.

Reciprocal Deletion and Duplication of 17p11.2-11.2: Korean Patients with Smith-Magenis Syndrome and Potocki-Lupski Syndrome

Deletion and duplication of the -3.7-Mb region in 17p11.2 result in two reciprocal syndrome, Smith-Magenis syndrome and Potocki-Lupski syndrome. Smith-Magenis syndrome is a well-known developmental disorder. Potocki-Lupski syndrome has recently been recognized as a microduplication syndrome that is a reciprocal disease of Smith-Magenis syndrome. In this paper, we report on the clinical and cytogenetic features of two Korean patients with Smith-Magenis syndrome and Potocki-Lupski syndrome. Patient 1 (Smith-Magenis syndrome) was a 2.9-yr-old boy who showed mild dysmorphic features, aggressive behavioral problems, and developmental delay. Patient 2 (Potocki-Lupski syndrome), a 17-yr-old boy, had only intellectual disabilities and language developmental delay. We used array comparative genomic hybridization (array CGH) and found a 2.6 Mb-sized deletion and a reciprocal 2.1 Mb-sized duplication involving the 17p11.2. These regions overlapped in a 2.1 Mb size containing 11 common genes, including RAI1 and SREBF.

Supernumerary Marker Chromosome in a Child with Microcephaly and Mental Retardation.

A de novo supernumerary marker chromosome (SMC) was identified in a 13- month-old girl who presented with microcephaly and mild mental retardation. On further characterization by oligo-nucleotide array-comparative genomic hybridization [array-CGH], the SMC was confirmed to be 18p.

Replication of the Association between Copy Number Variation on 8p23.1 and Autism by Using ASD-specific BAC Array

To discover genetic markers for autism spectrum disorder (ASD), we previously applied genome-wide BAC array comparative genomic hybridization (array-CGH) to 28 autistic patients and 62 normal controls in Korean population, and identified that chromosomal losses on 8p23.1 and on 17p11.2 are significantly associated with autism. In this study, we developed an 8.5K ASD-specific BAC array covering 27 previously reported ASD-associated CNV loci including ours and examined whether the associations would be replicated in 8 ASD patient cell lines of four different ethnic groups and 10 Korean normal controls. As a result, a CNV-loss on 8p23.1 was found to be significantly more frequent in patients regardless of ethnicity (p<0.0001). This CNV region contains two coding genes, DEFA1 and DEFA3, which are members of DEFENSIN gene family. Two other CNVs on 17p11.2 and Xp22.31 were also distributed differently between ASDs and controls, but not significant (p=0.069 and 0.092, respectively). All the other loci did not show significant association. When these evidences are considered, the association between ASD and CNV of DEFENSIN gene seems worthy of further exploration to elucidate the pathogenesis of ASD. Validation studies with a larger sample size will be required to verify its biological implication.

Chromosomal aberrations in peripheral T-cell lymphoma, not otherwise specified: an array comparative genomic hybridization approach / 白血病·淋巴瘤

Objective To analyze the genetic changes in peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS) and to find the key molecular aberrations underlying its pathogenesis. Methods A total of 37 cases of PTCL-NOS were investigated by 1Mb resolution array comparative genomic hybridisation (Array-CGH), in which 9 cases were further studied by using a Tile path array-CGH. DNA extraction, clonality analysis and histologic review were conducted to exclude 6 cases with polyploidy and without obvious genetic imbalances from this study. Results In general, there was a considerable overlap in the CGH profiles in many PTCL-NOS cases. The most recurrent regions of genomic gains were lp36.13-1p36.32, 7q22.1, 7q36.1-7q36.3, 7q32.1-7q32.3, 7q22.1-7q34,9p11 .2-9q12 and 9q33.3-9q34.3. The most recurrent regions of genomic losses were 1p12-1p21.1 and 13q14.11-13q14.3. Conclusion Genomic gains and losses are frequently identified in PTCL-NOS with array-CGH, in which patients with multiple chromosomal alterations (≥6regions) have poor prognosis. These genomic profiles are broadly important to reveal a distinct subgroup with genetic alterations and to find the key genomic imbalance of PTCL-NOS.

Genomic Alterations Detected in Colon Cancer Cell Lines by Using Array-Comparative Genomic Hybridization / 대한해부학회지

Cancer development is accompanied by genetic events like losses, gains and amplification of certain chromosome regions or alterations of chromatin structure. Array-based CGH (Array-CGH) is a highly comprehensive, sensitive and fast technique to allow investigation of general changes in target oncogenes and tumor suppressor genes. Recently, the prevalence of colon cancer is rapidly increasing in Korea and now it is the fourth leading cause of cancer death. So, the purpose of this study is to examine genomic alterations in colon cancer cell lines and to search novel genes which might be related to the development of colon cancer. In this study, genomic alterations are analyzed by using array-CGH in three colon cell lines from Korean, SNU-81, SNU-407 and SNU-1047. We observed numerous chromosomal imbalances from all cell lines. The common chromosomal gains were observed in 1p36.33, 1q22, 1q32.1, 2q35, 8p12, 8q22.3, 14q32.33, 16p13.3, and 16q24. Common chromosomal losses were found in 4q22.1, 9q13, 14q21.1, 14q32.33, 20p12.1, Xq21.1, and Yq11.223. Gains of 1p, 2q, 8p, and 8q or losses of 4q, 14q and 20p are already known to be associated with the colon cancer development. For gene alterations, we could see gains of some genes such as ELF3 and AAMP, which were already reported to be associated with colon cancer. Also, we could find some gene alterations which were known to be associated with other cancer types. These genes were GON4L, RNPEP, TMBIM1, TIMM17A, GPBAR1, PPP1R13B and SOX8. Besides, we found alterations of new genes such as PKND and LEPROTL1. The association of these genes with colon cancer is first demonstrated here. These genes may be the novel candidate genes functioning in the development of colon cancer. In conclusion, array-CGH demonstrated the complexity of genetic aberrations in several colon cell lines. These data about the patterns of genomic alterations could be a basic step for understanding more detailed genetic events in the carcinogenesis and also provide information about possible target genes for diagnosis and treatment in colon cancer.

Copy Number Variations in the Human Genome: Potential Source for Individual Diversity and Disease Association Studies

The widespread presence of large-scale genomic variations, termed copy number variation (CNVs), has been recently recognized in phenotypically normal individuals. Judging by the growing number of reports on CNVs, it is now evident that these variants contribute significantly to genetic diversity in the human genome. Like single nucleotide polymorphisms (SNPs), CNVs are expected to serve as potential biomarkers for disease susceptibility or drug responses. However, the technical and practical concerns still remain to be tackled. In this review, we examine the current status of CNV DBs and research, including the ongoing efforts of CNV screening in the human genome. We also discuss the characteristics of platforms that are available at the moment and suggest the potential of CNVs in clinical research and application.

Copy Number Variations in the Human Genome: Potential Source for Individual Diversity and Disease Association Studies

The widespread presence of large-scale genomic variations, termed copy number variation (CNVs), has been recently recognized in phenotypically normal individuals. Judging by the growing number of reports on CNVs, it is now evident that these variants contribute significantly to genetic diversity in the human genome. Like single nucleotide polymorphisms (SNPs), CNVs are expected to serve as potential biomarkers for disease susceptibility or drug responses. However, the technical and practical concerns still remain to be tackled. In this review, we examine the current status of CNV DBs and research, including the ongoing efforts of CNV screening in the human genome. We also discuss the characteristics of platforms that are available at the moment and suggest the potential of CNVs in clinical research and application.

Unbalanced translocation der(8)t(8:13)(p23.3;q32.1)dn identified by array CGH and subtelomeric FISH in a patient with mental retardation

Molecular cytogenetics allows the identification of unknown chromosome rearrangements, which is clinically useful in patients with mental retardation and/or development delay. We report on a 31-year- old woman with severe mental retardation, behavior development delay, and verbal performance delay. Conventional cytogenetic analysis showed a 46,XX,add(8)(p23.3) karyotype. To determine the origin of this unbalanced translocation, we performed array CGH and subtelomeric FISH. The results showed that the distal region of chromosome 8p was added to the terminal of chromosome 13q. This was confirmed the final result of 46,XX,der(8)t(8:13)(p23.3;q32.1)dn.

Analysis of Genomic Alterations in Retinoblastoma Cell Lines by Array-CGH / 대한해부학회지

Retinoblastoma is the most common intraocular malignancy in young children, arising in approximately 1 per 20,000 live births. Although it is established that the functional loss of both alleles of the RB1 gene is a prerequisite for the development of retinoblastoma, little is known about the genetic events that are required for tumor progression. To screen the genomic aberrations, two retinoblastoma cell lines, Y-79 and WERI-Rb-1, were analysed by using array-CGH. As a result, gains of AHRR, EXOC3, CEP72, TRIP13, TERT, SEMA5A, TAS2R1, MARCH6, CTNND2, CDH12, NHLRC1, TPMT, AOF1, FANCC, NCBP1, XPA, TGFBR1, BAAT, MRPL50, ZNF189, ALDOB, ABCA1, FCMD, TAL2, ZNF462, COL27A1, ORM1, ORM2, AKNA, ASTN2, TRIM32, GSN, STOM, LHX2, PBX3, ABL1, FIBCD1, WNK4, CCDC56, CNT1, BECN1, PSME3, AOC2, LOXHD1, ST8SIA5, SMAD2, KIAA0427, COL18A1, COL6A2, FTCD and LSS were found in both cell lines. Lost clones detected in both cell lines were RB1, ZDHHC3, EXOSC7, CLEC3B, CACNA2D3, DEFB106A, FAM90A6P, FAM90A7, ZMYND11, LARP5, GTPBP4, IDI2, IDI1, KLF6, AKR1CL2, FBXO18, IL15RA, IL2RA, TAF3, GATA3, CUGBP2, DHTKD1, SEC61A2, NUDT5, ITGA8, PTER, C1QL3, RSU1, DNMT2, PTPLA, PLXDC2, NEBL, MLLT10, DNAJC1, PIP5K2A, PRTFDC1, NRP1, PARD3, MGMT, RFP2OS, RFP2, KCNRG, IGHV, CDH19, TXNDC10 and RTTN. Through this study, it is confirmed that many genomic aberrations are involved in the development and progression of retinoblastoma. Genomic profiling of retinoblastoma cell lines by array-CGH revealed numerous imbalanced regions and novel candidate genes. These data provide a basis for more detailed molecular characterization and testing their pathologic roles of these candidates.

Array-CGH testing in spontaneous abortions with normal karyotypes

In about 50 percent of first trimester spontaneous abortion the cause remains undetermined after standard cytogenetic investigation. We evaluated the usefulness of array-CGH in diagnosing chromosome abnormalities in products of conception from first trimester spontaneous abortions. Cell culture was carried out in short- and long-term cultures of 54 specimens and cytogenetic analysis was successful in 49 of them. Cytogenetic abnormalities (numerical and structural) were detected in 22 (44.89 percent) specimens. Subsequent, array-CGH based on large insert clones spaced at ~1 Mb intervals over the whole genome was used in 17 cases with normal G-banding karyotype. This revealed chromosome aneuplodies in three additional cases, giving a final total of 51 percent cases in which an abnormal karyotype was detected. In keeping with other recently published works, this study shows that array-CGH detects abnormalities in a further ~10 percent of spontaneous abortion specimens considered to be normal using standard cytogenetic methods. As such, array-CGH technique may present a suitable complementary test to cytogenetic analysis in cases with a normal karyotype.