TY - JOUR. T1 - 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. AU - Greshock, Joel. AU - Naylor, Tara L.. AU - Margolin, Adam. AU - Diskin, Sharon. AU - Cleaver, Stephen H.. AU - Futreal, P. Andrew. AU - deJong, Pieter J.. AU - Zhao, Shaying. AU - Liebman, Michael. AU - Weber, Barbara L.. PY - 2004/1/1. Y1 - 2004/1/1. N2 - Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for disease-gene discovery in cancer and developmental disorders as well as numerous other applications. However, widespread utilization of aCGH has been limited by the lack of well characterized, high-resolution clone sets optimized for consistent performance in aCGH assays and specifically designed analytic software. We have assembled a set of ∼4100 publicly available human bacterial artificial chromosome (BAC) clones ...
TY - JOUR. T1 - High Resolution Array Comparative Genomic Hybridization in Sporadic and Celiac Disease-Related Small Bowel Adenocarcinomas. AU - Carvalho, B.. AU - Diosdado Calvo, M.B.. AU - Buffart, T.E.. AU - Watkins, R.. AU - Ylstra, B.. AU - Tijssen, M.. AU - Bolijn, J.S.. AU - Lewis, F.. AU - Maude, K.. AU - Verbeke, C.. AU - Nagtegaal, I.D.. AU - Grabsch, H.. AU - Mulder, C.J.J.. AU - Quirke, P.. AU - Howdle, P.. AU - Meijer, G.A.. PY - 2010. Y1 - 2010. M3 - Meeting Abstract. VL - 32. SP - 182. EP - 182. JO - Cellular Oncology. JF - Cellular Oncology. SN - 2211-3428. IS - 3. ER - ...
Recent genome-wide microarray-based research investigations have revealed a high frequency of submicroscopic copy number alterations (CNAs) in the myelodysplastic syndromes (MDS), suggesting microarray-based comparative genomic hybridization (aCGH) has the potential to detect new clinically relevant genomic markers in a diagnostic laboratory. We performed an exploratory study on 30 cases of MDS, myeloproliferative neoplasia (MPN) or evolving acute myeloid leukemia (AML) (% bone marrow blasts ≤ 30%, range 0-30%, median, 8%) by aCGH, using a genome-wide bacterial artificial chromosome (BAC) microarray. The sample data were compared to corresponding cytogenetics, fluorescence in situ hybridization (FISH), and clinical-pathological findings. Previously unidentified imbalances, in particular those considered submicroscopic aberrations (| 10 Mb), were confirmed by FISH analysis. CNAs identified by aCGH were concordant with the cytogenetic/FISH results in 25/30 (83%) of the samples tested. aCGH revealed new
Comparative genomic hybridization analysis of adrenocortical tumors.: Comparative genomic hybridization (CGH) is a molecular cytogenetic technique that allows t
TY - JOUR. T1 - Molecular and clinical characterization of a recurrent cryptic unbalanced t(4q;18q) resulting in an 18q deletion and 4q duplication. AU - Horbinski, Craig. AU - Carter, Erika M.. AU - Heard, Patricia L.. AU - Sathanoori, Malini. AU - Hu, Jie. AU - Vockley, Jerry. AU - Gunn, Shelly. AU - Hale, Daniel. AU - Surti, Urvashi. AU - Cody, Jannine D.. PY - 2008/11/15. Y1 - 2008/11/15. N2 - Recurrent constitutional non-Robertsonian translocations are very rare. We present the third instance of cryptic, unbalanced translocation between 4q and 18q. This individual had an apparently normal karyotype; however, after subtelomere fluorescence in situ hybridization (FISH), he was found to have a cryptic unbalanced translocation between 4q and 18q [ish der(18)t(4;18)(q35;q23) (4qtel+, 18qtel-)]. Oligonucleotide array comparative genomic hybridization (aCGH) refined the breakpoints in this child and in the previously reported child and indicated that the breakpoints were within 20 kb of each ...
Lim, G., J. Karaskova, et al. (2005). "An integrated mBAND and submegabase resolution tiling set (SMRT) CGH array analysis of focal amplification, microdeletions, and ladder structures consistent with breakage-fusion-bridge cycle events in osteosarcoma." Genes Chromosomes Cancer 42(4): 392-403. Coe, B. P., L. J. Henderson, et al. (2005). "High-resolution chromosome arm 5p array CGH analysis of small cell lung carcinoma cell lines." Genes Chromosomes Cancer 42(3): 308-13. Garnis, C., B. Coe, et al. (2004). "Construction and optimization of chromosome arm-specific comparative genomic hybridization arrays for identifying genetic alterations in preinvasive lung cancers." Chest 125(5 Suppl): 104S-5S. Garnis, C., B. P. Coe, et al. (2004). "Overexpression of LRP12, a gene contained within an 8q22 amplicon identified by high-resolution array CGH analysis of oral squamous cell carcinomas." Oncogene 23(14): 2582-6. de Leeuw, R. J., J. J. Davies, et al. (2004). "Comprehensive whole genome array CGH ...
Background: When abnormalities are found during the anatomy scan most patients are offered amniocentesis and conventional karyotyping, using Giemsa (G)-banding of metaphase chromosomes to detect aneuploidies and large structural changes in the prenatal diagnosis. The use of fluorescent in situ hybridization (FISH) reduces the time to obtain a result because culture is not necessary, but can only detect a limited number of prespecified targets. Small studies have shown that array comparative genomic hybridization (aCGH) can detect all unbalanced chromosomal abnormalities as well as smaller deletions and duplications that cannot be detected with routine cytogenetic analysis. Should aCGH screening be used instead of karyotyping to diagnose prenatal chromosomal abnormalities in pregnant patients with abnormal ultrasound? Methods: An exhaustive search of available medical literature from the past 5 years was conducted using Medline-OVID, CINAHL, Web of Science. Key words included: comparative genomic
Uveal melanomas (UM) are aggressive ocular tumours of adults that are typically characterized by chromosomal aberrations such as loss of 1p, 3, 6q, and gain 6p, and 8q. Of these monosomy 3 (M3) and 8q+ are powerful predictors of prognosis. The relationship of changes affecting chromosome 6 is however more ambivalent, having been linked to both good and poor prognosis, and yet both regions have not been well defined, which suggest the presence of one or more oncogenes in 6p and tumour suppressor gene in 6q. Therefore, different chromosome 6 alterations may have a variable impact on the prognosis of UM, and ultimately contain genes that contribute to the development and metastasis of this disease. It is likely that these changes can act as moderators to the tumour outcome. Although UM disseminates haematogenous with high propensity for the liver, and hepatic involvement reported in over 90% of patients, infrequently some patients will however initially present with metastases in sites other than ...
Abnormal genomic losses detected by array comparative genomic hybridization are prevalent in adults with unexplained intellectual disability. Our data showing abnormalities in 22% and 17% of overall patients and of cases with normal karyotypes, respectively, suggest that the yield of array comparati …
Detection of submicroscopic genomic copy number variation is now considered the first-tier clinical test-in place of standard G-banded karyotyping-in the evaluation of children with unexplained developmental delay, intellectual disability, autism spectrum disorders, or congenital anomalies. Fluorescence in situ hybridization (FISH) was the first molecular method for detection of submicroscopic genomic copy number variants (CNVs), but microarray-based comparative genomic hybridization (array CGH) has a much higher diagnostic yield for these patients when compared to traditional cytogenetic methods such as karyotype and FISH. This unit focuses on oligonucleotide arrays, including updated information about detection of long contiguous stretches of homozygosity (LCSH) through inclusion of single-nucleotide polymorphism (SNP) probes. Most clinical laboratories now offer arrays with some level of probe coverage throughout the genome, and many are offering detection of LCSH. Updated guidelines for array design
TY - JOUR. T1 - Overlay analysis of the oligonucleotide array gene expression profiles and copy number abnormalities as determined by array comparative genomic hybridization in medulloblastomas. AU - Lo, Ken C.. AU - Rossi, Michael R.. AU - Burkhardt, Tania. AU - Pomeroy, Scott L.. AU - Cowell, John K.. PY - 2007/1/1. Y1 - 2007/1/1. N2 - Combined analysis of gene expression array data and array-based comparative genomic hybridization data have been used in a series of 26 pediatric brain tumors to define up- and downregulated genes that coincide with losses, gains, and amplifications involving specific chromosome regions. Frequent losses were defined in chromosome arms 3q, 6q, 8p, 10q, 16q, 17p, and gains were identified in chromosome 7, and chromosome arms 9p and 17q. Amplification of a 2p region was seen in only one tumor, which corresponded to increased expression of the MYCN and DDX1 genes. To facilitate the analysis of the two data sets, we have developed a custom overlay tool that defines ...
Br J Haematol. 2010 Nov;151(4):336-45. doi: 10.1111/j.1365-2141.2010.08341.x. Epub 2010 Aug 31. Comparative Study; Multicenter Study; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Govt
Array-based comparative genomic hybridization (CGH) allows high-throughput genome-wide survey for DNA copy number aberrations, providing a powerful tool for investigating genetic disorders and for developing diagnostic and therapeutic targets. Arrays used in this study consist of approximately 43,000 60-mer oligonucleotide probes that span coding and noncoding regions of the whole human genome with an average spatial resolution of around 35 kb. Furthermore, the sensitivity of these arrays is capable of detecting and mapping regions of single-copy losses, homozygous deletions, and amplicons of various sizes even when using full-complexity genomic samples. In this study, the investigators will conduct an array-based comparative genomic hybridization (CGH) with genomic DNA of many affected members from schizophrenia families (the investigators classified families according to the presence or absence of two or more affected members) to identify a set of candidate genes associated with this ...
Background: Genome-wide analysis of sequence divergence among species offers profound insights into the evolutionary processes that shape lineages. When full-genome sequencing is not feasible for a broad comparative study, we propose the use of array-based comparative genomic hybridization (aCGH) in order to identify orthologous genes with high sequence divergence. Here we discuss experimental design, statistical power, success rate, sources of variation and potential confounding factors. We used a spotted PCR product microarray platform from Drosophila melanogaster to assess sequence divergence on a gene-by-gene basis in three fully sequenced heterologous species (D. sechellia, D. simulans, and D. yakuba). Because complete genome assemblies are available for these species this study presents a powerful test for the use of aCGH as a tool to measure sequence divergence. Results: We found a consistent and linear relationship between hybridization ratio and sequence divergence of the sample to the ...
The Cytogenetics Laboratory performs chromosome analysis, fluorescence in situ hybridization (FISH), and array comparative genomic hybridization (array CGH) on cells prepared from a wide variety of tissues including amniotic fluid, chorionic villi, products of conception, peripheral blood leukocytes, bone marrow, lymph node, and skin/muscle biopsy.. Learn more. ...
Leukaemia is often associated with genetic alterations such as translocations, amplifications and deletions, and recurrent chromosome abnormalities are used as markers of diagnostic and prognostic relevance. However, a proportion of acute myeloid leukaemia (AML) cases have an apparently normal karyotype despite comprehensive cytogenetic analysis. Based on conventional cytogenetic analysis of banded chromosomes, we selected a series of 23 paediatric patients with acute myeloid leukaemia and performed whole genome array comparative genome hybridization (aCGH) using DNA samples derived from the same patients. Imbalances involving large chromosomal regions or entire chromosomes were detected by aCGH in seven of the patients studied. Results were validated by fluorescence in situ hybridization (FISH) to both interphase nuclei and metaphase chromosomes using appropriate bacterial artificial chromosome (BAC) probes. The majority of these copy number alterations (CNAs) were confirmed by FISH and found ...
There is merit in each of these predictions. For example, profiling has re-emerged in clinical testing in the form of protein, tissue and nucleic acid arrays (e.g., cytokine profiles, array comparative genomic hybridization analysis) [49-52]. Computers and automation have played an increasingly important role in improving the efficiency and effectiveness of testing. More recently, pharmacogenetics, popularized by the slogan "right patient, right drug, right time" [53], has moved into mainstream testing (e.g., CYP2C9 for warfarin dosing) [54]. Since 1969, there have been many predictions and views of the future development of laboratory medicine and its sub-specialties. A summary of these predictions is provided in Table 1 [12-48]. A number of common themes and buzz-words can be identified in the prognostications such as nanotechnology, biosensors, microchips, genomics, and proteomics. These topics, together with the more specific predictions, are discussed in greater detail below. ...
BACKGROUND: Currently, two main technologies are used for screening of DNA copy number; the BAC (Bacterial Artificial Chromosome) and the recently developed oligonucleotide-based CGH (Chromosomal Comparative Genomic Hybridization) arrays which are capable of detecting small genomic regions with amplification or deletion. The correlation as well as the discriminative power of these platforms has never been compared statistically on a significant set of human patient samples. RESULTS: In this paper, we present an exhaustive comparison between the two CGH platforms, undertaken at two independent sites using the same batch of DNA from 19 advanced prostate cancers. The comparison was performed directly on the raw data and a significant correlation was found between the two platforms. The correlation was greatly improved when the data were averaged over large chromosomic regions using a segmentation algorithm. In addition, this analysis has enabled the development of a statistical model to discriminate BAC
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Background: Mental retardation can be caused by copy number variations (deletions, insertions, duplications), ranging in size from 1 kb to several megabases. Array based comparative genomic hybridisation (array-CGH) allows detection of an increasing number of genomic alterations.. Methods: A series of 46 patients with mental retardation and congenital abnormalities (previously screened for subtelomeric rearrangements) were evaluated for cryptic chromosomal imbalances by array-CGH. This array contains 6465 large-insert BAC/PAC clones, representing sequences uniformly distributed throughout the human genome. The results were confirmed by alternative techniques.. Results: Four pathogenic rearrangements were detected: two of them were novel, a deletion at 2q31.2 and a duplication at 8q12 band; the other two have been previously reported-a duplication of the Williams-Beuren region and a deletion of 3q29. By adding the subtelomeric alterations previously identified, a total rate of 18% of pathogenic ...
The new whitepaper explains how utilising a range of available tools builds a more complete picture of inherently complex genetic disorders, providing the insights necessary to drive novel discoveries and research into potential therapeutic strategies. At the forefront of this approach is Professor Madhuri Hegde, Professor of Human Genetics at Emory Genetics Laboratory (EGL, Atlanta, USA), whose success in applying such an integrated strategy is also explored. The paper highlights that while targeted DNA sequencing presents a valuable approach for genomic analysis, it is unable to detect copy number variations (CNV) with certainty. In contrast, comparative genomic hybridisation arrays (aCGH) are the gold-standard for CNV detection and the 60-mer oligonucleotide probes utilised by OGTs aCGH platform have been shown to deliver superior CNV detection compared with alternative platforms.. In collaboration with experts at EGL, OGT has designed a range of molecular arrays that are the ideal ...
Chromosomal abnormalities are diagnostic and prognostic key factors in acute myeloid leukemia (AML) patients, as they play a central role for risk stratification algorithms. High hyperdiploidy (HH), a rare cytogenetic abnormality seen commonly in elder male AML patients, is normally categorized under AML with complex karyotype (CK). Accordingly, patients with HH generally are associated with low remission rates and a short overall survival. Here we report a case of 21-year-old female, diagnosed with a de novo AML-M1 according to WHO classification and a CK at diagnosis. Cytogenetic, molecular cytogenetic approaches (standard fluorescence in situ hybridization (FISH), array-proven multicolor banding (aMCB)) and high resolution array comparative genomic hybridization (aCGH) analyses revealed a unique complex but still near diploid karyotype involving eleven chromosomes was identified. It included pentasomy 4, three yet unreported chromosomal aberrations t(1;2)(p35;p22), t(1;3)(p36.2;p26.2), and t(10;12)
In countries where comparative genomic hybridization arrays (aCGH) and next generation sequencing are not widely available due to accessibility and economic constraints, conventional 400-500-band karyotyping is the first-line choice for the etiological diagnosis of patients with congenital malformations and intellectual disability. Conventional karyotype analysis can rule out chromosomal alterations greater than 10 Mb. However, some large structural abnormalities, such as derivative chromosomes, may go undetected when the analysis is performed at less than a 550-band resolution and the size and banding pattern of the interchanged segments are similar. Derivatives frequently originate from inter-chromosomal exchanges and sometimes are inherited from a parent who carries a reciprocal translocation. We present two cases with derivative chromosomes involving a 9.1 Mb 5p deletion/14.8 Mb 10p duplication in the first patient and a 19.9 Mb 5p deletion/ 18.5 Mb 9p duplication in the second patient. These long
The treatment strategy usually depends on the disease state in the individual patient. However, it is difficult to estimate the disease state before treatment in many patients. The purpose of this study was to develop a BAC (bacterial artificial chromosome) mini-array allowing for the estimation of node metastasis, liver metastasis, peritoneal dissemination and the depth of tumor invasion in gastric cancers. Initially, the DNA copy number aberrations (DCNAs) were analyzed by array-based comparative genomic hybridization (aCGH) in 83 gastric adenocarcinomas as a training-sample set. Next, two independent analytical methods were applied to the aCGH data to identify the BAC clones with DNA copy number aberrations that were linked with the disease states. One of the methods, a decision-tree model classifier, identified 6, 4, 4, 4, and 7 clones for estimating lymph node metastasis, liver metastasis, peritoneal dissemination, depth of tumor invasion, and histological type, respectively. In the other method, a
Understanding tumors as evolutionary systems is an important area of study with far-reaching implications in diagnostic and treatment paradigms. Computational phylogenetics is a valuable method for inferring tumor evolution in terms of evolutionary trees, phylogenies, where paths in a tree correspond to possible tumor progression pathways. The location of specific cell-types and patient samples in the tree provide information on tumor sub-types and development of heterogeneity. We previously developed a tumor phylogeny inference pipeline for array comparative genome hybridization (aCGH)-based tumor copy number profiles. Steps in the pipeline included extraction of robust progression markers from the data, which could differentiate stages of tumor evolution or the different paths in the tree, and assigning amplification states to the inferred markers in those stages. We introduced a novel multi-sample model for amplicon identification and calling, HMMCNA, which jointly extracted markers from and ...
Comparative genomic hybridization (CGH) is a modern genetic method which enables a genome‐wide survey of chromosomal imbalances. For each chromosome region, one obtains the information whether there is a loss or gain of genetic material, or whether t
Comparative genomic hybridization is a molecular cytogenetic method for analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample, without the need for culturing cells. The aim of this technique is to quickly and efficiently compare two genomic DNA samples arising from two sources, which are most often closely related, because it is suspected that they contain differences in terms of either gains or losses of either whole chromosomes or subchromosomal regions (a portion of a whole chromosome). This technique was originally developed for the evaluation of the differences between the chromosomal complements of solid tumor and normal tissue, and has an improved resoIution of 5-10 megabases compared to the more traditional cytogenetic analysis techniques of giemsa banding and fluorescence in situ hybridization (FISH) which are limited by the resolution of the microscope utilized. This is achieved through the use of competitive ...
Comparative genomic hybridization (CGH) is a technique used to detect unbalanced chromosome rearrangements based on the use o f in situ hybridization of differentially labeled DNA. This technique can be used to analyze complex clinical cases which have constitutional chromosomal abnormalities that do not lend themselves to routine chromosomal analysis. CGH was examined in order to develop a reliable and reproducible protocol that can be used as an additional diagnostic tool in Shodair Hospitals clinical lab. CGH involves the isolation o f both test and reference DNA and the differentially labeling o f the different DNA with fluorescent probes. Then those samples o f DNA were hybridized onto a normal metaphase spread. The slide was examined under a fluorescent microscope and analyzed using Perceptive Scientific Instruments MacProbe fluorescent imaging software. It appears that a slightly modified version o f the published Vysis Protocol (1998) yields the best CGH results in our clinical diagnostic
臺大位居世界頂尖大學之列,為永久珍藏及向國際展現本校豐碩的研究成果及學術能量,圖書館整合機構典藏(NTUR)與學術庫(AH)不同功能平台,成為臺大學術典藏NTU scholars。期能整合研究能量、促進交流合作、保存學術產出、推廣研究成果。. To permanently archive and promote researcher profiles and scholarly works, Library integrates the services of "NTU Repository" with "Academic Hub" to form NTU Scholars.. ...
Chromosome abnormalities are common in oocytes derived from patients undergoing IVF treatment. The proportion of oocytes displaying aneuploidy is closely related to maternal age and may exceed 60% in patients over 40 years old. However, little information currently exists concerning the incidence of such anomalies in oocytes derived from young fertile women. A total of 121 metaphase II oocytes and their corresponding first polar bodies (PB) were analysed with the use of a comprehensive cytogenetic method, comparative genomic hybridization (CGH). The oocytes were donated from 13 young women (average age 22 years) without any known fertility problems. All oocytes were mature at the time of retrieval and were unexposed to spermatozoa. A low aneuploidy rate (3%) was detected. These results clearly indicate that meiosis I segregation errors are not frequent in oocytes of young fertile women. The higher aneuploidy rates reported in embryos derived from donor oocytes could be due to aggressive hormonal
Chromosome abnormalities are common in oocytes derived from patients undergoing IVF treatment. The proportion of oocytes displaying aneuploidy is closely related to maternal age and may exceed 60% in patients over 40 years old. However, little information currently exists concerning the incidence of such anomalies in oocytes derived from young fertile women. A total of 121 metaphase II oocytes and their corresponding first polar bodies (PB) were analysed with the use of a comprehensive cytogenetic method, comparative genomic hybridization (CGH). The oocytes were donated from 13 young women (average age 22 years) without any known fertility problems. All oocytes were mature at the time of retrieval and were unexposed to spermatozoa. A low aneuploidy rate (3%) was detected. These results clearly indicate that meiosis I segregation errors are not frequent in oocytes of young fertile women. The higher aneuploidy rates reported in embryos derived from donor oocytes could be due to aggressive hormonal
Patrick Buckley graduated with a Bsc. Hons in Biochemistry and Molecular Biology from DIT. In 2005, he completed a PhD in Clinical Genetics entitled "Development and Application of Microarray-Based Comparative Genomic Hybridization - Analysis of Neurofibromatosis Type-2, Schwannomatosis and related tumours" in the group of Professor Jan Dumanski at the Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden.. Moving back to Ireland, he spent two years in the Medical Devices Department within the Irish Medicines Board (now HPRA), before moving to the Department of Cancer Genetics at The Royal College of Surgeons in Ireland. Patrick received an Irish Research Council for Science, Engineering and Technology (IRCSET) Post-Doctoral Fellowship in 2007 and was appointed to a lecturering position in the Department of Molecular and Cellular Therapeutics, RCSI in 2010.. In 2011, Patrick moved to Beaumont Hospital to establish the Molecular Pathology Laboratory, which is now an ...
This observational study shows that comparative genomic hybridization and reflex microsatellite analysis are effective DNA technologies to determine chromosome results of preserved miscarriage tissue.
4183 Array comparative genomic hybridization (CGH) is a high-resolution technique that allows a genome-wide screen to identify regions of genomic imbalances. The technique has been widely used to characterize recurrent genomic copy number alterations in cancers, typically detected through the application of gain and loss thresholds. However, to date, the effect of sample ploidy on the detection accuracy of these thresholds towards single copy alterations (SCAs) has not been evaluated. Here, we describe a method to evaluate the detection accuracy of thresholds towards SCAs in array CGH data. Through the application of a Hidden Markov Model based method, we segment array CGH data from well-karyotyped cell lines, and generate ploidy-specific sensitivity-specificity plots, from which we identify optimum thresholds relevant to sample ploidy. We demonstrate that commonly used non-ploidy-specific thresholds are sub-optimal in their ability to call SCAs, partic ularly when applied to tetraploid samples ...
Copy number variation (CNV) comprises a recently discovered kind of variation involving deletion and duplication of DNA segments of variable size, ranging from a few hundred basepairs to several million. By altering gene dosage levels or disrupting proximal or distant regulatory elements CNVs create human diversity. They represent also an important factor in human evolution and play a role in many disorders including cancer. Array-based comparative genomic hybridization as well as expression arrays are powerful and suitable methods for determination of copy number variations or gene expression changes in the human genome. In paper I we established a 32K clone-based genomic array, covering 99% of the current assembly of the human genome with high resolution and applied it in the profiling of 71 healthy individuals from three ethnic groups. Novel and previously reported CNVs, involving ~3.5% of the genome, were identified. Interestingly, 87% of the detected CNV regions overlapped with known genes ...
Array-based comparative genomic hybridization analysis was performed on 21 malignant mesothelioma (MM) samples (16 primary cell cultures and 5 cell lines) and two reactive mesothelial hyperplasia (RM) primary cell cultures. The RM samples did not have any genomic losses or gains. In MM samples, deletions in 1p, 3p21, 4q, 9p21, 16p13 and 22q were detected frequently. We focused on 3p21 because this deletion was specific to the epithelioid type. Especially, a deletion in 3p21.1 region carrying seven genes including SEMA3G was found in 52% of MM samples (11 of 14 epithelioid samples). The allele loss of 3p21.1 might be a good marker for the epithelioid MM. A homozygous deletion in this region was detected in two MM primary cell cultures. A heterozygous deletion detected in nine samples contained the 3p21.1 region and 3p21.31 one carrying the candidate tumor suppressor genes such as semaphorin 3F (SEMA3F), SEMA3B and Ras association (RalGDS/AF-6) domain family member 1 (RASSF1A). SEMA3B, 3F and 3G ...
Array-based comparative genomic hybridization (aCGH) is a powerful tool to detect genomic imbalances in the human genome. The analysis of aCGH data sets has revealed the existence of a widespread technical artifact termed as waves, characterized by an undulating data profile along the chromosome.
Crete Fertility Centre is one of the very few centres in Greece which perform the new method, Array-CGH (Array Comparative Genomic Hybridization), with excellent results.. Array CGH is the only method able to detect unbalanced chromosomal abnormalities. This is because balanced chromosomal abnormalities such as reciprocal translocations, inversions or ring chromosomes do not affect copy number, which is what is detected by CGH technologies. CGH enables the exploration of all 46 human chromosomes in single test and the discovery of deletions and duplications, even on microscopic scale which may lead to the identification of candidate genes to be further explored by other cytological techniques.. Array CGH can help in cases of advanced maternal age, multiple miscarriages and failed embryo transfers.. Humans generally have 46 chromosomes that come as 23 pairs, one of each pair from our Mum and one of each from our Dad. Problems arise when an embryo misses out on a chromosome or picks up an extra ...
Paulette Mhawech-Fauceglia, Tanja Pejovic, Daniel Dim, Xueping Fang, Jeffrey Conroy, Shashikant Lele, Richard Cheney, and Kunle Odunsi. Array-based comparative genomic hybridization (aCGH) analysis is a useful tool for distinguishing primary pulmonary from metastatic neuroendocrine carcinoma to the lung. Applied Immunohistochemistry and Molecular Morphology. 2008 May; 16(3): 291-5 ...
Gain a deeper understanding of array comparative genomic hybridization, how it works and how it is being applied in clinical research today.
(2005) Lai et al. Bioinformatics. MOTIVATION: Array Comparative Genomic Hybridization (CGH) can reveal chromosomal aberrations in the genomic DNA. These amplifications and deletions at the DNA level are important in the pathogenesi...
Current models suggest that colon cancer initiation and progression are secondary to both the activation of oncogenes and the deletion of tumor suppressor genes. The role of each, however, is still poorly understood, particularly with regard to the induction of metastasis. We hypothesized that genetic differences exist between tumors that metastasize distantly and those that do not, and that oncogenes and tumor suppressor genes participate equally in this process. To address this hypothesis, human tumor specimens from localized [tumor-node-metastasis (TNM) stage I-III] and primary colon cancers (n = 10) were directly compared with metastatic (TNM stage IV) lesions (n = 10) using comparative genomic hybridization analysis. Although several alterations were shared equally between primary tumors and metastases (+7q, +19q, and +20q), two patterns of distinguishing alterations were observed: (a) alterations that were more extensive in liver metastases than in primary tumors (+8q, +13q, -4p, -8p, ...
The biomedical literature is an incredibly rich resource for researchers. Information obtained from previous scientific studies helps researchers focus their own efforts. To obtain the maximal benefit from studies in genetics and genomics there is a need to link this data with the information available in the associated biomedical literature. In particular, microarray gene expression, comparative genomic hybridization, and genetic mapping studies depend on an integrated pool of information to drive output analysis. In mining the literature to find regions previously associated with Prostate Cancer, one can define focus points for future research efforts. Subsequent analytical methods include actual placement of gene expression patterns on metabolic pathways, and the use of comparative genomic hybridization information along with genetic mapping data to determine localized genomic structure. The latter approach promises the added benefit of associating differential gene expression profiles with ...
European Journal of Gastroenterology & Hepatology. 10(12):A34, DECEMBER 1998. Issn Print: 0954-691X. Publication Date: December 1998. ...
In the present study, we examined DNA copy number alterations in 106 invasive cancers using 4 × 44K Agilent arrays. Our CGH analysis correctly identified clinical HER-2 amplification status with 96% to 99% accuracy, depending on the cutoff value used to determine HER-2 status by our CGH data. In addition, we report that 3,007 genes presented a significant correlation between copy number and mRNA levels. Interestingly, a high number of molecular targets (HER-2, EGFR, PTEN, VEGFA, AURKA, CHEK, AKT…) currently under investigation presented such correlation. Altogether, these two data suggest that (a) the occurrence of a DNA gain and/or lost leads to an unregulated overexpression or underexpression of mRNA and (b) high-resolution CGH array is a reliable technology to assess such copy number anomalies. CGH array, as complement to other technologies, could be an interesting approach in clinical practice to identify some subsets of patients who are candidates to targeted therapies.. We could ...
SANTA CLARA, Calif., July 28, 2016 Agilent Technologies Inc. (NYSE: A) today announced that scientists using the companys comparative genomic hybridization (CGH) technology have shown that cancer cell lines, which are broadly used in all aspects of biomedical research, may have vast differences in their genetic makeup, even when grown in the same batch.. As a result, the scientists have recommended that cell culture banks use advanced genomic technologies, such as array CGH, to ensure the consistency of the cells they provide to the research community.. Researchers have long been aware that some popular cell lines are not stable. That is, their biological properties and genetic makeup change as cultures are propagated in laboratories. While standard precautions and quality assurance methods are being used to control such changes and validate authenticity of the cell lines, they may not be sufficient, according to a paper published July 26 in Scientific Reports, an online journal from the ...
Comparative genomic analysis is the only way to determine the authenticity of industrial biotechnology in misappropriation litigation.
Scientists using Agilent Technologies comparative genomic hybridization CGH technology have shown that cancer cell lines, which are broadly used in all aspects of biomedical research, may have vast differences in their genetic makeup, even when grown in the same batch. As a result, the scientists have recommended that cell culture banks use...
Develop molecular markers that will facilitate accurate diagnosis (including prenatal diagnosis) and permit correlation of phenotypic variation with specific mutations by localizing the gene(s) for CDH to specific chromosomal segments using linkage analysis in familial cases. In sporadic cases, characterize the role of somatic mutations in CDDs by using a candidate gene approach, and comparative genomic hybridization (CGH) arrays ...
A comparison of the conceptual steps in aCGH and CNV-seq methods. 1. Starting material in both cases is genomic fragments from two genomes. 2. In CNV-seq the fr