Relevant bibliographies by topics / Array CGH

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  2. Dissertations / Theses
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Academic literature on the topic 'Array CGH'

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Published: 4 June 2021
Last updated: 4 May 2024

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Journal articles on the topic "Array CGH"

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Caliebe, A., K. Platzer, L. Argyriou, S. Bens, Y. Hellenbroich, N. Husemeyer, I. Nagel, et al. "Array-CGH." medizinische genetik 24, no. 2 (June 2012): 99–107. http://dx.doi.org/10.1007/s11825-012-0330-3.

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Bejjani, Bassem A., and Lisa G. Shaffer. "Targeted Array CGH." Journal of Molecular Diagnostics 8, no. 5 (November 2006): 537–39. http://dx.doi.org/10.1016/s1525-1578(10)60341-8.

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Climent, J., J. L. Garcia, J. H. Mao, J. Arsuaga, and J. Perez-Losada. "Characterization of breast cancer by array comparative genomic hybridizationThis paper is one of a selection of papers published in this Special Issue, entitled 28th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process." Biochemistry and Cell Biology 85, no. 4 (August 2007): 497–508. http://dx.doi.org/10.1139/o07-072.

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Cancer progression is due to the accumulation of recurrent genomic alterations that induce growth advantage and clonal expansion. Most of these genomic changes can be detected using the array comparative genomic hybridization (CGH) technique. The accurate classification of these genomic alterations is expected to have an important impact on translational and basic research. Here we review recent advances in CGH technology used in the characterization of different features of breast cancer. First, we present bioinformatics methods that have been developed for the analysis of CGH arrays; next, we discuss the use of array CGH technology to classify tumor stages and to identify and stratify subgroups of patients with different prognoses and clinical behaviors. We finish our review with a discussion of how CGH arrays are being used to identify oncogenes, tumor suppressor genes, and breast cancer susceptibility genes.
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Tadros, Shereen, Deborah Morrogh, and Richard H. Scott. "What is array CGH?" Archives of disease in childhood - Education & practice edition 98, no. 4 (May 30, 2013): 134–35. http://dx.doi.org/10.1136/archdischild-2013-303962.

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Halilović-Alihodžić, Mervisa. "Comparative genomic hybridization (CGH) in molecular diagnostics." Bioengineering Studies 2, no. 2 (September 1, 2021): 37–41. http://dx.doi.org/10.37868/bes.v2i2.id194.

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Comparative genomic hybridization (CGH) is a powerful molecular cytogenetic approach for identifying chromosomal abnormalities. CGH allows researchers to scan whole genomes for changes in DNA copy numbers. Starting in 2004, the array CGH became an irreplaceable method for the detection of gene mutations in people with congenital and developmental abnormalities, such as intellectual disability, dysmorphic characteristics, developmental delay, or several congenital deformities without an obvious syndrome pattern. This review focuses on the evolution of array CGH technology and its use in molecular diagnostics and its advantages over older cytogenetic tools. This review further highlights special arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity.
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Shen, Yiping, David T. Miller, Sau Wai Cheung, Va Lip, Xiaoming Sheng, Keith Tomaszewicz, Hong Shao, et al. "Development of a Focused Oligonucleotide-Array Comparative Genomic Hybridization Chip for Clinical Diagnosis of Genomic Imbalance." Clinical Chemistry 53, no. 12 (December 1, 2007): 2051–59. http://dx.doi.org/10.1373/clinchem.2007.090290.

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Abstract Background: Submicroscopic genomic imbalance underlies well-defined microdeletion and microduplication syndromes and contributes to general developmental disorders such as mental retardation and autism. Array comparative genomic hybridization (CGH) complements routine cytogenetic methods such as karyotyping and fluorescence in situ hybridization (FISH) for the detection of genomic imbalance. Oligonucleotide arrays in particular offer advantages in ease of manufacturing, but standard arrays for single-nucleotide polymorphism genotyping or linkage analysis offer variable coverage in clinically relevant regions. We report the design and validation of a focused oligonucleotide-array CGH assay for clinical laboratory diagnosis of genomic imbalance. Methods: We selected >10 000 60-mer oligonucleotide features from Agilent’s eArray probe library to interrogate all subtelomeric and pericentromeric regions and 95 additional clinically relevant regions for a total of 179 loci. Sensitivity and specificity were measured for 105 patient samples, including 51 with known genomic-imbalance events, as detected by bacterial artificial chromosome–based array CGH, FISH, or multiplex ligation-dependent probe amplification. Results: Focused array CGH detected all known regions of genomic imbalance in 51 validation samples with 100% concordance and an excellent signal-to-noise ratio. The mean SD among log2 ratios of all noncontrol features without copy number alteration was 0.062 (median, 0.055). Clinical testing of another 211 samples from individuals with developmental delay, unexplained mental retardation, dysmorphic features, or multiple congenital anomalies revealed genomic imbalance in 25 samples (11.9%). Conclusions: This focused oligonucleotide-array CGH assay, a flexible, robust method for clinically diagnosing genetic disorders associated with genomic imbalance, offers appreciable advantages over currently available platforms.
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Rosolowski, M., H. Berger, C. Schwaenen, S. Wessendorf, M. Loeffler, D. Hasenclever, and M. Kreuz. "Development and Implementation of an Analysis Tool for Array-based Comparative Genomic Hybridization." Methods of Information in Medicine 46, no. 05 (2007): 608–13. http://dx.doi.org/10.1160/me9064.

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Summary Objectives: Array-comparative genomic hybridization (aCGH) is a high-throughput method to detect and map copy number aberrations in the genome. Multi-step analysis of high-dimensional data requires an integrated suite of bioinformatic tools. In this paperwe detail an analysis pipeline for array CGH data. Methods: We developed an analysis tool for array CGH data which supports single and multi-chip analyses as well as combined analyses with paired mRNA gene expression data. The functions supporting relevant steps of analysis were implemented using the open source software R and combined as package aCGHPipeline. Analysis methods were illustrated using 189 CGH arrays of aggressive B-cell lymphomas. Results: The package covers data input, quality control, normalization, segmentation and classification. For multi-chip analysis aCGHPipeline offers an algorithm for automatic delineation of recurrent regions. This task was performed manuallyup to now. The package also supports combined analysis with mRNA gene expression data. Outputs consist of HTML documents to facilitate communication with clinical partners. Conclusions: The R package aCGHPipeline supports basic tasks of single and multi-chip analysis of array CGH data.
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Buffart, Tineke E., Marianne Tijssen, Thijs Krugers, Beatriz Carvalho, Serge J. Smeets, Ruud H. Brakenhoff, Heike Grabsch, Gerrit A. Meijer, Henry B. Sadowski, and Bauke Ylstra. "DNA Quality Assessment for Array CGH by Isothermal Whole Genome Amplification." Analytical Cellular Pathology 29, no. 4 (January 1, 2007): 351–59. http://dx.doi.org/10.1155/2007/709290.

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Background: Array Comparative Genomic Hybridization (array CGH) is increasingly applied on DNA obtained from formalin-fixed paraffin-embedded (FFPE) tissue, but in a proportion of cases this type of DNA is unsuitable. Due to the high experimental costs of array CGH and unreliable methods for DNA quality testing, better prediction methods are needed. The aim of this study was to accurately determine the quality of FFPE DNA input in order to predict quality of array CGH outcome. Material and Methods: DNA quality was assessed by isothermal amplification and compared to array CGH quality on 59 FFPE gastric cancer samples, one FFPE colorectal cancer sample, two FFPE normal uvula samples, one fresh frozen and six FFPE HNSCC samples. Gastric cancer DNA was also quality tested by β-globin PCR. Results: Accurate prediction of DNA quality using the isothermal amplification was observed in the colorectal carcinoma, HNSCC and uvula samples. In gastric cancer samples, the isothermal amplification was a more accurate method for selecting good quality DNA for array CGH compared to using PCR product lengths. The isothermal amplification product was used for array CGH and compared to the results achieved using non-amplified DNA in four of the samples. DNAs before and after amplification yielded the same segmentation patterns of chromosomal copy number changes for both the fresh DNA sample and the FFPE samples. Conclusion: The efficiency of isothermal DNA amplification is a reliable predictor for array CGH quality. The amplification product itself can be used for array CGH, even starting with FFPE derived DNA samples.
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Baldocchi, R. A., R. J. Glynne, K. Chin, D. Kowbel, C. Collins, D. H. Mack, and J. W. Gray. "Design considerations for array CGH to oligonucleotide arrays." Cytometry Part A 67A, no. 2 (2005): 129–36. http://dx.doi.org/10.1002/cyto.a.20161.

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Lee, Chung-Lin, Chih-Kuang Chuang, Ru-Yi Tu, Huei-Ching Chiu, Yun-Ting Lo, Ya-Hui Chang, Yen-Jiun Chen, et al. "Increased Diagnostic Yield of Array Comparative Genomic Hybridization for Autism Spectrum Disorder in One Institution in Taiwan." Medicina 58, no. 1 (December 22, 2021): 15. http://dx.doi.org/10.3390/medicina58010015.

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Background and Objectives: Chromosomal microarray offers superior sensitivity for identification of submicroscopic copy number variants (CNVs) and is recommended for the initial genetic testing of patients with autism spectrum disorder (ASD). This study aims to determine the diagnostic yield of array comparative genomic hybridization (array-CGH) in ASD patients from a cohort of Chinese patients in Taiwan. Materials and Methods: Enrolled in this study were 80 ASD children (49 males and 31 females; 2–16 years old) followed up at Taipei MacKay Memorial Hospital between January 2010 and December 2020. The genomic DNA extracted from blood samples was analyzed by array-CGH via the Affymetrix GeneChip Genome-Wide Human single nucleotide polymorphism (SNP) and NimbleGen International Standards for Cytogenomic Arrays (ISCA) Plus Cytogenetic Arrays. The CNVs were classified into five groups: pathogenic (pathologic variant), likely pathogenic (potential pathologic variant), likely benign (potential normal genomic variant), benign (normal genomic variant), and uncertain clinical significance (variance of uncertain significance), according to the American College of Medical Genetics (ACMG) guidelines. Results: We identified 47 CNVs, 31 of which in 27 patients were clinically significant. The overall diagnostic yield was 33.8%. The most frequently clinically significant CNV was 15q11.2 deletion, which was present in 4 (5.0%) patients. Conclusions: In this study, a satisfactory diagnostic yield of array-CGH was demonstrated in a Taiwanese ASD patient cohort, supporting the clinical usefulness of array-CGH as the first-line testing of ASD in Taiwan.
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Dissertations / Theses on the topic "Array CGH"

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Shah, Sohrab P. "Model based approaches to array CGH data analysis." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/2808.

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DNA copy number alterations (CNAs) are genetic changes that can produce adverse effects in numerous human diseases, including cancer. CNAs are segments of DNA that have been deleted or amplified and can range in size from one kilobases to whole chromosome arms. Development of array comparative genomic hybridization (aCGH) technology enables CNAs to be measured at sub-megabase resolution using tens of thousands of probes. However, aCGH data are noisy and result in continuous valued measurements of the discrete CNAs. Consequently, the data must be processed through algorithmic and statistical techniques in order to derive meaningful biological insights. We introduce model-based approaches to analysis of aCGH data and develop state-of-the-art solutions to three distinct analytical problems. In the simplest scenario, the task is to infer CNAs from a single aCGH experiment. We apply a hidden Markov model (HMM) to accurately identify CNAs from aCGH data. We show that borrowing statistical strength across chromosomes and explicitly modeling outliers in the data, improves on baseline models. In the second scenario, we wish to identify recurrent CNAs in a set of aCGH data derived from a patient cohort. These are locations in the genome altered in many patients, providing evidence for CNAs that may be playing important molecular roles in the disease. We develop a novel hierarchical HMM profiling method that explicitly models both statistical and biological noise in the data and is capable of producing a representative profile for a set of aCGH experiments. We demonstrate that our method is more accurate than simpler baselines on synthetic data, and show our model produces output that is more interpretable than other methods. Finally, we develop a model based clustering framework to stratify a patient cohort, expected to be composed of a fixed set of molecular subtypes. We introduce a model that jointly infers CNAs, assigns patients to subgroups and infers the profiles that represent each subgroup. We show our model to be more accurate on synthetic data, and show in two patient cohorts how the model discovers putative novel subtypes and clinically relevant subgroups.
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Mohrmann, Inga [Verfasser]. "Array-CGH bei Patienten mit Intelligenzminderung / Inga Mohrmann." Lübeck : Zentrale Hochschulbibliothek Lübeck, 2014. http://d-nb.info/1046429280/34.

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Lee, Sansan. "Genetic counseling perspectives on prenatal array CGH testing." Waltham, Mass. : Brandeis University, 2009. http://dcoll.brandeis.edu/handle/10192/23259.

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VIDETTA, ALESSANDRO DAVIDE. "Molecular analysis: an invaluable approach to improve diagnosis and tailor therapy." Doctoral thesis, Università di Siena, 2017. http://hdl.handle.net/11365/1011505.

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Neoplastic transformation can start in nearly every cell type in the human body. It is recognisable as cells acquiring the ability to divide uncontrollably and to escape aging mechanisms and naturally occurring cell death, resulting in the growth of a tumour. Tumours have different features, depending on the organ of origin and the level of differentiation of the tumour cells. At certain points in development, a tumour will be influencing its microenvironment, ensuring, among other things, vascularisation and cooperation with the immune system. A tumour can progress further, evolving into malignant disease, by invading the surrounding tissue, disseminating into the bloodstream or lymphatic channels, and establishing metastases in other parts of the body, often with fatal consequences for the affected individual. The diversity of cancer, in both biological and clinical terms, is well acknowledged and has been extensively studied. Today, with increasingly sophisticated technologies at our disposal, highly detailed molecular features of individual tumours can be described. Such features are often referred to as being layered, occurring at the genomic (DNA), transcriptomic (mRNA) and functional proteomic (protein) levels. Proteins are the key functional elements of cells, resulting from transcription of a gene into mRNA, which is further translated into a protein. This simplistic way of describing the relationship between the layers has gradually changed during the past decades of functional and molecular insight. Protein synthesis is no longer perceived as a linear process, but as an intricate network of a multitude of operational molecules. Astonishing progress has been made in the discovery of molecules that are able to influence transcription and translation, such as DNA-modifying enzymes and non-translated RNAs, and of mechanisms that are able to control the processing, localisation and activation of proteins. A picture is emerging of individual cells within a tumour that can differ at the genomic, epigenomic and transcriptional levels, as well as at the functional level. Mutations and epigenetic alterations create the required phenotypic diversity that, under the influence of shifting selective pressures imposed by the environment, determines the sub-clonal expansion and selection of specific cells. The development of solid tumours thus follows the same basic principles as Darwinian evolution. Most single nucleotide polymorphism (SNP) variants that arise in human evolution are neutral with respect to survival advantage; over a period of time, these variants are typically fixed in or die out from the genome according to chance. Other variants provide a survival advantage and will, over time, dominate the cell population, leading to distinct haploid signatures. Cancer may involve hundreds or thousands of mutations, with each mutation potentially contributing to tumour fitness. Most of these mutations are assumed to be passengers, but a limited number have driver capability, sometimes only in a sub-population of cells. There is an intricate interplay between sub-populations of tumour cells and among tumour and normal cells in the microenvironment, and tumour topology is likely to play a role in this context. Our knowledge of molecular mechanisms in cancer development and progression are mainly derived from model systems such as in vitro cell cultures and animal models, as well as from descriptive molecular analyses of tissue samples. Model systems have been crucial for understanding molecular interactions and their implications in cancer, but they cannot fully mimic tumour conditions in vivo. Tissue samples, on the other hand, contain both a microenvironment and sub-populations of cancer cells, but they represent only a snapshot in an individual tumour’s life history. Until recently, cancer studies mainly considered only one or a few molecular levels at a time. Altered protein expression can have several causes; it can be due to copy number gain, a translocation event that combines the gene with an active promoter, alteration of factors that modify DNA or influence the transcription machinery, or modifications of mRNA or the protein itself. Revealing the various downstream effects of such alterations is potentially useful for tumour classification and for prediction of treatment response and prognosis.
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Rocha, Ana Laís Bignotto da. "Sequenciamento direto dos genes SIX3, SHH, TGIF1, ZIC2 e array-CGH no estudo de pacientes com holoprosencefalia." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/61/61132/tde-12112013-150520/.

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Objetivos: Analisar por meio da técnica de sequenciamento direto a presença de alterações moleculares nos genes SHH, SIX3, ZIC2 e TGIF1 em indivíduos com diagnóstico clínico de HPE. Analisar por meio da técnica de CGH-array a presença de alterações moleculares em indivíduos com diagnóstico clínico de HPE previamente submetidos à análise por sequenciamento direto. Local: Laboratório de Genética e Citogenética Humana HRAC/USP, Bauru-SP. Casuística e metodologia: Foram selecionados 50 indivíduos, de ambos os sexos com idades entre 03 meses a 50 anos com diagnóstico clínico para HPE. Todos foram analisados por meio da técnica de sequenciamento direto para os genes SHH e TGIF1 completamente e para os genes ZIC2 e SIX3 parcialmente. Dentre os indivíduos que não apresentaram alterações na técnica de sequenciamento oito indivíduos com fenótipo mais grave foram selecionados para a análise por CGH-array. Resultados e discussão: Foram analisados 50 indivíduos por meio da técnica de sequenciamento direto dos gene SHH e TGIF1, foram encontradas duas variantes patogênicas na análise do gene SHH, no caso 1 a variante p.24G>P foi identificada, e no caso 2 foi identificada a variante c.1031del C. No gene TGIF1 foram encontrados cinco polimorfismos já descritos na literatura. Foi identificada uma nova variante silenciosa no éxon 1 do gene ZIC2 p.Q46Q (c. 431 G>A) e um polimorfismo já descrito na literatura em dois indivíduos no gene SIX3. A análise por CGH-array revelou a presença de uma microdeleção no caso 37, de 1,5Mb no cromossomo 17p12 entre as posições genômicas 14,052,279-15,102,307. A mesma deleção foi encontrada na mãe, sendo que esta região nunca foi associada a HPE. Conclusão: A técnica de sequenciamento direto é uma ferramenta muito importante no diagnóstico molecular da HPE, a padronização do sequenciamento direto para os genes ZIC2 e SIX3 poderá auxiliar em diagnósticos mais precisos em estudos futuros dentro do HRAC/USP. O emprego de novas técnicas como CGH-array pode indicar novas relações entre regiões cromossômicas e os múltiplos fatores envolvidos na formação da HPE.
Objective: Analyze through direct sequencing technique the presence of molecular changes on the genes SHH, SIX3, ZIC2 and TGIF1 on individuals with clinical diagnosis of HPE. Analyze through array-CGH technique the presence of molecular changes on individuals with clinical diagnosis of HPE previously submitted to the direct sequencing analyzes. Local: Genetics and Human Cytogenetics Laboratory, HRAC/USP, Bauru-SP. Methods: Were selected 50 individuals from both genders with ages between 03 months and 50 years clinically diagnosed with HPE. Everyone was analyzed through the direct sequencing technique for the genes SHH and TGIF1 completely and for the genes ZIC2 and SIX3 partially. From those individuals which did not have shown changes on the direct sequencing technique, eight individuals with more severe phenotype were selected to the analysis through array-CGH. Results an Discussion: Were analyzed 50 individuals through the technique of direct sequencing of the genes SHH and TGIF1, were found two pathogenic variants in the analysis of SHH gene, in the case 1, the variant p.G24P was identified, and in the case 2 was identified the variant c.1031delC. On the TGIF1 gene were found five polymorphisms already described on the literature. Was identified a new silent variant on the exon 1 of the ZIC2 gene p. Q46Q(c.431G>A) and a polymorphism already described in the literature in two individuals on the gene SIX3. The analysis through array-CGH revealed the presence of one microdeletion in the case 37, of 1,5 Mb on the region 17p12 between the genomic positions 14,052,279-15,102,307. The same deletion was detected in the mother, though this region was never associated to the HPE. Conclusion: The direct sequencing technique is a very important tool for the molecular diagnosis of the HPE, and the direct sequencing standardization for the genes ZIC2 and SIX3 might help in more precise diagnostics on HRAC/USP future studies. The employ of new techniques such as array-CGH may indicate new relations between chromosomal regions and the multiple hit involved in the development of HPE.
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Marioni, John Carlo. "Statistical methods for array CGH and copy number variation experiments." Thesis, University of Cambridge, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611877.

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Sporns, Peter [Verfasser]. "Korrelation von Array-CGH-Befunden und klinischem Phänotyp / Peter Sporns." Kiel : Universitätsbibliothek Kiel, 2015. http://d-nb.info/1065669992/34.

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Grzesiuk, Juliana Dourado. "Caracterização Citogenética Molecular de Rearranjos Cromossômicos Aparentemente Equilibrados Associados ao Fenótipo de Infertilidade." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-22042013-151132/.

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A translocação recíproca é o rearranjo equilibrado mais comum em humanos. Frequentemente, indivíduos com rearranjos equilibrados não apresentam manifestações clínicas, entretanto, na meiose, o pareamento entre cromossomos translocados forma uma figura quadrivalente em forma de cruz que torna a disjunção cromossômica incerta e dependendo do rearranjo, o individuo pode vir a ser infértil, apresentar um risco aumentado de abortamento espontâneo e/ou da prole apresentar alterações fenotípicas. Neste projeto, investigamos duas famílias de pacientes inférteis, portadores de translocações cromossômicas. O objetivo foi caracterizar as alterações citogenéticas e citogenômicas relacionadas à infertilidade masculina em pacientes portadores de rearranjos aparentemente equilibrados, associando técnicas de citogenética clássica (bandeamento GTG), citogenética molecular (FISH) e citogenômica (array-CGH). Foram estudados sete indivíduos da família 1, sendo diagnosticados três portadores da translocação (X;22), sendo um deles azoospérmico. Nesta família foram ainda detectados dois casos de mosaicismo para síndrome de Turner. A família 2 foi composta por dois irmãos oligozoospérmicos, portadores de translocação (8;13). Com a aplicação da técnica de FISH, definimos o cariótipo final dos portadores dos rearranjos como 46,XX ou 46,XY,t(X;22)(p22.3;q11.2) para a família 1 e 46,XY,t(8;13)(q13;q14)para a família 2. A técnica de array-CGH (plataforma 2x400K, Agilent) detectou alterações no número de cópias de alguns genes candidatos relacionados ao fenótipo de infertilidade, sendo a sequência 132 de piRNAs, os genes DDX11, Jagged 2 e ADAM18 na família 1 e os genes candidatos ADAM18 e POTE nos pacientes da família 2.
Reciprocal translocations are the most common balanced rearrangement in humans. Often individuals with balanced rearrangements show no clinical findings. However, in meiosis, the pairing between translocated chromosomes forms a quadrivalent cross-shaped figure which has the effect of making chromosome disjunction uncertain and, depending on the rearrangement, and on the segregation of the unbalanced chromosomes, the individual can be infertile, can present with an increased risk of spontaneous abortions or can have an offspring with abnormal phenotype. We have studied two families of infertile patients, who were carriers of chromosomal translocations. The objective was to characterize the cytogenetic and cytogenomic alterations related to male infertility in patients with apparently balanced rearrangements using classical cytogenetic techniques (GTG banding), molecular cytogenetics (FISH) and cytogenomics (array-CGH). Seven subjects of the family 1 were studied, including three carriers of translocation (X;22), one azoospermic. Two cases of mosaicism for Turner syndrome were detected in this family. The second family consisted of two oligozoospermic brothers with translocation (8;13). FISH was used to characterize the karyotypes as 46, XX or 46,XY, t(X;22)(p22.3;q11.2) for the members of the family 1 and 46,XY,t(8;13)(q13;q14) for family 2. Array-CGH was also performed using the Agilent platform 2x400K, to detect associated copy number variations of some of the candidate genes that could be related to infertility. In the family 1 the candidate genes were 132 piRNAs sequences and DDX11,Jagged 2 and ADAM18 genes. The candidate genes for the family 2 were ADAM18 and POT.
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Castells, Sarret Neus. "Array CGH com a primera opció per al diagnòstic genètic postnatal." Doctoral thesis, Universitat Autònoma de Barcelona, 2015. http://hdl.handle.net/10803/325159.

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La citogenètica convencional detecta un 3-5% dels pacients amb retard global del desenvolupament / discapacitat intel·lectual (RGD / DI) i / o malformacions congènites (MC). L'amplificació de sondes múltiples dependents de lligació (MLPA) permet incrementar la taxa diagnòstica entre 2,4-5,8%. Actualment els arrays d'hibridació genòmica comparada (aCGH) constitueixen l'eina diagnòstica amb major rendiment en pacients amb RGD / DI, MC i trastorns de l'espectre autista (TEA). L'objectiu del present treball ha estat avaluar l'eficiència de l'ús dels aCGH com a tècnica de primera opció diagnòstica en aquestes i altres indicacions (epilèpsia, talla baixa). Per assolir aquest objectiu, s'han estudiat 1.000 pacients afectats de les patologies abans esmentades mitjançant la tècnica de aCGH, utilitzant una estratègia d'hibridació pacient versus pacient i afegint el suport de la tècnica de MLPA en el 50% dels pacients estudiats. En primer lloc es va validar la tècnica i es va escollir la plataforma d’oligoarrays. Per tal de minimitzar costos i incrementar la eficiència, es va utilitzar l’estratègia d’hibridació de pacient versus pacient amb MLPA confirmatòria i es van establir criteris de diagnòstic per optimitzar la detecció de desequilibris patogènics. Per facilitar la interpretació dels resultats es va dissenyar un programa informàtic EasyArray. Es van detectar desequilibris d'efecte patogènic en un 14% dels pacients (140 / 1.000). En funció del fenotip es van diagnosticar un 18,9% dels pacients afectats de RGD / DI; un 13,7% de les MC; un 9,75% de les patologies psiquiàtriques, 1 7,01% dels casos amb epilèpsia i un 13,3% dels pacients amb talla baixa. Dins de les MC destaquen les del sistema nerviós central amb un 14,9% i les cardiopaties congènites amb un 10,6% de diagnòstics. Dins de les patologies psiquiàtriques, destaquen els pacients amb TEA amb un 8.9% de diagnòstics. Podem concloure que la tècnica d’arrayCGH té un rendiment diagnòstic molt superior al del cariotip amb bandes G. La seva utilització com a eina diagnòstica de primera opció juntament amb el disseny d’estratègies d’hibridació no estàndards, suposa una reducció considerable de costos. Els nostres resultats demostren l'efectivitat i eficiència de la utilització de l’arrayCGH com a primera opció en el diagnòstic genètic dels pacients amb sospita de desequilibris genòmics. Tot això avala la seva inclusió dins del Sistema Nacional de Salut.
Conventional cytogenetics diagnoses 3-5% of patients with unexplained developmental delay / intellectual disability (DD / ID) and / or multiple congenital Anomalies (MCA). Multiplex ligation probes Amplification (MLPA) increases diagnostic rate between 2.4 to 5.8%. Currently the array comparative genomic Hybridization (CGH) is the highest performing diagnostic tool in patients with DD / ID, MC and autism spectrum disorders. Our aim was to evaluate the efficiency of the use of aCGH as first-line test replacing the karyotype and MLPA in these and other pathological indications (epilepsy, short stature). A total of 1000 patients referred by one or more of the above mentioned disorders were analysed by aCGH using a methodology / strategy hybrid alternative patient versus patients adding support MLPA technique in 50% of patients studied. Following a validation period, an oligoarray platform was chosen. In order to minimize costs and increase efficiency, a patient versus patient hybridization strategy plus MLPA confirmation was used, and analysis criteria were set to optimise detection of pathogenic imbalances. In order to facilitate interpretation of results, a database application named Easy Array was designed. Pathogenic genomic imbalances were detected in 14% of the cases (140/1000), with a variable distribution of diagnosis according to the phenotypes: 18.9% of patients with DD / ID, 13.7% of MCAS, 9.75% of Psychiatric pathologies, 7.01% of patients with Epilepsy and 13.3% of patients with short Stature. Within the MCA, central nervous system abnormalities and congenital heart diseases accounted for 14.9% and 10.6% of diagnosis respectively. Among the Psychiatric disorders, patients with ASD accounted for 8.9% of diagnosis. We can conclude that Array-CGH provides a substantially higher diagnostic yield tan G-banded chromosomes analysis. Its use as first line test and the development of non-standard hybridization strategies reduces consumable costs considerably. Our results demonstrate the effectiveness and efficiency of the use of arrayCGH as the first line test in genetic diagnosis of patients suspected of genomic imbalances, supporting its inclusion within the National Health System.
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Zhang, Yunyu. "Hidden Markov Model inference copy number change in array-CGH data." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/33086.

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Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2005.
Includes bibliographical references (p. 56-57).
Cancer development and progression typically features genomic instability frequently resulting in genomic changes involving DNA copy number gains or losses. Identifying the genomic location of these regional alterations provides important opportunities for the discovery of potential novel oncogenes and tumor suppressors. Recently, array based competitive genomic hybridization (array-CGH) has become available as a powerful approach for genome-wide detection of DNA copy number changes. Array-CGH assesses DNA copy number in tumor samples through competitive hybridization on microarrays containing probes for thousands of genes. The datasets generated are complex and require statistical methods to accurately define discrete and uniform copy number from the data and to identify transitions between genomic regions with altered copy number. Several approaches based on different statistical frameworks have been developed. However, a fundamental informatic issue in array-CGH analysis remains unsolved by these methods. In particular, sample-specific data compression, a result of tumor cells being commonly admixed with normal cells in many tumor types, must be accounted for in each sample analyzed. Additionally, in order to accurately assess deviations from normal copy number, the copy number readout must be shifted to faithfully represent the baseline copy number in each tumor sample. Failure to appropriately address these issues reduces the accuracy of the data in hard-threshold based high-level analysis.
(cont.) By using the natural framework Hidden Markov Models (HMM) to model the distribution of array-CGH signals, a method infer the absolute copy number and identify change points has been developed to address the above problems. This method has been validated on independent dataset and its utility in inference on array-CGH data is demonstrated here.
by Yunyu Zhang.
S.M.
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Books on the topic "Array CGH"

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Kim, Ho-jung. array-CGH rŭl iyong han piso sepʻo pʻyeam ŭi chogi chaebal pʻyojija mit chindan mohyŏng kaebal =: Development of early-recurrence detection marker and diagnostic model using array-CGH in NSCLC. [Seoul]: Pogŏn Pokchibu, 2007.

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McDaniel, Samuel Alexander. The analyses of array CGH data and current status data. 2007.

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Mohammed, Mansoor S. CGH Arrays (Nuts & Bolts series). Dna Press, 2006.

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Book chapters on the topic "Array CGH"

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Arnemann, J. "Array-CGH." In Springer Reference Medizin, 206–7. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-48986-4_3439.

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Calistri, Daniele. "Array CGH." In Encyclopedia of Cancer, 1–3. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-642-27841-9_401-2.

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Arnemann, J. "Array-CGH." In Lexikon der Medizinischen Laboratoriumsdiagnostik, 1. Berlin, Heidelberg: Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-662-49054-9_3439-1.

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Dimitriadou, Eftychia, and Joris R. Vermeesch. "Array CGH." In Springer Protocols Handbooks, 567–86. Berlin, Heidelberg: Springer Berlin Heidelberg, 2016. http://dx.doi.org/10.1007/978-3-662-52959-1_55.

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Calistri, Daniele. "Array CGH." In Encyclopedia of Cancer, 362–64. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-662-46875-3_401.

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Kashork, Catherine D., Aaron Theisen, and Lisa G. Shaffer. "Prenatal Diagnosis Using Array CGH." In Prenatal Diagnosis, 59–70. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-066-9_5.

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Tauscher, Marcel, Inka Praulich, and Doris Steinemann. "Array-CGH in Childhood MDS." In Methods in Molecular Biology, 267–78. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-281-0_17.

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Mohapatra, Gayatry, Julia Sharma, and Stephen Yip. "Array CGH in Brain Tumors." In Methods in Molecular Biology, 325–38. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-281-0_20.

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Vermeesch, Joris R. "Array CGH: Opening New Horizons." In Fluorescence In Situ Hybridization (FISH) — Application Guide, 421–37. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-70581-9_35.

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Szuhai, Karoly. "Array-CGH and SNP-Arrays, the New Karyotype." In Microarrays in Diagnostics and Biomarker Development, 39–52. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-662-45800-6_5.

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Conference papers on the topic "Array CGH"

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"ROBUSTNESS OF EXON CGH ARRAY DESIGNS." In International Conference on Bioinformatics Models, Methods and Algorithms. SciTePress - Science and and Technology Publications, 2011. http://dx.doi.org/10.5220/0003153201730182.

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Feldman, Michael R., and Clark C. Guest. "Iterative discrete on-axis encoding for computer-generated holograms." In OSA Annual Meeting. Washington, D.C.: Optica Publishing Group, 1989. http://dx.doi.org/10.1364/oam.1989.tuff4.

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Iterative discrete on-axis (IDO) encoding of Fourier transform type computer-generated holograms (CGHs) to produce spot arrays has been described previously.1 This method has been extended to encode more general Fourier transform type CGHs and to encode Fresnel holograms for optical connection networks. The IDO encoding method is based on either an iterative improvement or a simulated annealing optimization routine. It has been shown that computation time for IDO encoding is reduced by employing an iterative improvement routine and by setting the initial CGH transmittance to a pattern (determined analytically) similar to the expected near-optimum pattern. Using this method, high performance large space-bandwidth product (SBWP) holograms can be encoded in a reasonable time. Several IDO encoded holograms have been fabricated. Experimental measurements have been performed to verify computer simulation results. A Fourier transform type binary phase CGH produced a 3 × 3 array of spots with 59% diffraction efficiency.1 Experimental Fresnel type IDO encoded binary phase optical interconnect holograms have demonstrated that high efficiency, high connection density holograms can be made.
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Ylipaa, Antti, Matti Nykter, Virpi Kivinen, Limei Hu, David Cogdell, Kelly Hunt, Wei Zhang, and Olli Yli-Harja. "Finding common aberrations in array CGH data." In 2008 3rd International Symposium on Communications, Control and Signal Processing (ISCCSP). IEEE, 2008. http://dx.doi.org/10.1109/isccsp.2008.4537408.

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Morrison, R. L., S. L. Walker, F. A. P. Tooley, F. B. McCormick, and T. J. Cloonan. "Computer generated holograms for free-space digital optics." In OSA Annual Meeting. Washington, D.C.: Optica Publishing Group, 1991. http://dx.doi.org/10.1364/oam.1991.turr1.

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AT&T's photonics switching technology group has demonstrated a series of prototype systems of increasing complexity to test and illustrate the feasibility of free-space digital optical systems. Computer generated holograms (CGH) were incorporated into a multistage system demonstration (i) to distribute optical power and illuminate an array of optical processors,1 and (ii) to form interconnections between stages. A 64 × 64 spot array was generated by illuminating a CGH with a collimated laser beam. The spot array intensity was required to vary by <20% between minimum and maximum intensity spots. A characterization system was used to ensure that this objective was met. To provide connectivity between channels, the information from each device was routed between modules using a scheme similar to a banyan network. By selectively shielding areas on the processor array, the interconnection was achieved using space invariant 1 × 3 CGHs. Some 1 × 3s were designed for reduced intensities at several higher-order spots.
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Chao, Tien-Hsin. "Optical correlator using a LCTV CGH filter and a thresholding photodetector array chip." In OSA Annual Meeting. Washington, D.C.: Optica Publishing Group, 1991. http://dx.doi.org/10.1364/oam.1991.thl2.

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An optical correlator using a CGH filter encoded in a liquid crystal television spatial light modulator (LCTV SLM) and a custom designed VLSI photodetector array chip is reported. A Burckhardt-type CGH filter was written in a commercially available thin film transistor-type LCTV SLM that contains 320 × 220 pixels and has a contrast ratio of ~100:1. Both gray scale and binary holographic images are reconstructed from the LCTV CGH. This CGH filter is successfully used in an optical correlator for pattern recognition experiments. To further enhance the system speed and discrimination capability, a novel CMOS 32 × 32 postprocessing photodetector array chip is designed and fabricated for the correlator peak detection. The two main novel features of this detector array are its thresholding capability and high speed. The thresholding capacity is achieved by building a comparator and logic circuits around each pixel of the detector array. Parallel detection across the entire output plane is done in each clock cycle. Digitized addresses of locations of all the correlation peaks that exceed the thresholding level are present in the output port. The speed of the detector is ~1-10 msec, depending upon the level of the thresholding current.
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Shah, Shishir. "Statistical Framework for Quantitative Analysis of Array CGH." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.259843.

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Blume, Matthias, Frederick B. McCormick, Jr., Philippe J. Marchand, and Sadik C. Esener. "Array interconnect systems based on lenslets and CGH." In SPIE's 1995 International Symposium on Optical Science, Engineering, and Instrumentation, edited by Jose M. Sasian. SPIE, 1995. http://dx.doi.org/10.1117/12.216383.

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Shah, Shishir. "Statistical Framework for Quantitative Analysis of Array CGH." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.4398777.

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Zuna, Rosemary E., and Christopher E. Aston. "Abstract 3904: Array CGH analysis of cervical cancer." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-3904.

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Nguyen, Nha, Heng Huang, Soontorn Oraintara, and An Vo. "A New Smoothing Model for Analyzing Array CGH Data." In 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering. IEEE, 2007. http://dx.doi.org/10.1109/bibe.2007.4375683.

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Reports on the topic "Array CGH"

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Cavalli, Luciane R. Detection of Genetic Alterations in Breast Sentinel Lymph Node by Array-CGH. Fort Belvoir, VA: Defense Technical Information Center, October 2005. http://dx.doi.org/10.21236/ada444833.

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Cavalli, Luciane R. Detection of Genetic Alterations in Breast Sentinel Lymph Node by Array-CGH. Fort Belvoir, VA: Defense Technical Information Center, October 2006. http://dx.doi.org/10.21236/ada460808.

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Seroussi, Eyal, and George Liu. Genome-Wide Association Study of Copy Number Variation and QTL for Economic Traits in Holstein Cattle. United States Department of Agriculture, September 2010. http://dx.doi.org/10.32747/2010.7593397.bard.

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Copy number variation (CNV) has been recently identified in human and other mammalian genomes and increasing awareness that CNV might be a major source for heritable variation in complex traits has emerged. Despite this, little has been published on CNVs in Holsteins. In order to fill this knowledge-gap, we proposed a genome-wide association study between quantitative trait loci (QTL) for economic traits and CNV in the Holstein cattle. The approved feasibility study was aimed at the genome-wide characterization of CNVs in Holstein cattle and at the demonstrating of their possible association with economic traits by performing the activities of preparation of DNA samples, Comparative Genomic Hybridization (CGH), initial association study between CNVs and production traits and characterization of CNVSNP associations. For both countries, 40 genomic DNA samples of bulls representing the extreme sub-populations for economically important traits were CGH analyzed using the same reference genome on a NimbleGen tiling array. We designed this array based on the latest build of the bovine genome (UMD3) with average probe spacing of 1150 bases (total number of probes was 2,166,672). Two CNV gene clusters, PLA2G2D on BTA2 and KIAA1683 on BTA7 revealed significant association with milk percentage and cow fertility, respectively, and were chosen for further characterization and verification in a larger sample using other methodologies including sequencing, tag SNPs and real time PCR (qPCR). Comparison between these four methods indicated that there is under estimation of the number of CNV loci in Holstein cattle and their complexity. The variation in sequence between different copies seemed to affect their functionality and thus the hybridization based methods were less informative than the methods that are based on sequencing. We thus conclude that large scale sequencing effort complemented by array CGH should be considered to better detect and characterize CNVs in order to effectively employ them in marker-assisted selection.
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Eshed, Yuval, and Sarah Hake. Exploring General and Specific Regulators of Phase Transitions for Crop Improvement. United States Department of Agriculture, November 2012. http://dx.doi.org/10.32747/2012.7699851.bard.

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The transition of plants from a juvenile to adult growth phase entails a wide range of changes in growth habit, physiological competence and composition. Strikingly, most of these changes are coordinated by the expression of a single regulator, micro RNA 156 (miR156) that coordinately regulates a family of SBP genes containing a miR156 recognition site in the coding region or in their 3’ UTR. In the framework of this research, we have taken a broad taxonomic approach to examine the role of miR156 and other genetic regulators in phase change transition and its implication to plant development and crop improvement. We set to: Determine the common and unique factors that are altered upon juvenile to adult phase transition. Determine the functions of select miR156 target genes in tomato and maize, and identify those targets that mediate phase transition. Characterize the role of miR172 and its targets in tomato phase change. Determine the relationships between the various molecular circuits directing phase change. Determine the effects of regulated manipulation of phase change genes on plant architecture and if applicable, productivity. In the course of the study, a new technology for gene expression was introduced – next generation sequencing (NGS). Hence some of the original experiments that were planned with other platforms of RNA profiling, primarily Affymetrix arrays, were substituted with the new technology. Yet, not all were fully completed. Moreover, once the initial stage was completed, each group chose to focus its efforts on specific components of the phase change program. The Israeli group focused on the roles of the DELAYED SYMPODIAL TERMINATION and FALSIFLORA factors in tomato age dependent programs whereas the US group characterized in detail the role of miR156 (also termed Cg) in other grasses and in maize, its interplay with the many genes encoding miR172.
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