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Relevant bibliographies by topics / Comparative genomic hybridization

Academic literature on the topic 'Comparative genomic hybridization'

Author: Grafiati

Published: 4 June 2021

Last updated: 20 February 2023

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Journal articles on the topic "Comparative genomic hybridization"

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Barrett, Irene J., Brenda L. Lomax, Tatiana Loukianova, Steven S. Tang, Valia S. Lestou, and Dagmar K. Kalousek. "Comparative Genomic Hybridization." Archives of Pathology & Laboratory Medicine 125, no. 1 (January 1, 2001): 81–84. http://dx.doi.org/10.5858/2001-125-0081-cgh.

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Abstract Objective.—To demonstrate the effectiveness of comparative genomic hybridization (CGH) for analysis of reproductive pathology specimens in clinical cytogenetics laboratories. Design.—A total of 856 CGH analyses were performed on various placental and fetal tissues derived from 368 specimens of spontaneous abortions and on placentas from 219 pregnancies with live-born infants. The live-born infants were clinically evaluated as normally developed, with either a normal birth weight or with intrauterine growth restriction; some live-born infants had an abnormal prenatal triple screen with normal cytogenetic results on amniotic fluid cell cultures. Results.—Comparative genomic hybridization analysis was successfully performed on 856 samples from spontaneously aborted specimens and term placentas. Failure of analysis occurred in 1.6% of samples and was due to an insufficient amount of tissue for DNA extraction. Comparative genomic hybridization identified aneuploidy in 53% of spontaneous abortion samples and 3.1% of term placentas. Conclusions.—Comparative genomic hybridization analysis is a useful clinical tool for detection of aneuploidy in placental and fetal tissues. It provides a genome-wide screen while eliminating tissue culture failures, culture artifacts, and maternal cell contamination. We present practical guidelines for interpreting CGH profiles derived from human reproductive specimens.

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Kellner, Udo, Anja Jacobsen, Angela Kellner, René Mantke, Albert Roessner, and Christoph Röcken. "Comparative Genomic Hybridization." American Journal of Clinical Pathology 119, no. 2 (February 2003): 265–71. http://dx.doi.org/10.1309/ef69vndlvpwve4qv.

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Pinkel, Daniel, and Donna G. Albertson. "COMPARATIVE GENOMIC HYBRIDIZATION." Annual Review of Genomics and Human Genetics 6, no. 1 (September 2005): 331–54. http://dx.doi.org/10.1146/annurev.genom.6.080604.162140.

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Pinkel, D., R. Segraves, D. Sudar, L. van Vliet, S. Clark, C. Chen, Y. Zhai, J. W. Gray, and D. G. Albertson. "Comparative Genomic Hybridization to Dna Microarrays." Microscopy and Microanalysis 3, S2 (August 1997): 205–6. http://dx.doi.org/10.1017/s1431927600007911.

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Comparative genomic hybridization (CGH), which involves the simultaneous hybridization of differentially labeled total genomic DNA from test cells and reference normal cells to metaphase chromosomes, has been used extensively to screen tumor genomes for regions of DNA sequence copy number variation. Analysis of these hybridizations requires quantitative analysis of the ratio of intensities of the fluorescent hybridization signals as a function of position along the chromosomes, which basically serve as a convenient genetic map. The ratios need to be measured very accurately since changes of about ± 20% from the average for the genome indicate important genetic events. Widespread use of CGH over the past several years has identified numerous regions of the genome that may contain currently unknown cancer genes. For example, regions of increased copy number may indicate sites of oncogenes, while regions of copy number decrease relative to average for the genome may signify the presence of a tumor suppressor gene.

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Fiorentino, Francesco. "Array comparative genomic hybridization." Current Opinion in Obstetrics and Gynecology 24, no. 4 (August 2012): 203–9. http://dx.doi.org/10.1097/gco.0b013e328355854d.

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Done, Susan B. "Diagnostic Array Comparative Genomic Hybridization." Journal of Molecular Diagnostics 8, no. 5 (November 2006): 527. http://dx.doi.org/10.2353/jmoldx.2006.060152.

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Jeuken, Judith W. M., Sandra H. E. Sprenger, and Pieter Wesseling. "Comparative Genomic Hybridization: Practical Guidelines." Diagnostic Molecular Pathology 11, no. 4 (December 2002): 193–203. http://dx.doi.org/10.1097/00019606-200212000-00002.

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Toraman, Ahter Dilsad, Keser, Güven Lüleci, Nurdan Tunalı, and Tekinalp Gelen. "Comparative genomic hybridization in ganglioneuroblastomas." Cancer Genetics and Cytogenetics 132, no. 1 (January 2002): 36–40. http://dx.doi.org/10.1016/s0165-4608(01)00521-0.

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Koschny, Ronald, Thomas Koschny, Ursula G. Froster, Wolfgang Krupp, and Margit A. Zuber. "Comparative genomic hybridization in glioma." Cancer Genetics and Cytogenetics 135, no. 2 (June 2002): 147–59. http://dx.doi.org/10.1016/s0165-4608(01)00650-1.

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Rienstein, Shlomit, Eric F. Adams, David Pilzer, Ayala Aviram Goldring, Boleslaw Goldman, and Eitan Friedman. "Comparative genomic hybridization analysis of craniopharyngiomas." Journal of Neurosurgery 98, no. 1 (January 2003): 162–64. http://dx.doi.org/10.3171/jns.2003.98.1.0162.

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Object. Craniopharyngioma is the most common childhood brain tumor and is thought to arise from embryonic remnants of the Rathke pouch. Some craniopharyngiomas are monoclonal in origin and hence presumably harbor somatic genetic alterations, although the precise molecular mechanisms involved in craniopharyngioma development are unknown. The goal of this study was to identify genetic alterations in craniopharyngiomas. Methods. To gain insight into the molecular mechanisms involved in development of these tumors, the authors analyzed nine adamantinomatous craniopharyngiomas by using comparative genomic hybridization. Six tumors (67%) displayed at least one genomic alteration, and three had six or more alterations. Only two tumors displayed a decrease in DNA copy number, and in all others an increase in DNA copy number was noted. Conclusions. The authors conclude that a subset of craniopharyngiomas consists of monoclonal tumors arising from activation of oncogenes located at specific chromosomal loci.

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Dissertations / Theses on the topic "Comparative genomic hybridization"

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Stanczak, Krzysztof M. "Detection of genomic deletions by single-nucleotide polymorphism array comparative genomic hybridization." Diss., Restricted to subscribing institutions, 2007. http://proquest.umi.com/pqdweb?did=1320950331&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.

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Mantripragada, Kiran K. "Microarray-Based Comparative Genomic Hybridization in Neurofibromatoses and DiGeorge Syndrome." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5743.

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Burke, Natalie. "Genetic Imbalances in Endometriosis Detected by Oligonucleotide-Array Based Comparative Genomic Hybridization." Digital Commons @ East Tennessee State University, 2013. https://dc.etsu.edu/etd/1129.

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Endometriosis is one of the most common gynecological diseases as it is thought to affect up to 15% of the female population. Characterized by the growth and proliferation of endometrial tissue outside of the uterine cavity, it is a complex condition with varying degrees of severity and can affect multiple regions of the body with symptoms ranging from a total lack of symptoms to debilitating pain and infertility. The most accepted theory of how endometriosis initiates is that of retrograde menstruation; however, approximately 90% of women with unobstructed fallopian tubes are thought to have some menstrual debris in the peritoneal cavity. Therefore, this theory does not explain in full why endometriosis occurs in some but not all women who experience retrograde bleeding. Genetic factors are thought to play a major role in the pathogenesis of endometriosis as women with a family history are 5 to 10 times more likely to develop the disease. The goal of this study was to determine if common chromosomal aberrations in the form of additions, deletions, or regions of loss of heterozygosity that may contribute to the establishment or progression of the disease are present in a population of endometriosis patients. DNA was isolated from the peripheral blood of endometriosis patients and endometriosis tissue biopsies, and it was analyzed using oligonucleotide based array comparative genomic hybridization. The results suggest that an addition on chromosome 17p13.3 may play a role in the biological mechanisms involved in endometriosis as it was identified in 75% of the DNA samples obtained from the peripheral blood and 100% of the DNA samples obtained from the tissue biopsies. This chromosomal imbalance is of particular interest as it is located in a region that harbors the tumor suppressor gene, hypermethylated in cancer-1 (HIC-1), whose aberrant expression has been reported in multiple cancers. Endometriosis has long been thought of as a benign disease despite its malignant characteristics, and individuals with endometriosis have been demonstrated to have an increased chance of developing ovarian cancer. This was the first study to examine the DNA from endometriosis patients using oligonucleotide based array comparative genomic hybridization to investigate genetic abnormalities in endometriosis. The findings may provide a novel target for future therapeutic options as well as indicate a link between endometriosis and cancer that has not been previously reported.

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錢文偉 and Man-wai Gary Chien. "Cytogenetic analysis of head and neck cancer by comparative genomic hybridization." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2001. http://hub.hku.hk/bib/B31224209.

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Valentine, Erin L. "Microarray-based comparative genomic hybridization of three Adams Oliver syndrome families." Oklahoma City : [s.n.], 2009.

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Chien, Man-wai Gary. "Cytogenetic analysis of head and neck cancer by comparative genomic hybridization /." Hong Kong : University of Hong Kong, 2001. http://sunzi.lib.hku.hk:8888/cgi-bin/hkuto%5Ftoc%5Fpdf?B23440041.

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文詠賢 and Wing-yin Cornelia Man. "Genomic aberrations in lung cancer: a study with comparative genomic hybridization and analysis of loss ofheterozygosity." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B31227697.

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Martin, Mallory N. "Microduplication 22q syndrome : investigation of intergenerational change using microarray-based comparative genomic hybridization /." Oklahoma City : [s.n.], 2009.

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Alshammari, Nawal. "Genetic biomarkers in uveal melanoma : an exploration using high-resolution array comparative genomic hybridization." Thesis, University of Sheffield, 2017. http://etheses.whiterose.ac.uk/16803/.

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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 the liver. The aim of this thesis was to address both central issues. Firstly to better understand how genetic biomarkers identify UM that will metastasize, and whether they can be used to further subtype UM. Secondly to see if potential driver genes could be identified that may lead both to an improved understanding of UM metastasis and how to treat it. The approach taken was to use customised high-resolution aCGH. Which, because it was specifically designed for UM, was hoped to identify recurrent focal SCNA that could have been missed by previous studies using lower resolution and unfocussed approaches, such as chromosomal CGH, classical karyotyping, or even BAC arrays. Altogether 137 primary UM were analysed, and as part of a small pilot study possible drivers were further investigated using IHC.

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Glen, McGillivary. "Comparative Genomic Analysis Between the Haemophilus influenzae biogroup aegyptius Brazilian Purpuric Fever Invasive Strain F3031 and the Haemophilus influenzae biogroup aegyptius Non-invasive Strain F1947." Miami University / OhioLINK, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=miami1088607238.

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Books on the topic "Comparative genomic hybridization"

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Banerjee, Diponkar, and Sohrab P. Shah, eds. Array Comparative Genomic Hybridization. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-281-0.

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Array Comparative Genomic Hybridization Protocols And Applications. Humana Press Inc., 2013.

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Banerjee, Diponkar, and Sohrab P. Shah. Array Comparative Genomic Hybridization: Protocols and Applications. Humana Press, 2016.

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Ghazani, Arezou Akhlaghi. Investigation of the molecular alterations in synchronous breast cancer using array and chromosomal comparative genomic hybridization. 2005.

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Molecular cytogenetic analysis of non-small cell lung carcinoma: By comparative genomic hybridization and spectral karyotyping. Ottawa: National Library of Canada, 1999.

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Ghazani, Arezou Akhlaghi. Investigation of the molecular alterations in synchronous breast cancer using array and chromosomal comparative genomic hybridization. 2005.

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Forsyth, Rob, and Richard Newton. Neurodiagnostic tools. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198784449.003.0002.

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This chapter explains the principles of how best to use the main diagnostic tools in paediatric neurology in the context of evidence-based medicine. The description of neuroradiology includes the principles of DWI, SWI, MRS, ASL and fMRI, and the usefulness of ultrasound, CT and PET scanning; neuroradiological anatomy, terminology, common incidental findings and normal myelination patterns. An approach to white matter and developmental brain abnormalities is depicted. Neurogenetic testing discusses the capabilities and limitations of microarray for Comparative Genomic Hybridization (copy-number variants), gene panel testing, and whole exome and whole genome next generation sequencing. The chapter offers the theory, practicality and pitfalls of electroencephalography, peripheral neurophysiology and evoked potential testing. Common practical procedures are described, including lumbar puncture, muscle biopsy and shunt tapping with an understanding of the place of special investigations on CSF, blood, urine, and skin. The scope of neuropsychological testing is described.

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Book chapters on the topic "Comparative genomic hybridization"

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Feuerstein, Burt G., Yuichi Hirose, Malgorzata Pellarin, and Gregg Magrane. "Comparative Genomic Hybridization." In FISH Technology, 197–217. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/978-3-642-56404-8_16.

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Presti, Joseph C. "Comparative Genomic Hybridization." In Renal Cancer, 69–80. Totowa, NJ: Humana Press, 2001. http://dx.doi.org/10.1385/1-59259-144-2:069.

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IJssel, Paul, and Bauke Ylstra. "Oligonucleotide Array Comparative Genomic Hybridization." In Comparative Genomics, 207–21. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-515-2_14.

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Hopman, Anton H. N., Christina E. M. Voorter, Ernst J. M. Speel, and Frans C. S. Ramaekers. "In Situ Hybridization and Comparative Genomic Hybridization." In Human Cytogenetic Cancer Markers, 45–69. Totowa, NJ: Humana Press, 1997. http://dx.doi.org/10.1007/978-1-4612-3952-9_3.

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Taboada, Eduardo N., Christian C. Luebbert, and John H. E. Nash. "Studying Bacterial Genome Dynamics Using Microarray-Based Comparative Genomic Hybridization." In Comparative Genomics, 223–53. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-515-2_15.

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Redon, Richard, Tomas Fitzgerald, and Nigel P. Carter. "Comparative Genomic Hybridization: DNA Labeling, Hybridization and Detection." In Methods in Molecular Biology, 267–78. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-538-1_17.

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Gorman, Patricia, and Rebecca Roylance. "Fluorescence In Situ Hybridization and Comparative Genomic Hybridization." In Breast Cancer Researh Protocols, 269–95. Totowa, NJ: Humana Press, 2006. http://dx.doi.org/10.1385/1-59259-969-9:269.

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Coe, Bradley P., William W. Lockwood, Raj Chari, and Wan L. Lam. "Comparative Genomic Hybridization on BAC Arrays." In Microarray Analysis of the Physical Genome, 7–19. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-192-9_2.

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Voullaire, Lucille, and Leeanda Wilton. "Comparative Genomic Hybridization on Single Cells." In Methods in Molecular Medicine™, 101–15. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-298-4_9.

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Baumgartner, Adi, Veronika Hartleb, and Jim D. Taylor. "Comparative Genomic Hybridization (CGH) in Genotoxicology." In Methods in Molecular Biology, 209–34. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9646-9_11.

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Conference papers on the topic "Comparative genomic hybridization"

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Wach, Sven, Christina Ellmann, Robert Stoehr, Katrin Weigelt, Peter J. Goebell, Frank Kunath, Helge Taubert, Arndt Hartmann, Bernd Wullich, and Bastian Keck. "Abstract 3937: Comparative genomic hybridization reveals complex genomic changes in plasmacytoid urothelial carcinoma." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-3937.

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Singh, Sher, Hung-i. Chen, Fang-han Hsu, Mong-hsun Tsai, Eric Chuang, and Yidong Chen. "Development of a normalization algorithm for array comparative genomic hybridization." In 2006 IEEE International Workshop on Genomic Signal Processing and Statistics. IEEE, 2006. http://dx.doi.org/10.1109/gensips.2006.353150.

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Liu, Jun, Sanjay Ranka, Tamer Kahveci, Onur Seref, O. Erhun Kundakcioglu, and Panos Pardalos. "A web server for mining Comparative Genomic Hybridization (CGH) data." In DATA MINING, SYSTEMS ANALYSIS AND OPTIMIZATION IN BIOMEDICINE. AIP, 2007. http://dx.doi.org/10.1063/1.2817337.

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Ly, M., G. Diallo, A. Valente, D. Diallo, K. Dumke, V. Marty, V. Scott, et al. "Genomic Profiling of Breast Cancer (BC) in Mali by Oligonucleotide Comparative Genomic Hybridization (CGH) Array." In Abstracts: Thirty-Second Annual CTRC‐AACR San Antonio Breast Cancer Symposium‐‐ Dec 10‐13, 2009; San Antonio, TX. American Association for Cancer Research, 2009. http://dx.doi.org/10.1158/0008-5472.sabcs-09-3059.

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Tsukamoto, Yoshiyuki, Masahiro Uchida, Tsuyoshi Noguchi, Tomohisa Uchida, Naoki Hijiya, Chisato Nakada, Keiko Matsuura, Kazunari Murakami, Toshio Fujioka, and Masatsugu Moriyama. "Abstract 3908: Genomic profiling of gastric carcinoma in situ and adenomas by array-based comparative genomic hybridization." 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.am2011-3908.

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Edelman, Daniel C., Holly Stevenson, Miiia Suuriniemi, Parvati Singh, Jamie Rodriguez-Canales, Jeffery C. Hanson, Robert Walker, Michael R. Emmert-Buck, and Paul Meltzer. "Abstract 4862: Whole genome amplification allows for testing of valuable specimens by array comparative genomic hybridization." 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.am2011-4862.

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Vollebergh, MA, PM Nederlof, LF Wessels, MK Schmidt, SA Joosse, E. van Beers, F. Froklage, et al. "Predicting response to alkylating chemotherapy in breast cancer patients using array comparative genomic hybridization." In CTRC-AACR San Antonio Breast Cancer Symposium: 2008 Abstracts. American Association for Cancer Research, 2009. http://dx.doi.org/10.1158/0008-5472.sabcs-6050.

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Liu, Jonathan H. W., Yang Washington Shao, Sam D. Molyneux, Rama Khokha, and Geoffrey A. Wood. "Abstract 398: Genome-wide comparison of matched canine osteosarcoma primary tumours and metastases by array comparative genomic hybridization." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-398.

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Chen, Eleanor, Kimberly P. Dobrinski, Kim H. Brown, Ryan Clagg, Elena Edelman, Myron Ignatius, Jillian Brockmann, et al. "Abstract 1412: Cross-species array comparative genomic hybridization identifies novel driver genes in embryonal rhabdomyosarcoma." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-1412.

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Needham, Rachel H. V., Arturo B. Ramirez, Iman Kishawi, Jackie L. Stilwell, and Eric P. Kaldjian. "Abstract 3615: Comparison of whole genome amplification methods on single and pooled cells for comparative genomic hybridization array analysis." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-3615.

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Reports on the topic "Comparative genomic hybridization"

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Clark, Steven M. Comparative Genomic Hybridization Onto Dense Arrays of DNA Clones: Development and Application to Breast Cancer Genomes. Fort Belvoir, VA: Defense Technical Information Center, September 1998. http://dx.doi.org/10.21236/ada357608.

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Ramaswamy, Anbazhagan. High Throughput Analysis of the Role of Genomic Methylation in Breast Cancer by Methylation-Sensitive Comparative Genomic Hybridization. Fort Belvoir, VA: Defense Technical Information Center, September 2001. http://dx.doi.org/10.21236/ada397004.

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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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Katzir, Nurit, James Giovannoni, and Joseph Burger. Genomic approach to the improvement of fruit quality in melon (Cucumis melo) and related cucurbit crops. United States Department of Agriculture, June 2006. http://dx.doi.org/10.32747/2006.7587224.bard.

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Fruit quality is determined by numerous genetic traits that affect taste, aroma, texture, pigmentation, nutritional value and duration of shelf-life. The molecular basis of many of these important traits is poorly understood and it’s understanding offers an excellent opportunity for adding value to agricultural products. Improvement of melon fruit quality was the primary goal of the project. The original objectives of the project were: The isolation of a minimum of 1000 fruit specific ESTs. The development of a microarray of melon fruit ESTs. The analysis of gene expression in melon using melon and tomato fruit enriched microarrays. A comprehensive study of fruit gene expression of the major cucurbit crops. In our current project we have focused on the development of genomics tools for the enhancement of melon research with an emphasis on fruit, specifically the first public melon EST collection. We have also developed a database to relay this information to the research community and developed a publicly available microarray. The release of this information was one of the catalysts for the establishment of the International Cucurbit Genomic Initiative (ICuGI, Barcelona, Spain, July 2005) aimed at collecting and generating up to 100,000 melon EST sequences in 2006, leveraging a significant expansion of melon genomic resources. A total of 1000 ESTs were promised under the original proposal (Objective 1). Non-subtracted mature fruit and young fruit flesh of a climacteric variety in addition to a non-climacteric variety resulted in the majority of additional EST sequences for a total of 4800 attempted reads. 3731 high quality sequences from independent ESTs were assembled, representing 2,467 melon unigenes (1,873 singletons, 594 contigs). In comparison, as of June 2004, a total of 170 melon mRNA sequences had been deposited in GENBANK. The current project has thus resulted in nearly five- fold the number of ESTs promised and ca. 15-fold increase in the depth of publicly available melon gene sequences. All of these sequences have been deposited in GENBANK and are also available and searchable via multiple approaches in the public database (http://melon.bti.cornell.edu). Our database was selected as the central location for presentation of public melon EST data of the International Cucurbit Genomic Initiative. With the available unigenes we recently constructed a microarray, which was successfully applied in hybridizations (planned public release by August 2006). Current gene expression analyses focus on fruit development and on comparative studies between climacteric and non-climacteric melons. Earlier, expression profiling was conducted using macroarrays developed at the preliminary stage of the project. This analysis replaced the study of tomato microarray following the recommendations of the reviewers and the panel of the original project. Comparative study between melon and other cucurbit crops have begun, mainly with watermelon, in collaboration with Dr. Amnon Levi (USDA-ARS). In conclusion, all four objectives have been addressed and achieved. In the continuation project that have been approved we plan to apply the genomic tools developed here to achieve detailed functional analyses of genes associated with major metabolic pathway.

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Xu, Jin-Rong, and Amir Sharon. Comparative studies of fungal pathogeneses in two hemibiotrophs: Magnaporthe grisea and Colletotrichum gloeosporioides. United States Department of Agriculture, May 2008. http://dx.doi.org/10.32747/2008.7695585.bard.

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Plant pathogenic fungi have various life styles and different plant infection strategies. Hemibiotrophs like Magnaporthe grisea and Colletotrichum species develop specialized structures during plant infection. The goal of this study was to identify, characterize, and compare genes required for plant infection in M. grisea and C. gloeosporioides. Specific objectives are to: 1) further characterize genes identified in the preliminary studies of C. gloeosporioides and M. grisea;2) identify and characterize additional fungal genes tagged by GFP; and 3) identify in planta growth and appressorium-specific genes by subtractive hybridization and transcript profiling by the LongSAGE method. In this study, the PI and Co-PI collaborated closely on studies in M. grisea and C. gloeosporioides. In M. grisea, REMI and ATMT were used to transform the wildtype with promoter-less EGFP constructs. A total of 28 mutants defective in different plant infection processes or expressing EGFP during plant infection were identified. Genes disrupted in five selected mutants have been identified, including MG03295 that encodes a putative Rho GTPase. In transformant L1320, the transforming vector was inserted in the MIRI gene that encodes a nuclear protein. The expression of MIRI was highly induced during infection. Deletion and site-directed mutagenesis analyses were used to identify the promoter regions and elements that were essential for induced in planta expression of MIRI. This was the first detailed characterization of the promoter of an in planta gene in M. grisea and the MIRI promoter can be used to monitor infectious growth. In addition, the Agilent whole-genome array of M. grisea was used for microarray analyses with RNA samples from appressoria formed by the wild-type shain and the pmkl and mstl2 mutants. Over 200 genes were downregulated in the mst I 2 and pmkl mutants. Some of them are putative transcription factors that may regulate appressorium formation and infectious hyphal growth. In C. gloeosporioides, various REMI mutants showing different pathogenic behavior were identified and characterized. Mutants N3736 had a single insertion and was hyper-virulent. The gene disrupted in mutant3736 (named CgFMOI) encodes a FAD-dependent monooxygenase. Expression analyses linked the expression of the CgFMOI gene with the necrotrophic phase of fungal infection, and also suggest that expression of CgFMOl is unnecessary for the first stages of infection and for biotrophy establishment. All CgFMOl-silenced mutants had reduced virulence. In REMI mutant N159, the tagged gene encodes a putative copper transporter that is homologue of S. cerevisiae CTR2. In yeast, Ctr2 is a vacuolar transporter for moving copper from the vacuole to the cytoplasm. The gene was therefore termed CgCTR2. In addition to characterization of CgCTR2, we also conducted comparative analyses in M. grisea. The M. grisea CgCTR-2 homolog was isolated, knockout strains were generated and characterized and the M. grisea was used to complement the Nl 59 C. gloeosporioides mutant. Overall, we have accomplished most of proposed experiments and are in the process of organizing and publishing other data generated in this project. For objective 3, we used the microarray analysis approach. Several genes identified in this study are novel fungal virulence factors. They have the potential to be used as targets for developing more specific or effective fungicides. In the long run, comparative studies of fungal genes, such as our CgCTR2 work, may lead to better disease control strategies.

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