Tesis: "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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7

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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8

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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9

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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Chen, Beichen. "Identification of copy number variants associated with renal agenesis using array-based comparative genomic hybridization." Thesis, University of Iowa, 2010. https://ir.uiowa.edu/etd/655.

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Copy Number Variants (CNVs) are defined as DNA segments of 1kb or more in length and present in a variable number of copies in the human genome. It has been recently shown that many human genetic diseases including organ malformations are caused by CNVs in a patient's genome. However, the genetic and molecular basis for Renal Agenesis (RA), which is a medical condition whereby unilateral or bilateral fetal kidneys fail to develop, has not yet been extended to CNV studies. By using array-based Comparative Genomic Hybridization, we are analyzing DNA from patients who have RA in order to identify CNVs that are causative for RA; genes within the CNVs will then be assessed for their potential involvement in RA by altering their dose in Xenopus embryos.

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Benetkiewicz, Magdalena. "Development and Application of Human Chromosome 22 Genomic Microarray : Chromosome 22-Associated Disorders Analyzed by Array-Based Comparative Genomic Hybridization." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6272.

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13

Locke, Devin Paul. "SEGMENTAL DUPLICATIONS PROMOTE GENOMIC INSTABILITY IN HUMAN CHROMOSOME 15q11-q13." Case Western Reserve University School of Graduate Studies / OhioLINK, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=case1088114861.

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14

Luk, Catherine Yuen Yee. "Molecular cytogenetic analysis of non-small cell lung carcinoma, by comparative genomic hybridization and spectral karyotyping." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0007/MQ45531.pdf.

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15

Maydan, Jason Stephen. "High-resolution mutation detection in Caenorhabditis elegans mutants and natural isolates using array comparative genomic hybridization." Thesis, University of British Columbia, 2009. http://hdl.handle.net/2429/6683.

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An essential requirement of genetic research is the ability to identify mutations. Forward genetic screens begin by selecting for a phenotype and proceed to search for the causative mutation. Reverse genetics experiments first identify the mutation and then seek to derive the mutant phenotype, if any. Both approaches depend on efficient means of detecting mutations. This thesis describes the development of methods to facilitate the detection of mutations in the model organism, Caenorhabditis elegans, using array Comparative Genomic Hybridization (aCGH). Exon-centric oligonucleotide microarrays targeting specific chromosomes and the whole genome were designed and used to detect both large multi-gene and small single-gene deletions. Both homozygous and heterozygous deletions were identified using this technique. I showed that even single nucleotide transitions and transversions are detectable when using microarrays with sufficient probe densities, which are achievable with target regions of two Mbp or less. I also used aCGH to detect extensive natural gene content variation between the N2 Bristol strain and twelve wild C. elegans isolates. Most of the DNA copy number alterations in these strains are deletions relative to Bristol. Over 5% of the genes present in the Bristol strain are absent in at least one of the natural isolates that were examined. This represents a significant increase in the number of genes with known null alleles. These deletions were then used to infer relationships among the natural isolates, which proved to be complex. The methods described in this thesis will greatly assist in the identification of mutations in C. elegans and are also applicable to other organisms with sequenced reference genomes.

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Castelli, Luciana Caricati Veiga. "Hibridação Genômica Comparativa em Endometriose." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-30052008-104355/.

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A endometriose é uma doença ginecológica benigna comum, mas agressiva, caracterizada pela presença de tecido endometrial ectópico. A teoria mais aceita para explicá-la é a teoria de Sampson, na qual o tecido endometrial descamado durante a menstruação sofre refluxo através das tubas uterinas, adere e se prolifera em sítios ectópicos da cavidade peritoneal. Por outro lado, apenas o refluxo tubário não é capaz de estabelecer a doença e vários estudos sugerem uma etiologia multidimensional incluindo fatores hereditários, hormonais e imunológicos. Várias metodologias têm sido propostas com o objetivo de identificar genes candidatos para a endometriose. A hibridação genômica comparativa (CGH) é uma técnica que permite que o genoma inteiro seja analisado em um só experimento, sem a necessidade de cromossomos metafásicos obtidos por cultura celular. Nossa proposta foi avaliar, por CGH, amostras de endometriomas ovarianos e de tecido endometrial eutópico de dez pacientes com diagnóstico firmado de endometriose, para screening do genoma. No grupo eutópico, 6/10 amostras apresentaram alterações caracterizadas por perdas ou ganhos de regiões cromossômicas e no grupo ectópico foram encontradas alterações em 7/10 casos. A presença de perdas e ganhos de regiões cromossômicas no endométrio eutópico, histologicamente normal, de mulheres com endometriose ovariana, pode ser considerada como alteração primária ao desenvolvimento da doença. A metodologia de CGH permitiu a detecção das regiões cromossômicas 11q12.3-q13.1, 17p11.1-p12 e 17q25.3-qter como regiões críticas, direcionando investigações futuras para identificação de genes associados à endometriose. Endometriosis is a common benign gynecological disease, very aggressive, characterized by the presence of ectopic endometrial tissue. The most accepted theory to explain it is Sampson\'s implantation theory, which says that the endometrial tissue exfoliated during menstruation undergoes reflux through the uterine tubes, adheres and proliferates in ectopic sites of the peritoneal cavity. On the other hand, only reflux is not enough to the establishment of the disease and a number of studies suggest a multidimensional etiology including hereditary, hormonal and immunological factors. Several methodologies have been proposed for the identification of candidate genes for endometriosis. The comparative genomic hybridization (CGH) is a versatile technique that allows the entire genome to be analyzed in only one experiment without the necessity of metaphasic chromosomes from the sample, excluding the cell culture. We aimed to evaluate, by CGH, ovarian endometriomas and eutopic endometrial tissue samples from 10 patients with confirmed diagnosis of endometriosis, for a genomic screening. In the eutopic group, 6/10 samples presented genomic imbalances and 7/10 cases showed alterations in the ectopic group. The presence of losses and gains of chromosomic regions in the histologically normal eutopic endometrium from women with ovarian endometriosis can be considered as a primary alteration in the development of the disease. The CGH methodology allowed the detection of chromosomic regions 11q12.3-q13.1, 17p11.1-p12 and 17q25.3-qter as critical regions, leading to future investigations for the identification of genes associated to endometriosis.

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17

Buckley, Patrick. "Development and Application of Microarray-Based Comparative Genomic Hybridization : Analysis of Neurofibromatosis Type-2, Schwannomatosis and Related Tumors." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4786.

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18

Mahas, Ahmed Ibrahim. "Distinguishing Melanocytic Nevi From Melanoma by DNA Copy Number Changes: Array-Comparative Genomic Hybridization As a Research Tool." Wright State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=wright1437782090.

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19

Alwohhaib, M. "Detection of somatic mutations in breast cancer and non-cancerous chromosomal disorders by the application of comparative genomic hybridization." Thesis, Swansea University, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.635770.

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The aim of this study was to detect chromosomal imbalances in breast cancer and non-cancerous chromosomal disorders by comparative genomic hybridization (CGH). Initially, the technique was developed to be used on different types of samples. The samples used include DNA of patients suffering from different syndromes, frozen breast tumours tissue samples, and archival paraffin - embedded breast-tumour tissue sections. CGH application on the different syndromes have shown copy number changes in chromosome Y in two kabuki syndrome patients, imbalances at the X and Y chromosomes of the fragile X patients, a deletion at 15q11-q13 of a Prader-Willi syndrome patient, and gain in 7q21 qter of a cystic fibrosis patient. Furthermore, the CGH technique was able to detect an accumulation of genetic changes in the paraffin embedded archival samples for women who are under 40 years of age suffering from breast cancer. CGH was also applied to look for the copy number changes in the genome of 21 Kuwaiti women who have been diagnosed with primary breast cancer at Kuwait cancer control centre. Chromosomal regions 1q, 8p, 8q and 6q are detected to be abnormal in these patients which need further investigation. Finally, PCR-SSCP was used to detect the mutations in exons 5, 6, 7 and 8 of the P53 gene in 21 breast cancer patients. SSCP detected 3/21 mutations. They were then characterised by direct sequencing. These mutations were a transition of G → A at codon 77 of exon 5, insertion of fair nucleotides between codons 163 and 164 of exon 5, and insertion of two nucleotides into codons 241 of exon 7.

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20

Potluri, Keerti. "Improving DNA quality using FFPE tissues for Array Comparative Genomic Hybridization to find Single Nucleotide Polymorphisms (SNPs) in Melanoma." Wright State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=wright1438267267.

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21

Toujani, Saloua. "Du chromosome au gène par un criblage global des altérations génomiques dans la malignité pour isoler de nouvelles cibles thérapeutiques." Thesis, Paris 11, 2012. http://www.theses.fr/2012PA11T027/document.

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Le cancer est désormais considéré comme une maladie génomique de la cellule. Les moyens d’étude de l’oncogénome étaient basés sur les différentes modalités du caryotype, peu résolutif. L’application des techniques de micromatrices d’oligonucléotides, notamment l’aCGH, a permis une avancée majeure dans la caractérisation des génomes des cancers.La première partie de notre travail a porté sur les lymphomes de Burkitt (LB), caractérisés par une translocation entre un gène d'immunoglobuline et MYC. L’étude portait sur 12 tumeurs primaires et 15 lignées cellulaires. L’aCGH (44K et 244K), concordait avec les cytogénétiques morphologique et moléculaire (FISH) sauf pour les translocations. Plus de la moitié des variations du nombre de copies (<2Mb) étaient des polymorphismes (CNV). Les anomalies pathologiques (CNA) (n=136) intéressaient les régions suivantes : gains 1q, 13q, 7q, 8q, 2p, 11q et 15q ; pertes 3p, 4p, 4q, 9p, 6p, 17p, 6q, 11pterp13 et 14q12q21.3. Vingt régions minimales critiques (MCR) d’une taille varie entre 0.07-71.36 Mb, étaient délimitées. Trois MCR étaient identifiées sur le 1q : 1q21.1q25.2, 1q32.1 et 1q44. La région proximale de 1q21.1q25.2 était le siège d’une amplification, contenant entre autres les gènes BCA2, PIAS, BCL9. L’étude par transcriptome, sur 15 lignées, a démontré la surexpression uniquement de BCL9, remanié dans les LAL B et faisant partie de la voie de signalisation de MYC. Sur la région 11q23.1, le gain intéressait le gène POU2AF1 dont le messager était élevé. La MCR 13q31.3q32.1 était le siège d’une amplification contenant ABCC4, et le polycistron miR17-92. La corrélation des résultats d’aCGH à ceux du transcriptome et du mirnome ont démontré une surexpression du miR17-92 qui contrôle le développement des lymphocytes B et intervient dans la voie de signalisation de MYC. Sur le 9p21.3, la perte emportait le locus p16INK4A/p15INK4B. Le transcriptome avait démontré une sous expression de p15INK4B. Le locus p16INK4A/p15INK4B contrôle les 2 voies majeures, pRB et p53.La seconde partie de notre travail a consisté à étudier 17 tumeurs congelées de carcinomes adénoïdes kystiques (CAK) par aCGH 44K. Les CNA étaient validées par FISH et/ou MLPA. L’expression protéique était étudiée par immunohistochimie. Les pertes excédaient les gains (41 versus 24). La t(6;9)(q23;p22) récurrente dans les CAK était indétectable car équilibrée. Dans un seul cas, le der(6)t(6;9) est probablement présent sur le profil aCGH. Les MCR les plus fréquentes (-6q22 et -6q24) n’incluaient pas 6q23. Treize MCR étaient identifiées. La MCR délétée en 8q impliquait le miR-124A2 qui régule les gènes CDK6 et MMP2. Sur le 9p21.3, le locus p16INK4A/p15INK4B était de nouveau perdu. Des gains isolés étaient observés au niveau des locus CCND1, KIT/PDGFRA/KDR, MDM2 et JAK2. Le gène MDM2, qui était amplifié sous forme de double minutes, est un élément clé de l’axe p16INK4A-ARF-p53.Pour la troisième partie de notre travail nous avons étudié 60 tumeurs primaires d’adénocarcinomes pulmonaires (AD) de non fumeur par aCGH (244K). Dans 50/60 tumeurs, le nombre de MCR était de 14. Cinq MCR contenaient un seul gène (MOCS2, NSUN3, KHDRBS2, SNTG1 et ST18). Une MCR gagnée, 5q35, contenait le gène NSD1. Une amplification, sous forme de HSR et mise en évidence par FISH, intéressait l’oncogène FUS. Une PCR quantitative avait permis de confirmer la surexpression FUS. A notre connaissance, c’est la première étude qui incrimine le gène FUS dans la carcinogenèse de l’AD du non-fumeur. D’autres gènes étaient également impliqués : ARNT, BCL9, CDK4, p15INK4B, EGFR, ERBB2, MDM2, MDM4, MET, MYC, NKX2-1 et KRAS. Un clustering non supervisé avait permis de dégager un groupe avec un gain de MYC ; un autre groupe caractérisé par la perte des gènes suppresseurs RB et WRN et un dernier groupe caractérisé par un gain 7p et 7q, et présentait une fréquence élevée de mutations de l’EGFR. Dans 10/60, le nombre de CNA était très rare et aucune MCR n’était détectée Much of our current understanding of cancer is based on the hypothesis that it is a genetic disease, arising as a clone of cells that expand in an unregulated fashion because of somatically acquired mutations. High-throughput tools for nucleic acid characterization, such as array comparative genomic hybridization (aCGH), now provide the means to conduct comprehensive analyses of somatic anomalies in the oncogenome.In the first part of our work we have carried out a fine mapping of additional chromosomal anomalies in Burkitt lymphoma (BL). The hallmark of this disease is the translocation t(MYC;IG). We have applied whole-genome 244K and 44k oligonucléotides aCGH to 15 cells lines and 12 primary tumors of BL respectively. Karyotype and FISH analysis were used to validate aCGH results. As expected, all translocations remained undetectable with aCGH. More than half of the copy number alterations (CNAs) < 2 Mb were mapped to Mendelian CNVs, including GSTT1, and BIRC6. Somatic cell line-specific CNVs localized to the IG locus were consistently observed with the 244 K aCGH platform. Among 136 CNAs, gains were found in 1q, 13q, 7q, 8q, 2p, 11q and 15q. Losses were found in 3p, 4p, 4q, 9p, 13q, 6p, 17p, 6q,11pterp13 and 14q12q21.3. Twenty one minimal critical regions (MCR), (range 0.04–71.36 Mb), were delineated in tumors and cell lines. Three MCRs were localized to 1q: 1q21.1q25.2, 1q32.1 et 1q44. The proximal one was mapped to 1q21.1q25.2 with a 6.3 Mb amplicon (1q21.1q21.3) harboring BCA2, BCL9 and PIAS3. Only BCL9 high level transcrit was noted on oligonucleotide microarray gene expression that was done on 15 cells lines. BCL9, was implicated in a LAL B translocation t(1;14)(q21;q32) and it is a member of MYC pathway. The 13q31.3q32.1, 89.58–96.81 Mb MCR contained an amplicon with several genes. The miR-17-92 cluster, upregulated on mirnome analysis that was done on 15 cells lines, is the gene driver of 13q MCR. The miR-17-92 cluster is a member of MYC pathway. The 9p21.3 MCR harbored p16INK4A/p15INK4B locus which is downregulated. MYC activates ARF,a protein encodes by p16INK4A/p15INK4B locus. . On the second part of our work, a 44k aCGH was applied on 17 frozen adenoid cystic carcinoma (ACC) to delineate with a high resolution the CNA associated with ACC. aCGH results were validated with FISH and/or MLPA. Protein expression was screened with immunohistochemistry analysis. The translocation t(6;9)(q23;p23p24)/ MYB-NFIB recurrent in ACC, was not detected with aCGH. In one case, the der(6)t(6;9) was suspected in the aCGH pattern. There were recurrent gains at 7p15.2, 17q21–25, 22q11–13, and recurrent losses at 1p35, 6q22–25, 8q12–13, 9p21, 12q12–13, and 17p11–13. Thirteen MCR were detected. The recurrent deletion at 8q12.3–13.1 contained miRN124A2 gene, whose product regulates MMP2 and CDK6. The 9p21.3 MCR harbored p16INK4A/p15INK4B locus which was deleted. On 17p11p13, the MCR contained several genes and TP53 was deleted in 2 cases. The MDM2 gene, a member of p16INK4A-ARF-p53 pathway, was amplified and overexpressed in one case. Among the other unique CNAs, gains harbored CCND1, KIT/PDGFRA/KDR, and JAK2. On the third part of this these, a high-resolution 244K aCGH was conducted on 60 frozen lung adenocarcinoma (AD) of never smokers patients in order to establish a catalog of CNA. In 50/60 tumors, fourteen new MCR of gain or loss was noted. One larger MCR of gain contained NSD1.One focal amplification and nine gains contained FUS. NSD1 and FUS are oncogenes hitherto not known to be associated with lung cancer. FUS was over-expressed in 10 tumors with gain of 16p11.2 compared to 30 tumors without that gain. A FUS hsr was observed with FISH screening. FUS was over-expressed in 10 tumors with gain of 16p11.2 compared to 30 tumors without that gain. Other cancer genes present in aberrations included ARNT, BCL9, CDK4, p15INK4B, EGFR, ERBB2, MDM2, MDM4, MET, MYC, NKX2-1 and KRAS

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Gatto, Kaleb Pretto 1987. "Análise dos cromossomos sexuais de Pseudis tocantins (Anura, Hylidae)." [s.n.], 2013. http://repositorio.unicamp.br/jspui/handle/REPOSIP/317686.

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Orientadores: Luciana Bolsoni Lourenço, Carmen Silvia Busin Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia Made available in DSpace on 2018-08-23T12:08:20Z (GMT). No. of bitstreams: 1 Gatto_KalebPretto_M.pdf: 33988822 bytes, checksum: 7e3f3565dac9a540ea7c353f51068d4f (MD5) Previous issue date: 2013 Resumo: O resumo poderá ser visualizado no texto completo da tese digital Abstract: The abstract is available with the full electronic document Mestrado Biologia Celular Mestre em Biologia Celular e Estrutural

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23

Adhikari, Bishwo. "Genomic Analysis of Nematode-Environment Interaction." BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2578.

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The natural environments of organisms present a multitude of biotic and abiotic challenges that require both short-term ecological and long-term evolutionary responses. Though most environmental response studies have focused on effects at the ecosystem, community and organismal levels, the ultimate controls of these responses are located in the genome of the organism. Soil nematodes are highly responsive to, and display a wide variety of responses to changing environmental conditions, making them ideal models for the study of organismal interactions with their environment. In an attempt to examine responses to environmental stress (desiccation and freezing), genomic level analyses of gene expression during anhydrobiosis of the Antarctic nematode Plectus murrayi was undertaken. An EST library representative of the desiccation induced transcripts was established and the transcripts differentially expressed during desiccation stress were identified. The expressed genome of P. murrayi showed that desiccation survival in nematodes involves differential expression of a suite of genes from diverse functional areas, and constitutive expression of a number of stress related genes. My study also revealed that exposure to slow desiccation and freezing plays an important role in the transcription of stress related genes, improves desiccation and freezing survival of nematodes. Deterioration of traits essential for biological control has been recognized in diverse biological control agents including insect pathogenic nematodes. I studied the genetic mechanisms behind such deterioration using expression profiling. My results showed that trait deterioration of insect pathogenic nematode induces substantial overall changes in the nematode transcriptome and exhibits a general pattern of metabolic shift causing massive changes in metabolic and other processes. Finally, through field observations and molecular laboratory experiments the validity of the growth rate hypothesis in natural populations of Antarctic nematodes was tested. My results indicated that elemental stoichiometry influences evolutionary adaptations in gene expression and genome evolution. My study, in addition to providing immediate insight into the mechanisms by which multicellular animals respond to their environment, is transformative in its potential to inform other fundamental ecological and evolutionary questions, such as the evolution of life-history patterns and the relationship between community structure and ecological function in ecosystems.

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Catelani, Ana Lúcia Pereira Monteiro. "Variação no número de cópias de segmentos de DNA (CNV) em pacientes com surdez sindrômica." Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-28062010-123759/.

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A perda auditiva é o defeito mais comum ao nascimento e cerca de 70 milhões de pessoas no mundo apresentam algum grau de perda auditiva. Além da alta incidência, as implicações da perda auditiva na linguagem, na cognição e no desenvolvimento emocional e social reforçam sua importância. No entanto, em grande parte dos pacientes, a causa da deficiência auditiva não é esclarecida. Nós usamos hibridação comparativa do genoma baseada em arrays (Array Comparative Genomic Hybridization aCGH) para investigar alterações no número de cópias de segmentos de DNA (Copy Number Variation CNV) em 31 indivíduos que apresentavam deficiência auditiva e sinais clínicos adicionais, mas que não puderam ser classificados em síndrome conhecida. A escolha de indivíduos sindrômicos se baseou no pressuposto de que, em média, apresentam alterações genômicas maiores e, portanto, mais provavelmente detectáveis com o uso de aCGH de 1 Mb, que era a plataforma disponível no início do projeto. CNVs não descrita em bancos de dados de indivíduos normais foram identificadas em oito pacientes, quatro delas ocorreram de novo enquanto as outras quatro foram herdadas de um genitor fenotipicamente normal. As alterações de novo definem segmentos cromossômicos que provavelmente contém genes relacionados à deficiência auditiva e sensíveis a dose, especificamente: 1q23.3-q25.2, 2q22q23, 6p25.3 e 11q13.2-q13.4. As alterações raras identificadas tanto nos pacientes quanto em um genitor normal poderiam ser um evento ao acaso, sem papel na deficiência auditiva; no entanto, a possibilidade de que essas alterações possam funcionar como fatores de predisposição não podem ser descartadas. Se considerarmos apenas as CNVs de novo como causativas dos fenótipos investigados, detectamos quatro pacientes portadores entre os 31 investigados (13%). Se considerarmos também as CNVs herdadas como possivelmente causativas, a taxa de desequilíbrios cromossômicos associados à surdez será de 26%. Esses resultados são provavelmente uma substimativa e esses números seriam possivelmente maiores com o uso de uma das plataformas de alta resolução disponíveis atualmente. Esses resultados, embora limitados, indicam que investigação por aCGH em pacientes com surdez sindrômica idiopática está entre os testes mais eficientes para detectar etiologia dos fenótipos, devendo ser incorporado à rotina no diagnóstico e aconselhamento genético. Hearing loss is the most common congenital deficiency and about 70 million people worldwide present some degree of hearing impairment. In addition to its high incidence, hearing loss impacts language, cognition and social and emotional development. However, in a large proportion of patients, the cause of the hearing deficiency cannot be elucidated. We screened copy number changes by 1 Mb-array Comparative Genomic Hybridization (aCGH) in 31 individuals with syndromic hearing impairment whose clinical features were untypical for known disorders. The choice of evaluating syndromic rather than non-syndromic individuals was based on the assumption that they are more likely to carry larger genomic alterations which could be more easily detected by the comparatively low resolution 1 Mb aCCG, which was the available platform when this project started. Copy number changes (CNV) not documented in the database of normal individuals were detected in eight patients, four de novo imbalances and four inherited from a normal parent. The de novo alterations define candidate chromosome segments likely to harbor dosage sensitive genes related to hearing impairment, namely 1q23.3-q25.2, 2q22q23, 6p25.3 and 11q13.2- q13.4. The rare imbalances also present in normal parents might be casually associated with hearing impairment, but also have a possible role as a predisposition factor. When only the de novo CNVs were considered causative for the disease phenotypes, our study revealed relevant copy number changes in 4 patients (13%). If we also count the rare CNVs that had been inherited as possibly causative, the frequency of chromosome imbalances associated with syndromic deafness in our sample becomes 26%. These figures are probably underestimates and will probably become larger when high resolution oligoarray platforms are applied. These results indicate that aCGH is an efficient tool for defining the etiology of syndromic deafness and its use in routine diagnosis of hearing impairment and for genetic counseling is highly recommended.

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25

Yano, Cassia Fernanda. "Estudos evolutivos no gênero Triportheus (Characiformes, Triportheidae) com enfoque na diferenciação do sistema de cromossomos sexuais ZZ/ZW." Universidade Federal de São Carlos, 2016. https://repositorio.ufscar.br/handle/ufscar/8567.

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Submitted by Alison Vanceto (alison-vanceto@hotmail.com) on 2017-02-23T13:20:14Z No. of bitstreams: 1 TeseCFY.pdf: 5114033 bytes, checksum: 6922d93e7dda82cee55aa69273fa7013 (MD5) Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2017-03-14T19:51:58Z (GMT) No. of bitstreams: 1 TeseCFY.pdf: 5114033 bytes, checksum: 6922d93e7dda82cee55aa69273fa7013 (MD5) Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2017-03-14T19:52:08Z (GMT) No. of bitstreams: 1 TeseCFY.pdf: 5114033 bytes, checksum: 6922d93e7dda82cee55aa69273fa7013 (MD5) Made available in DSpace on 2017-03-14T20:02:44Z (GMT). No. of bitstreams: 1 TeseCFY.pdf: 5114033 bytes, checksum: 6922d93e7dda82cee55aa69273fa7013 (MD5) Previous issue date: 2016-10-24 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Triportheus genus (Characiformes, Triportheidae) presents a particular scenario 1 in fishes, with a ZZ/ZW sex chromosomes system for all species until now investigated. The Z chromosome is metacentric and the largest one of the karyotype, remaining morphologically conserved in all species. In contrast, the W chromosome differs in shape and size among species, from almost identical to markedly reduced in size in relation to the Z, with a clear heterochromatin accumulation associated with its differentiation process. This scenario in Triportheus, along with a well defined phylogeny for this group, provided an excellent opportunity to investigate the evolutionary events associated with the sex chromosomes differentiation, a matter of increasing interest to evolutionary biology in recent years. Therefore, the purpose of this study was to investigate the origin and differentiation of sex chromosomes in eight Triportheus species, using diverse conventional and molecular cytogenetics tools, such as C-banding, chromosomal mapping of rDNAs and several other repetitive DNA sequences, comparat ive genomic hybridization (CGH), microdissection of Z and W chromosomes and whole chromosome painting (WCP). The preferential accumulation of repetitive DNAs on the W chromosome highlighted the predominant participation of these sequences in the differentiation of this chromosome. Notably, the differential accumulation of microsatellites, and a hybridization pattern with no direct correlation to the ancestry of the W chromosome, put in evidence the particular evolutionary processes that shaped the sex-specific chromosome among species. The chromosomal mapping of 5S and 18S rDNAs and U2 DNAsn highlighted a very particular scenario in the distribution of these multigene families in Triportheus. Indeed, the variability in number of the rDNA sites on the autosomes, as well as the syntenic "status" of these three multigene families, showed their intense dynamism in the karyotype evolution, revealing a much more complex organization of these genes than previously supposed for closely related species. In addition, the occurrence of U2 DNAsn on the W chromosome of T. albus appears as an evolutionary novelty, while the occurrence of 18S rDNA in the Wq terminal region of all species pointed to a conserved condition for the genus, as well as a peculiarity in the evolutionary process of the W chromosome. Noteworthy, the use of WCP, and especially CGH experiments, put in evidence sequences which are shared by both Z and W chromosomes and sequences that are unique to each one. Thus, the Wq terminal region stood out with a high concentration of female specific sequences, in coincidence with the location of the 18S rDNA genes, allowing inferences about the origin of these cistrons on the sex-specific chromosome. Our data also showed that the ZZ/ZW system had, in fact, a common origin in Triportheus, considering the homologies found in chromosomal paintings using the Z and W probes. Triportheus auritus is the direct representative of the first lineage to differentiate in the genus and WCP experiments, using the Z chromosome probe of this species, have showed how this chromosome is notably conserved in all investigated species. On the other hand, the W chromosome showed variable patterns of homology among species, highlighting the molecular divergence emerged along its evolutionary history. In conclusion, the results obtained in this study allowed to certify the common origin of the ZZ/ZW sex system in Triportheus and to evaluate the intra- and inter-specific genomic homologies and differences between the sex pair, resulting in significant advances in the knowledge of the origin and differentiation of the sex chromosomes among lower vertebrates. O gênero Triportheus (Characiformes, Triportheidae) apresenta um cenário 1 incomum entre os peixes, com a ocorrência de um sistema de cromossomos sexuais ZZ/ZW para todas as espécies já investigadas. O cromossomo Z é metacêntrico e o maior do cariótipo, permanecendo morfologicamente conservado em todas as espécies. Contrariamente, o cromossomo W apresenta formas variáveis e tamanhos distintos entre as espécies, podendo apresentar tamanho quase idêntico ao do cromossomo Z até acentuadamente reduzido em relação a ele, com um nítido acúmulo de heterocromatina associado ao processo de diferenciação desse cromossomo. Este cenário em Triportheus, juntamente com a filogenia já bem definida para este grupo, possibilitou uma oportunidade excelente para a investigação de eventos evolutivos associados aos cromossomos sexuais, aspecto este que vem despertando interesse crescente na biologia evolutiva nos últimos anos. Assim sendo, a proposta deste estudo foi investigar a origem e a diferenciação dos cromossomos sexuais em oito espécies de Triportheus, usando ferramentas diversificadas da citogenética convencional e molecular, como o bandamento-C, mapeamento cromossômico de DNAr e diversas outras classes de DNAs repetitivos, hibridização genômica comparativa (CGH), microdissecção dos cromossomos Z e W e pintura cromossômica total (WCP). O acúmulo preferencial de várias sequências de DNAs repetitivos no cromossomo W possibilitou destacar a participação preponderante deste componente do genoma na diferenciação do cromossomo sexo18 específico. Notadamente, o acúmulo diferencial de microssatélites colocou em evidência processos evolut ivos específicos do cromossomo W entre as espécies, bem como um padrão acumulativo que não apresenta correlação direta com a ancestralidade deste cromossomo. O mapeamento cromossômico do DNAr 5S e 18S e do DNAsn U2 evidenciou um cenário bastante particular na distribuição dessas famílias multigênicas em Triportheus. A variabilidade em relação ao número de sítios de DNAr nos autossomos, assim como o “status” sintênico dessas três famílias, evidenciaram o dinamismo evolutivo desses genes mesmo entre espécies proximamente relacionadas. Além disso, a ocorrência de DNAsn U2 no cromossomo W de T. albus evidenciou uma novidade evolutiva, enquanto a ocorrência de DNAr 18S na região Wq terminal confirmou uma condição conservada no gênero, assim como uma peculiaridade do processo evolut ivo do cromossomo W, visto que todas as espécies analisadas até o momento são portadoras dessas sequências. O emprego de WCP, e principalmente de CGH, possibilitou demonstrar a localização de sequências que são compartilhadas pelos cromossomos Z e W, bem como de sequências que são exclusivas de cada um deles. Assim, a região Wq terminal se destacou por apresentar uma grande concentração de sequências específicas de fêmeas, em coincidência com a localização do cluster de DNAr 18S, possibilitando inferências sobre a origem destes cístrons no cromossomo sexo-específico. Nossos dados também demonstraram que o sistema ZZ/ZW teve, de fato, uma origem comum em Triportheus, considerando as homologias encontradas nos mapeamentos cromossômicos com sondas dos cromossomos sexuais Z e W. Triportheus auritus é a espécie representante direta da primeira linhagem a se diferenciar no gênero e experimentos de WCP, utilizando a sonda do cromossomo Z desta espécie, mostrou que este cromossomo se encontra notavelmente conservado em todas as espécies investigadas. Por outro lado, o cromossomo W apresentou padrões variáveis de homologia entre as espécies, destacando divergências moleculares diferencialmente moldadas ao longo da sua história evolutiva. Em conclusão, os resultados obtidos no presente estudo possibilitaram atestar a origem comum do sistema ZZ/ZW em Triportheus, bem como avaliar divergências e similaridades genômicas intra- e interespecíficas quanto ao par sexual, obtendo-se avanços significativos no conhecimento da origem e diferenciação dos cromossomos sexuais entre os vertebrados inferiores. CAPES: 11744/13–8

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26

Ashton, Kevin John. "Genetic Aberrations in Non-Melanoma Skin Cancer." Thesis, Griffith University, 2002. http://hdl.handle.net/10072/367012.

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Genetic changes are hallmarks of cancer development involving the activation and/or inactivation of oncogenes and tumour suppressor genes, respectively. In non-melanoma skin cancer (NMSC) development, the initiation of genetic mutations results from exposure to solar ultraviolet radiation. Non-melanoma skin cancers are comprised of basal cell carcinoma (BCC) and squamous cell carcinoma (SCC). Several related cutaneous lesions also exist, of which solar keratoses (SK) are widely accepted as a precursor dysplasia to SCC development. The study of recurrent genetic changes present within NMSC and SK should help reveal causative mutations in skin cancer development. Such analysis could also elucidate links in the genetic similarity of these dysplasia. The rapid screening of numerical changes in DNA sequence copy number throughout the entire genome has been made possible by the advent of comparative genomic hybridisation (CGH). This technique enables the identification of net gains and loss of genetic material within a tumour DNA sample. Chromosomal regions of recurrent gain or loss identify loci containing putative oncogenes and tumour suppressor genes, respectively with potential roles in NMSC tumourigenesis. Used in conjunction with tissue microdissection and universal degenerate PCR techniques this can enable the elucidation of aberrations in small histologically distinct regions of tumour. Such a technique can utilize archival material such as paraffin embedded tissue, which is the major source of neoplastic material available for cancer research. This study used the CGH technique to investigate aberrations in BCC, SCC and SK samples. The screening of copy number abnormalities (CNAs) in BCC revealed that although these tumours were close to diploid and generally genetically stable, they did contain several recurrent aberrations. The loss of genetic material at 9q was identified in a third of BCC tumours studied. This is characteristic of inactivation of the PTCH tumour suppressor gene, a known attribute in some sporadic BCC development. Validation of this loss was performed via loss of heterozygosity, demonstrating good concordance with the CGH data. In addition the over-representation of the 6p chromosome arm was revealed in 47% of biopsies. This novel CNA is also commonly observed in other cutaneous neoplasias, including Merkel cell carcinoma and malignant melanoma. This suggests a possible common mechanism in development and or promotion in these cutaneous dysplasias, the mechanisms of which have yet to be clearly defined. In contrast to BCC, numerical genetic aberrations in SCC and SK were much more frequent. Several regions of recurrent gain were commonly shared between both dysplasias including gain of 3q, 4p, 5p, 8q, 9q, 14q, 17p, 17q and 20q. Common chromosomal regions of loss included 3p, 8p, 9p, 11p, 13q and 17p. In addition loss of chromosome 18 was significantly observed in SCC in comparison to SK, a possible defining event in SK progression to SCC. The identification of shared genetic aberrations suggests a clonal and genetic relationship between the two lesions. This information further supports the notion for re-classification of SK to an SCC in situ or superficial SCC. Finally, the CNAs detected have been similarly observed in other squamous cell-derived tumours, for example cervical and head and neck SCC. This provides further evidence to common mechanisms involved in the initiation, development and progression of SCC neoplasia. This study has identified a number of recurrent chromosomal regions, some of which are novel in NMSC development. The further delineation of these loci should provide additional evidence of their significance and degree of involvement in NMSC tumourigenesis. The identification of the cancer-causing genes mapped to these loci will further demarcate the genetic mechanisms of BCC and SCC progression. An understanding of the events involved in skin cancer formation and progression should shed additional light on molecular targets for diagnostics, management and therapeutic treatment. Thesis (PhD Doctorate) Doctor of Philosophy (PhD) School of Health Sciences Full Text

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27

Mixão, Verónica de Pinho 1991. "Hybridization in Candida yeast pathogens." Doctoral thesis, Universitat Pompeu Fabra, 2020. http://hdl.handle.net/10803/670103.

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Candida species are among the most important fungal pathogens. Although Candida albicans is the most common cause of Candida infections, many other Candida species have emerged as pathogens. How pathogenicity is evolutionary acquired is unknown, but previous studies point to a role of hybridization in its development. This thesis studied the genomic features of Candida pathogens, with a special focus on hybrids and their evolution. Specifically, it asked the questions of how spread are hybrids among Candida species, and what are the processes that drive the evolution of their genomes. To this end, genomes from 141 isolates belonging to 13 Candida species were analyzed and compared, to reconstruct their features and evolution. Overall, this thesis supports an important role of hybridization in the emergence of new yeast pathogens and provides novel insights on the evolutionary aftermath of hybridization. Candida spp. se encuentran entre los hongos patógenos más importantes. Candida albicans es la principal causante de infecciones por Candida, pero muchas otras especies del mismo género han emergido como patógenos. Los mecanismos evolutivos implicados en la adquisición de patogenicidad se desconocen, pero estudios precedentes apuntan a que la hibridación puede haber jugado un papel importante en este desarrollo. Esta tesis estudia las características genómicas de las especies patógenas del género Candida, centrándose en híbridos y su evolución. Específicamente, se analiza la presencia de híbridos entre las especies de Candida y se estudian los procesos que impulsan la evolución de sus genomas. Para ello, se analizaron y compararon los genomas de 141 cepas correspondientes a 13 especies con el propósito de reconstruir sus características genómicas y estudiar su evolución. En resumen, esta tesis respalda un papel importante de la hibridación en la aparición de nuevas levaduras patógenas y aporta nuevas ideas sobre las consecuencias evolutivas de dicha hibridación.

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28

Michelland, Sylvie. "Déséquilibres génétiques dans les cancers bronchiques : une analyse par hybridation génomique comparative." Université Joseph Fourier (Grenoble), 1998. http://www.theses.fr/1998GRE10181.

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Le cancer du poumon est un probleme de sante publique majeur et il represente la premiere cause de mort par cancer chez l'homme dans le monde. Nous nous sommes interesses a l'analyse des desequilibres genetiques dans les tumeurs bronchiques dans le but d'etablir une cartographie precise des zones du genome associees a cette pathologie. Nous avons utilise la technique d'hybridation genomique comparative in situ (cgh) qui met en evidence de maniere rapide et globale l'ensemble des desequilibres genetiques presents dans une tumeur. Nous avons mis au point un protocole permettant d'obtenir des preparations de chromosomes metaphasiques adaptees a l'hybridation de type cgh et determine les conditions optimales requises pour une analyse cgh fiable et reproductible. Nous avons realise une etude cgh sur 11 tumeurs neuroendocrines de haut garde de malignite et 11 tumeurs non neuroendocrines. Nous avons montre que ces deux phenotypes partagent des anomalies communes et que certaines anomalies sont retrouvees specifiquement dans un phenotype. Ces resultats renforcent la notion qu'il existerait deux voies differentes de tumorgenese conduisant a la formation de ces deux classes de cancers bronchiques. Nous avons analyse un ensemble de 74 tumeurs bronchiques incluant tous les types histologiques. Notre but etant d'une part, d'identifier les regions chromosomiques specifiques pour chaque type histologique et d'autre part, d'etablir des correlations entre les anomalies chromosomiques mises en evidence par cgh, le type de cancer (ne, non ne), le type histologique et le degre de malignite de la tumeur. Les resultats ont montre des anomalies chromosomiques communes et differentes dans les differents types histologiques et nous avons etabli un patron d'anomalies chromosomiques pour chaque type histologique. Le nombre, le type et la distribution des anomalies permet de distinguer les carcinomes de haut grade et de bas grade de malignite. De plus, certaines anomalies semblent etre plus particulierement impliquees dans le caractere agressif des tumeurs. Ces resultats permettront ainsi d'orienter les recherches moleculaires visant a caracteriser les genes impliques dans le processus de cancerogenese.

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29

Giraud, Delphine. "Dynamique des éléments transposables et évolution du génome des spartines polyploïdes." Thesis, Rennes 1, 2019. http://www.theses.fr/2019REN1B057.

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Les conséquences de la spéciation divergente ou réticulée (par hybridation) ont été explorées au cours de la diversification des spartines depuis 6-10MA à travers l’analyse des séquences répétées, de leur expression et régulation. Nous avons montré une corrélation entre éléments transposables, tailles de génome, et relations phylogénétiques, tout en mettant en évidence une dynamique variable des catégories d’éléments transposables ou de séquences satellites selon les lignées, et l’ancienneté des évènements de spéciation. L’abondance des éléments transposables a été mise en relation avec leur niveau d’expression et le rôle des petits ARN dans leur contrôle. Cette régulation se met rapidement en place suite à l’hybridation interspécifique et explique la « quiescence génomique » (absence de prolifération d’éléments transposables) détectée chez l’allododécaploïde récent S. anglica. Les annotations d’éléments transposables et de petits ARNs, les nouveaux transcriptomes de références réalisés chez différentes espèces au cours de ce travail représentent des ressources additionnelles qui permettront d’explorer de manière plus exhaustive la dynamique des génomes de spartines et de comprendre les mécanismes génomiques impliqués dans l’adaptation et l’écologie de ces espèces ingénieurs d’écosystèmes We explored the consequences of divergent speciation or reticulate evolution (resulting from hybridization) during diversification of the Spartina genus in the last 6-10 MY, based on the analysis of repeated sequences, their expression and regulation. Transposable element amounts, genome size, and phylogenetic relationships were found correlated, although differential dynamics of specific transposable element families or satellite sequences were encountered according to lineages, and to divergence times following the speciation events. The abundance of transposable elements appears related to their level of expression and the role of small RNAs in their control. This regulation is rapidly established following interspecific hybridization and explains the "genomic quiescence" (absence of transposable element “burst”) detected in the recent allododecaploid S. anglica. Annotations of transposable elements and small RNAs, new reference transcriptomes generated for different species during this work represent additional resources that will allow a more comprehensive exploration of the Spartina genome history and dynamics for a better understanding of the genomic mechanisms involved in the adaptation and ecology of these “ecosystem engineers” species

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30

Williams, Stephen. "IDENTIFICATION OF LOCI CONTRIBUTING TO THE SMITH-MAGENIS SYNDROME-LIKE PHENOTYPE AND MOLECULAR EVALUATION OF THE RETINOIC ACID INDUCED 1 GENE." VCU Scholars Compass, 2010. http://scholarscompass.vcu.edu/etd/65.

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Smith-Magenis syndrome (SMS) is a multiple congenital abnormalities intellectual disability syndrome that results from a deletion of chromosome 17p11.2 or mutation of the retinoic acid inducted one gene (RAI1). SMS is characterized by a multitude of phenotypic features including craniofacial defects, short stature, obesity, intellectual disability, self-abusive behavior, sleep disturbance and behavioral abnormalities. Interestingly, although SMS is a clearly defined syndrome with a known molecular change at its foundation, ~40% of all candidate cases sent to the Elsea lab for evaluation do not have a mutation or deletion of RAI1. We hypothesize that at least one other locus must be responsible for this Smith-Magenis-like (SMS-like) phenotype. To address this hypothesis, we first compiled a cohort of 52 subjects who had been referred to the Elsea lab for a clinical diagnosis of SMS. Once these individuals were confirmed to not have an RAI1 mutation or deletion, their phenotypes were compiled and statically analyzed to distinguish whether SMS and SMS-like cohorts are different in the prevalence of the core phenotypes of SMS such as, but not limited to, sleep disturbance, self-abusive behavior and developmental delay. SMS-like and SMS cohorts are not different in prevalence for these core features. Next, all SMS-like subjects were sent for whole genome array comparative genomic hybridization (aCGH) to identify duplications or deletions of each individual’s genome which contribute to the phenotype observed. We identified 6 pathogenic copy number variants (CNVs) in six individuals which contribute directly to the clinical phenotype, including two del(2)(q37). This study enabled us to draw relationships between SMS and other syndromes that had never been appreciated before and helped to identify pathways in which RAI1 may function. Using the data from our SMS-like study we were able to further characterize two known syndromes; Deletion 2q37 syndrome (brachydactyly mental retardation syndrome) and deletion 2q23 syndrome. With regard to deletion 2q37, syndrome we used genomic data from known and new deletion 2q37 subjects to refine the critical region to one gene: the histone deacetylase 4 gene (HDAC4). Using both clinical and molecular clues, we were able to identify one subject from our SMS-like cohort who has an insertion in HDAC4 which results in a premature stop codon. We conclude from this study that mutation of HDAC4 results in brachydactyly mental retardation syndrome. With regard to deletion 2q23 syndrome there were only five known cases in the published literature to which we were able to add two more. Using as similar approach to our del2q37 study we refined the critical region for this syndrome to one gene, the methyl binding domain 5 gene (MBD5). Using a molecular and clinical approach we were able to conclude that haploinsufficiency of MBD5 results in the core phenotypes seen in del2q23 syndrome including microcephaly, intellectual disabilities, severe speech impairment, and seizures. Using all the data generated from the three previous studies we set out to characterize the molecular function of RAI1. We hypothesize that RAI1 is a transcription factor that regulates gene expression of core genes involved in development, neurological function, and circadian rhythm. Using a ChIP-chip based approach we identified 257 transcripts we believe RAI1 regulates. Following up on these transcripts, using in vitro and in vivo methods, we have been able to conclude that RAI1 is a positive regulator of CLOCK, the master regulator of the central circadian cycle. Taken together, these studies have given us insight into the specific molecular changes that contribute to SMS and SMS-like syndromes. We have unveiled pathways and genes which are important to normal human development and behavior and identified novel functions of RAI1. These studies will provide the foundation for the future discovery of the pathways affected.

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31

Ashton, Kevin John, and K. Ashton@griffith edu au. "Genetic Aberrations in Non-Melanoma Skin Cancer." Griffith University. School of Health Science, 2002. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20030818.122305.

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Genetic changes are hallmarks of cancer development involving the activation and/or inactivation of oncogenes and tumour suppressor genes, respectively. In non-melanoma skin cancer (NMSC) development, the initiation of genetic mutations results from exposure to solar ultraviolet radiation. Non-melanoma skin cancers are comprised of basal cell carcinoma (BCC) and squamous cell carcinoma (SCC). Several related cutaneous lesions also exist, of which solar keratoses (SK) are widely accepted as a precursor dysplasia to SCC development. The study of recurrent genetic changes present within NMSC and SK should help reveal causative mutations in skin cancer development. Such analysis could also elucidate links in the genetic similarity of these dysplasia. The rapid screening of numerical changes in DNA sequence copy number throughout the entire genome has been made possible by the advent of comparative genomic hybridisation (CGH). This technique enables the identification of net gains and loss of genetic material within a tumour DNA sample. Chromosomal regions of recurrent gain or loss identify loci containing putative oncogenes and tumour suppressor genes, respectively with potential roles in NMSC tumourigenesis. Used in conjunction with tissue microdissection and universal degenerate PCR techniques this can enable the elucidation of aberrations in small histologically distinct regions of tumour. Such a technique can utilize archival material such as paraffin embedded tissue, which is the major source of neoplastic material available for cancer research. This study used the CGH technique to investigate aberrations in BCC, SCC and SK samples. The screening of copy number abnormalities (CNAs) in BCC revealed that although these tumours were close to diploid and generally genetically stable, they did contain several recurrent aberrations. The loss of genetic material at 9q was identified in a third of BCC tumours studied. This is characteristic of inactivation of the PTCH tumour suppressor gene, a known attribute in some sporadic BCC development. Validation of this loss was performed via loss of heterozygosity, demonstrating good concordance with the CGH data. In addition the over-representation of the 6p chromosome arm was revealed in 47% of biopsies. This novel CNA is also commonly observed in other cutaneous neoplasias, including Merkel cell carcinoma and malignant melanoma. This suggests a possible common mechanism in development and or promotion in these cutaneous dysplasias, the mechanisms of which have yet to be clearly defined. In contrast to BCC, numerical genetic aberrations in SCC and SK were much more frequent. Several regions of recurrent gain were commonly shared between both dysplasias including gain of 3q, 4p, 5p, 8q, 9q, 14q, 17p, 17q and 20q. Common chromosomal regions of loss included 3p, 8p, 9p, 11p, 13q and 17p. In addition loss of chromosome 18 was significantly observed in SCC in comparison to SK, a possible defining event in SK progression to SCC. The identification of shared genetic aberrations suggests a clonal and genetic relationship between the two lesions. This information further supports the notion for re-classification of SK to an SCC in situ or superficial SCC. Finally, the CNAs detected have been similarly observed in other squamous cell-derived tumours, for example cervical and head and neck SCC. This provides further evidence to common mechanisms involved in the initiation, development and progression of SCC neoplasia. This study has identified a number of recurrent chromosomal regions, some of which are novel in NMSC development. The further delineation of these loci should provide additional evidence of their significance and degree of involvement in NMSC tumourigenesis. The identification of the cancer-causing genes mapped to these loci will further demarcate the genetic mechanisms of BCC and SCC progression. An understanding of the events involved in skin cancer formation and progression should shed additional light on molecular targets for diagnostics, management and therapeutic treatment.

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Suzuki, Keli Tieko. "Investigação molecular por sequenciamento do gene CBP em portadores da síndrome de Rubinstein-Taybi." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/5/5141/tde-24052012-154642/.

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A Síndrome de Rubinstein-Taybi (RTSs) é uma doença rara de herança autossômica dominante, caracterizada por dismorfismos craniofaciais, polegares e háluces alargados, deficiência intelectual e de crescimento. RTSs tem sido associada com mutações no gene CREBBP (CBP) e mutações menos frequentes no gene EP300 que foram descritas em oito indivíduos. CBP e p300 possuem alta homologia e são extremamente importantes em várias vias de sinalização, principalmente como coativadores de transcrição e na acetilação das histonas. Nosso estudo baseou-se na análise de alterações moleculares por sequenciamento direto do CBP, FISH e array-CGH em 20 pacientes com RTSs. Dos 20 pacientes avaliados por sequenciamento direto foram identificadas oito alterações moleculares, dentre estas, seis são alterações moleculares novas as quais não foram descritas na literatura, são elas: i) duas deleções (p.M747fs STOP830 e p.G1011fs STOP1021) ii) duas alterações do tipo nonsense (p.Arg1341X, p.Arg1498X) iii) três do tipo missense (p.Arg1907Trp, p.Leu604Pro e p.His1291Arg). Também identificamos um polimorfismo de único nucleotídeo (SNP) (rs115594471/ c.5874CT). Dois pacientes apresentaram deleção do gene CBP em um dos alelos, identificado pelo método array-CGH. Outro, apresentou uma translocação aparentemente equilibrada t(2;16), cuja análise subsequente com FISH revelou uma quebra na região do CBP. Neste trabalho, a taxa de detecção de alteração molecular no CBP por sequenciamento direto foi de 40% (08/20). Porém, a taxa de detecção das alterações moleculares no CBP foi de 55% (11/20), considerando a combinação das diferentes técnicas utilizadas (FISH, sequenciamento direto e array-CGH). Não houve correlação genótipo-fenótipo, exceto por uma maior frequência da presença de epicanto nos pacientes com alteração no CBP. Os resultados obtidos neste trabalho servem como o diagnóstico molecular para os pacientes com RTSs atendidos no Ambulatório do Laboratório de investigação Médica 001 (ALIM 001) do Instituto da Criança - FMUSP, contribuindo para uma melhor orientação médica, como também para realização do aconselhamento genético às famílias Rubinstein-Taybi syndrome (RTSs) is a rare autosomal dominant disease characterized by craniofacial dysmorphisms, broad thumbs and toes, mental and growth deficiency. RTS has been associated with CREBBP (CBP) gene mutations and less frequently with mutations in EP300 gene, which have been reported in eight individuals. CBP and p300 have high homology and are extremely important in many signaling pathways especially as transcriptional coactivators and histone acetylation. Our study was based on the alteration analysis by direct sequencing of the CBP, by FISH and array-CGH in 20 RTSs patients. We identified eight molecular alterations in 20 RTSs patients evaluated by direct sequencing: i) two deletions (p.M747fs STOP830 and p.G1011fs STOP1021) ii) two nonsense alterations (p.Arg1341X and p.Arg1498X) iii) Three missense alteration (p.Arg1907Trp, p.Leu604Pro and p.His1291Arg). Single-nucleotide polymorphism were also identified (rs115594471 / c.5874CT), and six of these are new molecular alterations, not described in literature. Two RTSs patients studied had CBP gene deletion in one allele, identified by array-CGH method. Other patient, presented with apparent balanced translocation t(2;16) in which the subsequent analysis using FISH, showed a break in region of CBP. In this work, the rate of detection of molecular alteration in CBP by direct sequencing in RTSs patient was 40.0% (08/20). However, the rate of detection of molecular alteration in CBP was 55.0% (11/20), considering the combination of different techniques (FISH, direct sequencing and array-CGH. No significant correlation could be established in this study between the different types of mutations and genotype-phenotype of RTSs patients, except a higher frequency of the presence of epicanthus in the RTS patients with alteration in the CBP. The results of this study serve as a molecular diagnosis for RTSs patients treated at the Ambulatory of the Medical Investigation Laboratory 001 (ALIM 001) of the Instituto da Criança - FMUSP, and this contributes to better clinical management, such as making an appropriate genetic counseling for families

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Liu, Iris. "Comparative genome hybridization reveals widespread genome variation in pathogenic cryptococcus species." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/5646.

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Genome variability can influence the virulence of pathogenic microbes. The availability of genome sequences for strains of the AIDS-associated fungal pathogens Cryptococcus neoformans and C. gattii presented an opportunity to use Comparative Genome Hybridization (CGH) to examine genome variability between strains of different molecular subtypes and ploidy. CGH analysis of 15 strains revealed extensive genomic variation including regions of difference (deletions and amplifications) and chromosome copy number variability. Although no common genomic change was observed for these 15 strains, three key observations came out of these studies. First, CGH identified putative recombination sites and the origins of specific segments of the genome for the common laboratory strain, JEC21. Second, CGH and subsequent PCR-RFLP (PCR-Restriction Fragment Length Polymorphism) analysis on 33 clinical, environmental and laboratory-generated AD hybrid strains revealed that chromosome 1 from the serotype A genome is preferentially retained in clinical strains. Third, CGH and subsequent qRT-PCR (quantitative real-time PCR) analysis revealed disomy for chromosome 13 in two clinical strains: CBS7779 and WM626. Further qRT-PCR and phenotypic studies on CBS7779 revealed a correlation between variable melanin production and disomy. Specifically, highly melanized strains were monosomic for chromosome 13 and less melanized strains were disomic for this chromosome. This correlation, however, only held for the initial CBS7779 isolates. That is, subsequent screens of highly-melanized and less-melanized isolates derived from the initial CBS7779 strain no longer followed this pattern. These subsequent screens, however, did reveal that 1) disomy, once established, was a relatively stable trait and 2) having disomy at chromosome 13 seemed to increase the probability of developing disomy at chromosome 4. Finally, qRT-PCR of 13 additional strains from AIDS patients revealed that disomy of both chromosome 13 and chromosome 4 is common in freshly isolated, clinical strains. Overall, the data presented in this thesis reveal novel aspects of genome variability and lay the foundation for future studies on the relevance of variation in the virulence of C. neoformans.

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Eulálio, Inês Mariana Cardoso. "Developmente of a CNVs detection method through qPCR." Master's thesis, Universidade de Aveiro, 2017. http://hdl.handle.net/10773/22507.

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Mestrado em Biotecnologia Os copy number variations (CNVs) consistem em segmentos de DNA de uma kilobase ou mais, que se encontram num número variável de cópias, em comparação com um genoma de referência. A deteção de CNVs é convencionalmente realizada através de técnicas de citogenética, como fluorescence in situ hybridization e array comparative genomic hybridization, ou com base em PCR, como multiplex ligation-dependent probe amplification, SNP arrays ou deep sequencing. Porém, a evolução da técnica de PCR quantitativo em tempo real (qPCR) permitiu que fosse, actualmente, considerada o método gold standard para a detecção de CNVs devido, sobretudo, ao elevado rendimento, sensibilidade, precisão e versatilidade. O presente trabalho descreve o desenvolvimento e validação de um método de deteção de CNVs através da técnica de qPCR. A metodologia adotada provou ser um método preciso e sensível para a detecção de CNVs em regiões específicas. Copy number variations (CNVs) consist in DNA segments of one kilobase or larger, that are present in variable copy number, in comparison to a reference genome. CNVs detection is conventionally performed through cytogenetic, such as fluorescence in situ hybridization and array comparative genomic hybridization, or PCR-based techniques, like multiplex ligation-dependent probe amplification, SNP arrays or deep sequencing. However, the evolution of quantitative PCR (qPCR) allows it to be considered the gold standard for CNVs detection, mainly due to its high throughput, precision and versatility. The present work describes the development and validation of a qPCR method for CNVs detection. This method proved to be an accurate and sensitive method for CNVs detection in targeted regions.

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Berglund, Mattias. "Molecular Characterization of Diffuse Large B-cell Lymphoma and Aspects of Transformation." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4266.

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Serson, William Richard. "INCREASING RENEWABLE OIL CONTENT AND UTILITY." UKnowledge, 2017. http://uknowledge.uky.edu/pss_etds/89.

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Since the dawn of agriculture man has been genetically modifying crop plants to increase yield, quality and utility. In addition to selective breeding and hybridization we can utilize mutant populations and biotechnology to have greater control over crop plant modification than ever before. Increasing the production of plant oils such as soybean oil as a renewable resource for food and fuel is valuable. Successful breeding for higher oil levels in soybean, however, usually results in reduced protein, a second valuable seed component. We show that by manipulating a highly active acyl-CoA: diacylglycerol acyltransferase (DGAT) the hydrocarbon flux to oil in oilseeds can be increased without reducing the protein component. Compared to other plant DGATs, a DGAT from Vernonia galamensis (VgDGAT1A) produces much higher oil synthesis and accumulation activity in yeast, insect cells and soybean. Soybean lines expressing VgDGAT1A show a 4% increase in oil content without reductions in seed protein contents or yield per unit land area. Furthermore, we have screened a soybean fast neutrino population derived from M92-220 variety and found three high oil mutants that do not have reduced levels of protein. From the F2 plant populations we quantitatively pooled the high oil and low oil plants and performed comparative genomics hybridization (CGH). From the data it appears that two families have a 0.3 kb aberration in chromosome 14. We are performing further analysis to study this aberration and develop markers for molecular breeding. Mutagenic techniques are also useful for developing other traits such as early flowering varieties and adapting new high oil crops to a new region. Chia (Salvia hispanica) is an ancient crop that has experienced an agricultural resurgence in recent decades due to the high omega 3 fatty acid (ω-3) content of the seeds and good production potential. The area of cultivation has been expanded to Kentucky using mutagenized populations and the composition traits are similar to that of the original regions of cultivation in Central and South America.

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Kincaid, Smith Julien. "Modification des traits d'histoire de vie au cours de l’hybridation et analyse des mécanismes moléculaires sous- jacents chez les parasites plathelminthes du genre Schistosoma." Thesis, Perpignan, 2018. http://www.theses.fr/2018PERP0028/document.

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Les changements globaux ont en partie pour effet de modifier les aires de répartition géographique des espèces. Les interactions nouvelles entre espèces n’ayant jamais été en contact peuvent potentiellement mener à des cas atypiques de reproduction, notamment l’hybridation. Ce phénomène peut avoir des implications épidémiologiques fortes car il peut conduire à la genèse de pathogènes hybrides. La combinaison du matériel génétique d’espèces distinctes peut conférer de meilleures capacités à la progéniture (vigueur hybride ou hétérosis), pouvant à terme potentiellement mener à des changements adaptatifs et à l'émergence de pathogènes dans des zones non endémiques, ce qui en fait une menace émergente à l’échelle mondiale. Ce travail de thèse se focalise sur la schistosomiase, seconde maladie parasitaire humaine et sa récente émergence en Europe (Corse, France). Après l’identification et la caractérisation génomique d’un parasite hybride entre deux agents distincts de la maladie, S. haematobium chez l’homme et S. bovis chez les bovins, nous avons mené une approche intégrative afin de caractériser à plusieurs échelles les capacités invasives et la virulence de tels parasites. A partir de souches du terrain, nous avons mis en place un protocole d’évolution expérimentale visant à générer des hybrides de première et deuxième générations au laboratoire. Nous avons analysé les modifications de traits d’histoire de vie de ces parasites ainsi que les conséquences moléculaires (génomique et transcriptomique) de ce « clash génomique » et nous montrons que l’hybridation peut être une force évolutive majeure pour les parasites Global changes contribute in modifying species geographical distribution. New interactions between species that have never been in contact before can potentially lead to atypical cases of reproduction, including hybridization. This phenomenon can have strong epidemiological consequences as it can potentially lead to the genesis of hybrid pathogens. The combination of genetic material of distinct species can confer increased capacities to the offspring (hybrid vigor or heterosis), eventually leading to adaptive changes and the emergence of pathogens in non-endemic areas, making them an emerging global threat. This thesis work focuses on schistosomiasis, the second human parasitic disease after malaria and its recent emergence in Europe (Corsica, France). After the identification and genomic characterization of a hybrid parasite between two distinct agents of the disease, S. haematobium in humans and S. bovis in cattle, we conducted an integrative approach to characterize at several scales the invasive capacities and virulence of such parasites. Starting from the field, we set up an experimental evolution protocol aimed at generating first- and second-generation hybrids in the laboratory. We analysed life history trait modifications of these parasites as well as the molecular consequences (genomics and transcriptomics) of this "genomic clash" and we show that hybridization can be a major evolutionary force for parasites

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Aguiar, Simone dos Santos. "Pesquisa da amplificação e/ou deleção genica atraves da tecnica de hibridização genomica comparativa (CGH) e da leção dos genes P53 e RB1 atraves da tecnica de hibridação in situ fluorescente (FISH) no tecido do tumor de crianças e adolescentes com ost." [s.n.], 2006. http://repositorio.unicamp.br/jspui/handle/REPOSIP/312071.

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Orientador: Silvia Regina Brandalise Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas Made available in DSpace on 2018-08-06T21:43:20Z (GMT). No. of bitstreams: 1 Aguiar_SimonedosSantos_D.pdf: 43958145 bytes, checksum: b9dafbbd99ad0e567b3c1f03a0c7b37e (MD5) Previous issue date: 2006 Resumo: Introdução Os osteossarcomas (OS) são tumores agressivos, primários de osso, com prognóstico reservado. As deleções dos genes supressores de tumor, RBl e P53, localizados nos cromossomos 13 e 17 respectivamente, são freqüentemente encontradas neste tipo de tumor. As alterações citogenéticas encontradas nos OS são de alta complexidade, porém nenhuma delas é recorrente, não podendo caracterizá-lo. A técnica da Hibridização Genômica Comparativa (CGH) é uma ferramenta muito precisa para o estudo das deleções e amplificações gênicas ocorridas neste tumor. Materiais e Métodos. Tecido tumoral de 41 crianças com OS foi analisado pela técnica de CGH para pesquisar possíveis ganhos e/ou perdas gênicas . A técnica da Hibridização In Situ Fluorescente (FISH) foi realizada para estudar as deleções dos genes P53 e RBl. Vinte e quatro pacientes eram do sexo feminino e 17 do sexo masculino, com mediana de 12 anos e 4 meses. Resultados. As anormalidades cromossômicas observadas com a técnica de CGH foram diversas e variadas, especialmente ganhos nos cromossomos lp, 2p, 3q, 5q,5p e 6p e, perdas nos cromossomos 14q (50% no - 14q 11.2), 15q e 16p. Alto índice de perdas foi observado no cromossomo 21 (26 de 41 casos; p=0,008), sendo a região mais freqüentemente afetada a 21ql 1.2. Com relação ao estudo dos supressores tumorais, a deleção do P53 ocorreu em 68,3% dos casos (p=0,02) e do RBl em 87,5% dos casos (p=0,000001). Conclusão. Apesar de ambos supressores (PS3 e RBl) estarem deletados na maioria dos pacientes, este evento parece não estar associado ao prognóstico. Anormalidades ainda não reportadas presentes no cromossomo 21 nos OS pediátricos, sugerem que a seqüência mapeada nesta região cromossômica possa estar envolvida na patogênese deste tumor Abstract: Background. Osteosarcomas (OS) are aggressive bone tumors and often have a poor prognosis. It is already known that abnormalities in chromosomes 13 and 17 are frequently observed in OS patients, being also expected a deletion of RBI and P53 genes. The tumors exhibit karyotypes with a high degree of complexity, that has made it difficult to determine if any recurrent chromosomal aberrations could characterize OS. To address inherent difficulties associated with classical cytogenetic analysis, comparative genomic hybridization (CGH) has been applied to OS tissue. Patients and Methods. Forty one pediatric OS specimens were analyzed by CGH techniques, and the expression of RBI and P53 were analyzed by FISH . Twenty four patients were girls and 17 boys. Median age was 12 years and 4 months.Results. Chromosomal abnormalities were highly diverse and variable specially gains in chromosome lp, 2p, 3q, 5q , 5p and 6p and losses in chromosome 14q (50% in - 14q 11.2), 15q and 16p. High level of losses in chromosome 21 were present (26 of 41 cases; p-0,008), being 21 q 11.2 region the most frequent one. Concerning about genes expression, P53 is deleted in 68,3% of the cases (p=0,02) and RBI in 87,5% (p=0,000001) .Conclusion. Although both oncogenes (P53 and RBI) are deleted in OS population, it remains impossible to determine if this abnormality is a prognostic factor. These new and unreported findings in chromosome 21 of pediatric OS tumors, suggest that specific sequences mapping these chromosomal regions, would likely to play a role in the development of OS Doutorado Pediatria Mestre em Saude da Criança e do Adolescente

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39

Baumgartner, Adolf. "Comparative genomic hybridization (CGH) in genotoxicology." 2013. http://hdl.handle.net/10454/10121.

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No In the past two decades comparative genomic hybridization (CGH) and array CGH have become crucial and indispensable tools in clinical diagnostics. Initially developed for the genome-wide screening of chromosomal imbalances in tumor cells, CGH as well as array CGH have also been employed in genotoxicology and most recently in toxicogenomics. The latter methodology allows a multi-endpoint analysis of how genes and proteins react to toxic agents revealing molecular mechanisms of toxicology. This chapter provides a background on the use of CGH and array CGH in the context of genotoxicology as well as a protocol for conventional CGH to understand the basic principles of CGH. Array CGH is still cost intensive and requires suitable analytical algorithms but might become the dominating assay in the future when more companies provide a large variety of different commercial DNA arrays/chips leading to lower costs for array CGH equipment as well as consumables such as DNA chips. As the amount of data generated with microarrays exponentially grows, the demand for powerful adaptive algorithms for analysis, competent databases, as well as a sound regulatory framework will also increase. Nevertheless, chromosomal and array CGH are being demonstrated to be effective tools for investigating copy number changes/variations in the whole genome, DNA expression patterns, as well as loss of heterozygosity after a genotoxic impact. This will lead to new insights into affected genes and the underlying structures of regulatory and signaling pathways in genotoxicology and could conclusively identify yet unknown harmful toxicants.

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Santos, André Ferreira. "Development of a Database for Array Comparative Genomic Hybridization." Master's thesis, 2015. http://hdl.handle.net/10316/30808.

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Dissertação de Mestrado Integrado em Engenharia Biomédica apresentada à Faculdade de Ciências e Tecnologia da Universidade de Coimbra. A técnica de Microarray de Hibridização Genómica Comparativa (arrayCGH) permitiu um avanço significativo no diagnóstico de doenças de desenvolvimento incompreensíveis através da deteção de variações do número de cópia genómicas (CNVs) que antes eram indetetáveis por outros tipos de tecnologias citogenéticas. Através desta técnica são detetadas síndromes genéticas já identificadas mas também novos distúrbios e novas doenças genómicas causadas por CNVs. A avaliação da patogenicidade das CNVs detetadas por arrayCGH está direta ou indiretamente relacionada com a consulta de CNVs previamente classificadas e arquivadas. Quando é detetada uma CNV anteriormente não observada, os clínicos tem de interpretar uma variação de significado clínico incerto (VOUS) o que pode ser muito complicado para eles. No entanto, a partilha de CNVs classificadas entre laboratórios pode ajudar quando uma variação destas aparece, de modo a poder classificá-la como benigna ou patogénica. Guardar, consultar e partilhar informação sobre CNVs de uma forma fácil é muito importante para os clínicos e para os laboratórios de modo a que estes possam fazer um diagnóstico correto dos seus pacientes. Neste trabalho é apresentado o desenvolvimento de uma base de dados, usando a tecnologia LAMP (Linux, Apache, MySQL e PHP), para guardar registos de arrayCGH e para dar aos clínicos laboratoriais uma interface para consultar e gerir CNVs.

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Chen, Hung-I. Harry, and 陳鴻毅. "Development of a Normalization Algorithm for Array Comparative Genomic Hybridization." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/86066366982034436673.

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碩士 國立臺灣大學 電機工程學研究所 95 Genomic instability is one of fundamental factors in tumorigenesis and tumor progression. Many studies have shown that copy-number abnormalities at the DNA level are important in the pathogenesis of cancer. Array Comparative Genomic Hybridization (array CGH), developed based on expression microarray technology, can reveal the chromosomal aberrations in segmental copies at a high-resolution. However, due to the nature of array CGH, many standard expression data processing tools, such as data normalization, often failed to yield satisfactory results. We demonstrate a novel array CGH normalization algorithm, which provides an accurate array CGH data normalization by utilizing the dependency of neighboring probe measurements in array CGH experiments. To facilitate the study, we have developed a Hidden Markov Model (HMM) to simulate a series of array CGH experiments with random DNA copy number alterations that can be used to validate the performance of our normalization. In addition, we applied our algorithm to normalize real data from an array CGH study of CL1-0, CL1-1 and CL1-5 cell lines. CL1-0, CL1-1 and CL1-5 are closely related lung cancer cell lines which are classified according to their differential invasiveness. The normalization made significant improvement over data quality and enhanced the reliability of experimental results. By using this newly developed algorithm, the normalized data showed distinct patterns of DNA copy number alternations among those lung cancer cell lines. Finally, based on this new development; we are establishing a user-friendly web-based system to provide convenient online array CGH data analysis.

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Chen, Hung-I. Harry. "Development of a Normalization Algorithm for Array Comparative Genomic Hybridization." 2007. http://www.cetd.com.tw/ec/thesisdetail.aspx?etdun=U0001-1007200716470300.

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LIN, YI CHAO, and 林宜昭. "Analysis of chromosomal aberration in pancreatic carcinoma by comparative genomic hybridization." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/49141080339263080109.

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碩士 長庚大學 基礎醫學研究所 93 The mortality of pancreatic cancer in male is the ninth leading cause of cancer death during year 2003 in Taiwan, and that in female ranks eighth. In order to develop the new diagnostic, therapeutic and preventive methods of the disease, we ought to define the progression of the tumorigenesis mechanism of the cancer. However, what we know about the genetic mechanism of the disease is not enough. Hruban et al. (2000) proposed the genetic progression model for pancreatic intraepithelial neoplasias. It involved a set of genetic variations. The complicated copy number amplification and deletion in particular regions of chromosomes were difficult to detect with usual methods. Therefore, we used comparative genomic hybridization (CGH) to define the variant regions of chromosomes in pancreatic cancers, and tried to define the tumor suppressor genes and oncogenes involved. Twenty-three cases of pancreatic cancer were collected, including 16 cases of pancreatic ductal adenocarcinoma, 4 cases of endocrine carcinoma, a case of acinar cell carcinoma, and 2 cases of mucinous adenocarcinoma. After CGH analyses to the 23 cases the copy number abnormality showed that the gain occured in 14 cases (61%) at chromosomes 13q, in 13 cases (57%) at each of 7p, 8q and 14p, in 12 cases (52%) at each of 5q, 13p, 19p and 21p, in 11 cases (48%) at each of 1q, 5p, 6p and 11p, and the loss in 6 cases (26%) at chromosome 16q and 18q, and in 5 cases (22%) at 1p. We also noticed among 16 cases of pancreatic ductal adenocarcinoma, that the copy number gain occurred in chromosomes 8q (63%), 13q, 14p (56%), 1q, 5q, 7p, 11q, 13p and 21p (50%), and loss in chromosomes 18q (31%) and 16q (25%). Also, in 3 among 4 cases of endocrine carcinoma it showed the gain at chromosome 6q. The results imply that the particular type of tumor may be related to the certain genomic aberration in the identified specific regions. Further investigation with the array CGH, which increases the resolution in detecting the particular regions of chromosomes, may facilitate the understanding of the specific genes that may be involved. It can be then analyzed in correspondence with the various stages of the tumors, and the tumorigenesis progression of pancreatic carcinoma.

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Lin, Yu-Shu, and 林育澍. "An Integration of Statistical Methods for Array-based Comparative Genomic Hybridization." Thesis, 2006. http://ndltd.ncl.edu.tw/handle/71870029541893742750.

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碩士 國立臺灣大學 農藝學研究所 94 The DNA microarray is widely used to investigate gene expression profiles of many thousands of genes simultaneously. And it has become a common tool for exploring various questions in many areas of biological and medical sciences. Specifically, array-based comparative genomic hybridization (Array CGH) is applied to screen alteration of DNA copy numbers genomewide. The main purpose of such application is to detect the altered DNA segments among genome sequences from a control (reference) treatment to a test treatment. Typically, efficient statistical tools are developed to compare the intensity ratios of spots representing the competitive hybridization between the control mRNA sample and the test mRNA sample, which are separately labeled with red (Cy5) and green (Cy3) fluorescence dyes. Users usually focus on the gain region and the loss region on each chromosome. In consequence, the differentially altered regions are displayed by graphical plots. From the simulation results presented in Lai et al. (2005), several competing statistical methods are selected for analysis of Array CGH data, including Adaptive Weights Smoothing method, Circular Binary Segmentation method and CGH Segmentation method. Furthermore, we use Perl, PHP programming language and Apache web server to integrate the chosen statistical methods into an analysis platform under R language environment. The proposed platform offers normalization, identification of the differentially altered regions and plotting of the gain and loss regions genomewide. In addition, users can annotate information through UCSC Genome Browser and ID Converter for advanced analyses.

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45

Freitas, Marta Catarina Baptista. "Prenatal diagnosis: the clinical usefulness of Array Comparative Genomic Hybridization (aCGH)." Master's thesis, 2017. https://hdl.handle.net/10216/104446.

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Freitas, Marta Catarina Baptista. "Prenatal diagnosis: the clinical usefulness of Array Comparative Genomic Hybridization (aCGH)." Dissertação, 2017. https://hdl.handle.net/10216/104446.

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47

Lai, Jiunn-Jei, and 賴俊吉. "Study of Chromosomal Aberrations in Nasal Lymphoma By Comparative Genomic Hybridization Technique." Thesis, 2000. http://ndltd.ncl.edu.tw/handle/19102033855476926703.

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碩士 國立陽明大學 遺傳學研究所 88 Nasal lymphoma (nasal and nasal type T/NK cell lymphoma) is the most aggressive kind of lymphoma. It was most often occurred in nose or facial midline. And it is highly associated with Epstein Barr Virus. The incidence of nasal lymphoma in Asian and Native American are much higher than that of Caucasian. There are about three forth cases occurred in male. Besides, the prognosis of nasal lymphoma was very poor, and there was highly rate of relapse. Because of these reasons, we are interest in analyzing how it happens. Here, we want to realize the cytogenetics of nasal lymphoma by using the CGH (Comparative Genomic Hybridization) technique to achieve it. The principle of CGH technique is that labeling the equal amount DNA of cancer cells and that of normal cells with different fluorescence dye, and then hybridizing to normal metaphase chromosomes on the slide at the same time. By analyzing the ratio of fluorescence on metaphase chromosomes, we can realize that are there any gain or loss segments of DNA of cancer cells in chromosomes. And there were most likely oncogenes or tumor suppressor genes in these gain or loss segments. We analyzed 17 cases DNA of nasal lymphoma from NCKU, and one cell line -- HANK1 (offered by Dr. Kagami in Japan) by using CGH. The result indicated that the mainly chromosomal aberration is gain in X chromosome (29.4%). There were few researches done about chromosomal aberrations of nasal lymphoma before, and they were using conventional cytogenetic technique (karyotyping). The results have a common finding that the loss of chromosome 6q21-25 segment in the chromosomal aberrations of nasal lymphoma, but it did not appear in our CGH results. The X chromosomal aberrations are the common findings both in researches using earlier cytogenetic technique and our CGH experiments. Is there any oncogene or tumor suppressor gene on X chromosome? This is a good question for further research.

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48

Chen, Ming-Chih, and 陳明志. "Investigation on the People’s Willingness to Using the array-Comparative Genomic Hybridization." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/80244000447158336128.

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碩士 育達商業科技大學 行銷與流通管理所 101 Taiwan has been a highly developed country, where low birth rate has become an increasingly apparent phenomenon. More and more people choose not to have children, or insist on the spirit that one child is just enough and only have one child. In the trend of late marriage and late childbirth, middle and advanced maternal age has been quite common. However, the risk of preterm birth or congenital disease also increases with the age of women at childbirth. According to medical statistics, 4 in 100 newborns have birth defects in Taiwan, and it is estimated that more than 5000 babies with congenital abnormalities are born every year. Based on the concept of genetic health and the consideration of perfect fetus, array-Comparative Genomic Hybridization (aCGH) with higher resolution than that of traditional chromosome inspection technology, a new type of prenatal genome detection technology, can rely on chromosome chip inspection to make up for the deficiency in traditional chromosome inspection after first excluding possibility of these problems regarding clinical commonly known congenital abnormal genes, difficulty in detecting chromosome deficiency diseases in tiny fragments by traditional chromosome inspection technology, and even awareness of developmental retardation after birth. This study mainly took the Health Belief Model (HBM) as the theoretical basis to investigate the usage intention of the public on chromosome chip inspection and its influencing factors. A questionnaire survey was made among 430 pregnant couples attending mother class or undergoing prenatal examination in department of obstetrics and gynecology. With invalid questionnaires removed, 372 effective ones were obtained, and the recovery rate was 86.5%. The study found that the public’s knowledge of chromosome chip inspection, perceived susceptibility and cues to action have positive effects on usage intention, and perceived barriers have negative effects on usage intention. Finally, it is suggested that government, enterprises and philanthropic organizations should cooperate in establishing perfect prenatal examination items and providing enough health resources for the public, so as to reduce the incidence of congenital malformation and make the concept of genetic health and the wish of perfect fetus come true in every family.

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49

"Identification of genetic abnormalities in nasopharyngeal carcinoma by comparative genomic hybridization and interphrase cytogenetics." 1999. http://library.cuhk.edu.hk/record=b5889980.

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Fan Chung-sze. Thesis (M.Phil.)--Chinese University of Hong Kong, 1999. Includes bibliographical references. Abstracts in English and Chinese. Acknowledgements --- p.i Abstract --- p.ii List of Tables --- p.vii List of Figures --- p.viii List of Abbreviations --- p.x Table of Contents --- p.xi Chapter Chapter 1 --- Introduction Chapter 1.1 --- Nasopharyngeal Carcinoma --- p.1-1 Chapter 1.1.1 --- Histology of NPC --- p.1-1 Chapter 1.1.2 --- Etiological Factors --- p.1-2 Chapter 1.1.3 --- Genetic Changes in NPC --- p.1-5 Chapter 1.2 --- Background of Present Study --- p.1-14 Chapter 1.3 --- Aims of Study --- p.1-15 Chapter Chapter 2 --- Comparative Genomic Hybridization and Fluorescence In- Situ Hybridization Chapter 2.1 --- Introduction --- p.2-1 Chapter 2.2 --- Fluorescence In-Situ Hybridization (FISH) --- p.2-2 Chapter 2.2.1 --- Principle of FISH --- p.2-2 Chapter 2.2.2 --- Applications of FISH --- p.2-2 Chapter 2.2.3 --- Advantages and Limitations --- p.2-5 Chapter 2.3 --- Comparative Genomic Hybridization (CGH) --- p.2-7 Chapter 2.3.1 --- Principle of CGH --- p.2-7 Chapter 2.3.2 --- Applications of CGH --- p.2-8 Chapter 2.3.3 --- Advantages and Limitations --- p.2-10 Chapter 2.4 --- Method of CGH --- p.2-13 Chapter 2.4.1 --- CGH Probe Preparation --- p.2-13 Chapter 2.4.2 --- CGH Template Preparation --- p.2-21 Chapter 2.4.3 --- Hybridization --- p.2-23 Chapter 2.4.4 --- Post-hybridization --- p.2-23 Chapter 2.4.5 --- Fluorescence Detection --- p.2-24 Chapter 2.4.6 --- Image Acquisition and Analysis --- p.2-24 Chapter 2.5 --- Method of Interphase FISH --- p.2-29 Chapter 2.5.1 --- FISH Probe Preparation --- p.2-29 Chapter 2.5.2 --- FISH Template Preparation --- p.2-29 Chapter 2.5.3 --- Hybridization --- p.2-30 Chapter 2.5.4 --- Post-hybridization --- p.2-30 Chapter 2.5.5 --- Fluorescence Detection --- p.2-30 Chapter 2.5.6 --- Scoring of FISH Signals --- p.2-31 Chapter 2.5.7 --- Threshold Determination --- p.2-31 Chapter Chapter 3 --- FISH Studies on NPC Biopsies Guided by CGH Information Derived from Cell Lines and Xenografts Chapter 3.1 --- Introduction --- p.3-1 Chapter 3.2 --- Materials and Methods --- p.3-3 Chapter 3.2.1 --- CGH Analysis --- p.3-3 Chapter 3.2.2 --- Interphase FISH Analysis --- p.3-4 Chapter 3.2.3 --- Statistical Analysis --- p.3-7 Chapter 3.3 --- Results Chapter 3.3.1 --- CGH --- p.3-9 Chapter 3.3.2 --- Interphase FISH Analysis --- p.3-10 Chapter 3.3.3 --- Statistical Analysis --- p.3-11 Chapter 3.4 --- Discussion --- p.3-27 Chapter 3.4.1 --- CGH --- p.3-27 Chapter 3.4.2 --- Interphase FISH Analysis --- p.3-31 Chapter 3.5 --- Summary of This Chapter --- p.3-36 Chapter Chapter 4 --- CGH Studies on Universally Amplified DNA from Microdissected NPC Biopsies and Interphase FISH Analysis Chapter 4.1 --- Introduction --- p.4-1 Chapter 4.2 --- Materials and Methods --- p.4-4 Chapter 4.2.1 --- CGH on Universally Amplified DNA --- p.4-4 Chapter 4.2.2 --- Interphase FISH Analysis --- p.4-6 Chapter 4.2.3 --- Statistical Analysis --- p.4-8 Chapter 4.3 --- Results --- p.4-9 Chapter 4.3.1 --- CGH on Universally Amplified DNA --- p.4-9 Chapter 4.3.2 --- Interphase FISH Analysis --- p.4-10 Chapter 4.3.3 --- Statistical Analysis --- p.4-11 Chapter 4.3.4 --- Comparison of CGH and FISH Findings --- p.4-11 Chapter 4.4 --- Discussions --- p.4-30 Chapter 4.4.1 --- CGH Findings --- p.4-30 Chapter 4.4.2 --- Interphase FISH Analysis --- p.4-41 Chapter 4.4.3 --- Comparison of CGH and FISH Findings --- p.4-43 Chapter 4.5 --- Summary of This Chapter --- p.4-45 Chapter Chapter 5 --- Conclusion and Further Studies Chapter 5.1 --- Conclusion --- p.5-1 Chapter 5.2 --- Further Studies --- p.5-3 Chapter 5.2.1 --- Combination of Microdissection --- p.5-3 Chapter 5.2.2 --- Multicolor Karyotyping --- p.5-3 Chapter 5.2.3 --- Microarrays --- p.5-4 References --- p.R-1

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50

"Chromosomal aberrations in hepatocellular carcinoma: a study by comparative genomic hybridization and interphase cytogenetics." 2000. http://library.cuhk.edu.hk/record=b5890480.

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Lee Siu-wah. Thesis submitted in: December 1999. Thesis (M.Phil.)--Chinese University of Hong Kong, 2000. Includes bibliographical references (leaves [106]-116). Abstracts in English and Chinese. Abstract (in English) --- p.i Abstract (in Chinese) --- p.iii Acknowledgements --- p.v Table of Contents --- p.vi List of Figures --- p.ix List of Tables --- p.x Abbreviations --- p.xi Chapter Chapter 1 --- Introduction --- p.1 Chapter 1.1 --- Hepatocellular Carcinoma (HCC) --- p.2 Chapter 1.2 --- Etiology of Hepatocellular Carcinoma --- p.5 Chapter 1.2.1 --- Viral Infection --- p.5 Chapter 1.2.1.1 --- Hepatitis B Virus --- p.5 Chapter 1.2.1.2 --- Hepatitis C Virus --- p.7 Chapter 1.2.2 --- Cirrhosis and Chronic Inflammation --- p.8 Chapter 1.2.3 --- Aflatoxin --- p.9 Chapter 1.3 --- Genetic Studies of Hepatocellular Carcinoma --- p.9 Chapter 1.3.1 --- Conventional Cytogenetics --- p.9 Chapter 1.3.2 --- Molecular Cytogenetics --- p.12 Chapter 1.3.3 --- Molecular Genetic Studies --- p.12 Chapter 1.3.3.1 --- Proto-oncogenes --- p.12 Chapter 1.3.3.2 --- Tumour Suppressor Genes --- p.13 Chapter 1.3.3.3 --- Cell Cycle Genes --- p.14 Chapter 1.4 --- Background of Study --- p.16 Chapter 1.5 --- Objectives of Study --- p.17 Chapter Chapter 2 --- Material and Methods --- p.18 Chapter 2.1 --- Materials --- p.19 Chapter 2.2 --- Analysis of Chromosomal Imbalances by Comparative Genomic Hybridization --- p.23 Chapter 2.2.1 --- Comparative Genomic Hybridization --- p.23 Chapter 2.2.2 --- Methods Chapter 2.2.2.1 --- Preparation of Normal Metaphases --- p.30 Chapter 2.2.2.2 --- Extraction of High Molecular Weight DNA --- p.30 Chapter 2.2.2.3 --- Labeling of DNA by Nick Translation --- p.31 Chapter 2.2.2.4 --- Labeling Efficiency --- p.31 Chapter 2.2.2.5 --- Preparation of Probe --- p.33 Chapter 2.2.2.6 --- Hybridization --- p.33 Chapter 2.2.2.7 --- Washing and Detection of Signals --- p.35 Chapter 2.2.2.8 --- Image Acquisition and Analysis --- p.35 Chapter 2.2.2.9 --- Control Experiments --- p.36 Chapter 2.3 --- Positional Mapping of Novel Amplicon by Interphase Cytogenetics --- p.39 Chapter 2.3.1 --- Fluorescence in situ Hybridization --- p.39 Chapter 2.3.2 --- Using Yeast Artificial Chromosomes (YAC) as Probe --- p.41 Chapter 2.3.3 --- Methods --- p.48 Chapter 2.3.3.1 --- Culture of Yeast Artificial Chromosomes --- p.48 Chapter 2.3.3.2 --- Extraction of Total YAC DNA --- p.48 Chapter 2.3.3.3 --- Verification of YAC Clones for Chimerism by FISH --- p.49 Chapter 2.3.3.4 --- Inter-Alu-PCR --- p.49 Chapter Chapter 3 --- Assessment of Genetic Changes in HCC by Comparative Genomic Hybridization (CGH) --- p.57 Chapter 3.1 --- Introduction --- p.58 Chapter 3.2 --- Materials and Methods --- p.58 Chapter 3.2.1 --- Patients and Specimens --- p.58 Chapter 3.2.2 --- Comparative Genomic Hybridization --- p.60 Chapter 3.2.3 --- Statistical Analysis --- p.60 Chapter 3.3 --- Results --- p.61 Chapter 3.3.1 --- Overall Copy Number Aberrations in 67 HCC and Surrounding Cirrhotic Tissues --- p.61 Chapter 3.3.2 --- TNM Staging --- p.61 Chapter 3.3.3 --- Tumour Size --- p.72 Chapter 3.3.4 --- Serum AFP Elevation --- p.72 Chapter 3.3.5 --- Chromosomal Aberrations in HCC arising from Cirrhotic and Non- cirrhotic Livers --- p.72 Chapter 3.4 --- Discussion --- p.73 Chapter 3.4.1 --- Recurrent Gains --- p.73 Chapter 3.4.2 --- Recurrent Losses --- p.75 Chapter 3.4.3 --- Tumour Progression --- p.76 Chapter 3.5 --- Conclusion --- p.78 Chapter Chapter 4 --- Positional Mapping of a Novel Amplicon on Chromosome 1q21-q25 by Interphase Cytogenetics --- p.79 Chapter 4.1 --- Introduction --- p.80 Chapter 4.2 --- Materials --- p.82 Chapter 4.3 --- Methods --- p.82 Chapter 4.3.1 --- Preparation of Paraffin-embedded Tissue Sections --- p.82 Chapter 4.3.2 --- Verification of YAC Probes for Chimerism --- p.83 Chapter 4.3.3 --- Hybridization Efficiency of Test and Reference Probes --- p.83 Chapter 4.3.4 --- Slide Pretreatment and FISH with YAC Probes --- p.88 Chapter 4.3.5 --- Scoring of FISH Signals --- p.88 Chapter 4.4 --- Results --- p.89 Chapter 4.4.1 --- Relative Copy Number Gain --- p.89 Chapter 4.4.2 --- Intratumour Heterogeneity --- p.90 Chapter 4.5 --- Discussion --- p.90 Chapter 4.6 --- Further Studies --- p.104 Chapter 4.6.1 --- Fine Mapping of Chromosomal Region 1 q21 --- p.104 Chapter 4.6.2 --- Isolation of Novel Genes in the Amplicon --- p.105 Chapter 4.6.3 --- Expression Status of the EDC Genes --- p.105 References --- p.106

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