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Frater, Eric, and Eric Frater. "Optical Alignment with CGH Phase References." Diss., The University of Arizona, 2016. http://hdl.handle.net/10150/621452.
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The growing field of high-order aspheric and freeform optical fabrication has inspired the creation of optical surfaces and systems which are difficult to align. Advances in optical alignment technology are critical to fabricating and integrating aspheric components in advanced optical systems. This dissertation explores the field of optical alignment with a computer-generated hologram (CGH) used as a reference. A CGH is a diffractive optic which may be used to create a desired phase profile across a beam of light, project irradiance patterns, or serve as a mask for an incident beam. The alignment methods presented in this dissertation are concerned with the use of a CGH to create reference phase profiles, or "wavefronts" , in a beam. In one application a set of axisymmetric CGH references are co-aligned. Each CGH has also been aligned to an aspheric mirror so the co-alignment of the CGH references is also a co-alignment of the aspheric mirrors. Another application is concerned with aligning an interferometer to test an aspheric mirror surface. The interferometer measures a "null" interference pattern when its wavefront accommodates a known surface profile. In this alignment application the CGH creates wavefronts which accommodate a known set of small spherical reference features at the test surface. An interference null from all the "phase fiducial" reference features indicates an aligned projection of the CGH. The CGH co-alignment method is implemented on a 4-mirror prime focus corrector known as the Hobby-Eberly Telescope Wide Field Corrector (HET WFC). It is shown that this method was very successful for centration alignment of some mirrors, whereas mechanical stability was the hardware limitation for other degrees of freedom. The additional alignment methods used in this project are described in detail and the expected alignment of the HET WFC is reported.The fabrication, characterization and application of spherical phase fiducials is demonstrated in a CGH-corrected Fizeau test prototype. It is shown that these reference features achieve <±1.5µm transverse alignment precision. A pair of phase fiducials is also applied to constrain the clocking and magnification of a projected wavefront. Fabrication and coordinate measurement of the features present the dominant challenges in these demonstrations.
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Paiva, Greicy Helen Gambarini [UNESP]. "Genes candidatos a marcadores tumorais na progressão do adenocarcinoma de próstata indentificados por análise de HR-CGH e CGH-ARRAY." Universidade Estadual Paulista (UNESP), 2009. http://hdl.handle.net/11449/102718.
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O câncer de próstata (CaP) é a neoplasia mais comumente diagnosticada entre homens no ocidente. Embora tratamentos efetivos para a doença localizada estejam disponíveis atualmente, não há terapia curativa para tumores metastáticos. Além disso, os marcadores diagnósticos utilizados na clínica não conseguem discriminar totalmente a evolução diferencial da doença. Desta forma, o conhecimento das diferenças biológicas entre tumores primários confinados ao órgão e metástases é essencial para o desenvolvimento de novos marcadores e identificação de alvos terapêuticos. Neste estudo a análise baseada na metodologia de HR-CGH cromossômico foi realizada para identificar alterações de ganhos e perdas genômicas em três grupos de amostras: o grupo I, que compreende amostras pareadas de tumor primário e respectivas metástases (11 casos); o grupo II, constituído de pacientes que apresentaram seguimento clínico favorável por mais de 10 anos (5 casos); e o grupo III, constituído por diferentes biópsias do mesmo paciente (5 pacientes com 2 biópsias cada). As amostras foram microdissecadas (amostras a fresco: a partir de lâminas de referência; em blocos de parafina: a laser) e após a obtenção de DNA foram amplificadas (amostras de arquivo: PCR-SCOMP) ou marcadas por nick-translation para a realização de HR-CGH. Os resultados de HR-CGH foram comparados com os dados obtidos da análise de CGH-array num subgrupo de amostras e revelaram concordâncias significativas. Os resultados obtidos na presente investigação revelaram perdas dos cromossomos 1p, 2, 3q, 4p, 5q, 7, 8, 9q, 10q, 11q, 12q, 14q, 15q, 16q, 17q, 18q, 19, 20q e 22q em 80% dos casos avaliados. Além disso, perdas em 17q11.2-25, por exemplo, foram detectadas exclusivamente nos tumores do grupo I e nas suas metástases, e não nos tumores do grupo II, sugerindo que esta alteração deve ser importante...
Prostate cancer (PCa) is the most commonly diagnosed non-cutaneous malignancy and the second leading cause of cancer mortality in men from Occident. Although effective treatments for the localized disease are available, there is no efficient therapy for metastatic tumors. Additionally, clinical diagnostic markers are not able to completely discriminate the differential evolution of the disease. The knowledge of biological differences between localized primary tumors and metastasis can establish new molecular markers and therapeutic targets. In this study, an analysis based on HR-CGH methodology was performed to identify imbalances genomic in three groups of samples: group I, paired samples of primary tumors and its metastasis (11 cases); group II, patients that exhibited favorable follow-up over 10 years (5 cases); and group III, different biopsies from the same patient (5 patients with 2 biopsies each). The tumor samples were submitted to microdissection procedures (fresh samples: from reference slides; paraffin embedded samples: laser), DNA extracted and amplified (archive sample: PCR-SCOMP) or labeled by nick-translation to HR-CGH. The HRCGH results were compared with data obtained from CGH-array analysis of a subgroup of samples and revealed significant concordances. In the present investigation, there were observed losses on chromosomes 1p, 2, 3q, 4p, 5q, 7, 8, 9q, 10q, 11q, 12q, 14q, 15q, 16q, 17q, 18q, 19, 20q and 22q in 80% of the cases. Losses in 17q11.2-25, for instance, were detected exclusively in tumor from group I and its metastasis, but were not found in tumors from group II, suggesting that this alteration must be important in the progression of the disease. Five genes were selected after the comparison between the HR-CGH and CGH-array data. The tumor suppressor genes ARID1A, MTSS1, NME1 and S100A4 and TOP2A (oncogenes) were evaluated by quantitative real time... (Complete abstract click electronic access below)
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Paiva, Greicy Helen Gambarini. "Genes candidatos a marcadores tumorais na progressão do adenocarcinoma de próstata indentificados por análise de HR-CGH e CGH-ARRAY." Botucatu : [s.n.], 2009. http://hdl.handle.net/11449/102718.
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Orientador: Silvia Regina RogattoBanca: Spencer L. M. Payão
Banca: Carla Rosemberg
Banca: José Carlos de S. Trindade
Banca: Maria Aparecida M. Rodrigues
Resumo: O câncer de próstata (CaP) é a neoplasia mais comumente diagnosticada entre homens no ocidente. Embora tratamentos efetivos para a doença localizada estejam disponíveis atualmente, não há terapia curativa para tumores metastáticos. Além disso, os marcadores diagnósticos utilizados na clínica não conseguem discriminar totalmente a evolução diferencial da doença. Desta forma, o conhecimento das diferenças biológicas entre tumores primários confinados ao órgão e metástases é essencial para o desenvolvimento de novos marcadores e identificação de alvos terapêuticos. Neste estudo a análise baseada na metodologia de HR-CGH cromossômico foi realizada para identificar alterações de ganhos e perdas genômicas em três grupos de amostras: o grupo I, que compreende amostras pareadas de tumor primário e respectivas metástases (11 casos); o grupo II, constituído de pacientes que apresentaram seguimento clínico favorável por mais de 10 anos (5 casos); e o grupo III, constituído por diferentes biópsias do mesmo paciente (5 pacientes com 2 biópsias cada). As amostras foram microdissecadas (amostras a fresco: a partir de lâminas de referência; em blocos de parafina: a laser) e após a obtenção de DNA foram amplificadas (amostras de arquivo: PCR-SCOMP) ou marcadas por nick-translation para a realização de HR-CGH. Os resultados de HR-CGH foram comparados com os dados obtidos da análise de CGH-array num subgrupo de amostras e revelaram concordâncias significativas. Os resultados obtidos na presente investigação revelaram perdas dos cromossomos 1p, 2, 3q, 4p, 5q, 7, 8, 9q, 10q, 11q, 12q, 14q, 15q, 16q, 17q, 18q, 19, 20q e 22q em 80% dos casos avaliados. Além disso, perdas em 17q11.2-25, por exemplo, foram detectadas exclusivamente nos tumores do grupo I e nas suas metástases, e não nos tumores do grupo II, sugerindo que esta alteração deve ser importante... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Prostate cancer (PCa) is the most commonly diagnosed non-cutaneous malignancy and the second leading cause of cancer mortality in men from Occident. Although effective treatments for the localized disease are available, there is no efficient therapy for metastatic tumors. Additionally, clinical diagnostic markers are not able to completely discriminate the differential evolution of the disease. The knowledge of biological differences between localized primary tumors and metastasis can establish new molecular markers and therapeutic targets. In this study, an analysis based on HR-CGH methodology was performed to identify imbalances genomic in three groups of samples: group I, paired samples of primary tumors and its metastasis (11 cases); group II, patients that exhibited favorable follow-up over 10 years (5 cases); and group III, different biopsies from the same patient (5 patients with 2 biopsies each). The tumor samples were submitted to microdissection procedures (fresh samples: from reference slides; paraffin embedded samples: laser), DNA extracted and amplified (archive sample: PCR-SCOMP) or labeled by nick-translation to HR-CGH. The HRCGH results were compared with data obtained from CGH-array analysis of a subgroup of samples and revealed significant concordances. In the present investigation, there were observed losses on chromosomes 1p, 2, 3q, 4p, 5q, 7, 8, 9q, 10q, 11q, 12q, 14q, 15q, 16q, 17q, 18q, 19, 20q and 22q in 80% of the cases. Losses in 17q11.2-25, for instance, were detected exclusively in tumor from group I and its metastasis, but were not found in tumors from group II, suggesting that this alteration must be important in the progression of the disease. Five genes were selected after the comparison between the HR-CGH and CGH-array data. The tumor suppressor genes ARID1A, MTSS1, NME1 and S100A4 and TOP2A (oncogenes) were evaluated by quantitative real time... (Complete abstract click electronic access below)
Doutor
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Shah, Sohrab P. "Model based approaches to array CGH data analysis." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/2808.
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DNA copy number alterations (CNAs) are genetic changes that can produce
adverse effects in numerous human diseases, including cancer. CNAs are
segments of DNA that have been deleted or amplified and can range in size
from one kilobases to whole chromosome arms. Development of array
comparative genomic hybridization (aCGH) technology enables CNAs to be
measured at sub-megabase resolution using tens of thousands of probes.
However, aCGH data are noisy and result in continuous valued measurements of
the discrete CNAs. Consequently, the data must be processed through
algorithmic and statistical techniques in order to derive meaningful
biological insights. We introduce model-based approaches to analysis of aCGH
data and develop state-of-the-art solutions to three distinct analytical
problems.
In the simplest scenario, the task is to infer CNAs from a single aCGH
experiment. We apply a hidden Markov model (HMM) to accurately identify
CNAs from aCGH data. We show that borrowing statistical strength across
chromosomes and explicitly modeling outliers in the data, improves on
baseline models.
In the second scenario, we wish to identify recurrent CNAs in a set of aCGH
data derived from a patient cohort. These are locations in the genome
altered in many patients, providing evidence for CNAs that may be playing
important molecular roles in the disease. We develop a novel hierarchical
HMM profiling method that explicitly models both statistical and biological
noise in the data and is capable of producing a representative profile for a
set of aCGH experiments. We demonstrate that our method is more accurate
than simpler baselines on synthetic data, and show our model produces output
that is more interpretable than other methods.
Finally, we develop a model based clustering framework to stratify a patient
cohort, expected to be composed of a fixed set of molecular subtypes. We
introduce a model that jointly infers CNAs, assigns patients to subgroups
and infers the profiles that represent each subgroup. We show our model to
be more accurate on synthetic data, and show in two patient cohorts how the
model discovers putative novel subtypes and clinically relevant subgroups.
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Ghaffari, Saeed R. "Development and application of comparative genomic hybridisation (CGH)." Thesis, University of Glasgow, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390763.
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Mohrmann, Inga [Verfasser]. "Array-CGH bei Patienten mit Intelligenzminderung / Inga Mohrmann." Lübeck : Zentrale Hochschulbibliothek Lübeck, 2014. http://d-nb.info/1046429280/34.
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Lee, Sansan. "Genetic counseling perspectives on prenatal array CGH testing." Waltham, Mass. : Brandeis University, 2009. http://dcoll.brandeis.edu/handle/10192/23259.
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Gamero, Angel Mauricio Castro. "Desequilíbrios cromossômicos em nove casos de osteossarcoma detectados através de hibridação genômica comparativa (CGH)." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-22042013-095920/.
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O osteossarcoma (OS) é o tumor ósseo maligno mais freqüente da infância e adolescência com uma taxa de sobrevida livre de eventos de 50 70% após 3 anos.. O pico de incidência ocorre na segunda década da vida, característica que sugere uma relação entre o rápido crescimento ósseo da adolescência e o desenvolvimento da neoplasia. Ainda, o conhecimento das bases genéticas é insuficiente. Estudos de citogenética clássica têm demonstrado que o OS caracteriza-se por exibir alta heterogeneidade cariotípica, incluindo altos graus de aneuploidia e rearranjos estruturais complexos. A técnica de CGH constitui uma ferramenta valiosa na analise do perfil genômico de tumores sólidos, e tem confirmado a complexidade das alterações cariotípicas em OS, descrita pela citogenética convencional. Não obstante, os estudos existentes são divergentes, e poucos têm estudado as informações obtidas por CGH em relação com a progressão tumoral. O objetivo do presente estudo foi identificar a presença de desequilíbrios cromossômicos em amostras de OS por meio da técnica de CGH. Os experimentos de CGH foram realizados de acordo com o descrito por Kallioniemi et al (1994). Foram analisadas nove amostras (3 biópsias, 5 ixressecções após quimioterapia e 1 metástase). O CGH detectou desequilíbrios cromossômicos em todas as amostras. Os ganhos foram mais freqüentes que as perdas. Muitas alterações cromossômicas foram observadas, especialmente ganhos nos cromossomos 1q, 2, 3p, 4, 5p, 6, 7, 8, 11p, 14q, 16, 21q e X; e perdas nos cromossomos 1p, 2q, 3q, 5q, 9q, 11q e 17q. As regiões mínimas de sobreposição mais freqüentes foram ganhos de 2p13-p14, 2q36-q37, 4q21 e 8p22, e perdas de 1p34.2, 3q22-q23 e 3q24. Três pacientes apresentaram amostras pareadas, e as alterações cromossômicas detectadas foram muito variadas, refletindo a heterogeneidade cromossômica intratumoral em cada caso. A mais alta divergência clonal entre as amostras pareadas foi observada entre a amostra de ressecção e a amostra metastática correspondente, mostrando a complexidade cromossômica adquirida durante a progressão e metastatização no caso descrito. Ainda são necessárias investigações adicionais, que contribuíam para a caracterização completa dos genes localizados nessas regiões.Osteosarcoma (OS) is the most frequent aggressive bone malignancy affecting children and young adults with an event-free survival of 50-70% after 3 years. The incidence peak occurs during the second decade of life, suggesting a relationship between rapid bone growth and the development of this tumor. The knowledge of the genetic basis behind tumor progression is still limited. Conventional cytogenetic studies have demonstrated that OS exhibits high cariotipic heterogeneity, with different degrees of aneuploidy and complex structural rearrangements. The CGH is an important tool for studying the genomic profiles of solid tumors, and has confirmed the complexity of cariotipic alterations in OS. However, previous studies have shown divergent results and few have correlated them with tumor progression. The objective of present study was to identify chromosome unbalances in nine samples of OS by CGH. 3 biopsies, 5 resections before quimioterapy and 1 metastasis were analyzed. The experiments were performed accordingly with Kallioniemi et al (1994). CGH detected chromosomal imbalances in all samples. Gains were more frequent than losses. Many chromosomal alterations were observed, especially gains at 1q, xi2, 3p, 4, 5p, 6, 7, 8, 11p, 14q, 16, 21q and X; and losses at 1p, 2q, 3q, 5q, 9q, 11q and 17q. The minimal regions of superposition were gains of 2p13-p14, 2q36-q37, 4q21 and 8p22, and losses of 1p43.2, 3q22-q23 and 3q24. Three patients had consecutive samples, and the chromosomal alterations varied, reflecting the chromosomal heterogeneity for each case. The highest clonal divergence among the consecutive samples was observed between resection and the corresponding metastatic sample, showing the chromosomal complexity acquired during the progression and dissemination in this case. Additional investigations for the characterization of genes at these regions are necessary.
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Herr, Alexander [Verfasser]. "Hochauflösende CGH mit Hilfe von DNS-Mikrorastern / Alexander Herr." Berlin : Freie Universität Berlin, 2005. http://d-nb.info/1021667471/34.
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Marioni, John Carlo. "Statistical methods for array CGH and copy number variation experiments." Thesis, University of Cambridge, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611877.
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Sporns, Peter [Verfasser]. "Korrelation von Array-CGH-Befunden und klinischem Phänotyp / Peter Sporns." Kiel : Universitätsbibliothek Kiel, 2015. http://d-nb.info/1065669992/34.
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Rocha, Ana Laís Bignotto da. "Sequenciamento direto dos genes SIX3, SHH, TGIF1, ZIC2 e array-CGH no estudo de pacientes com holoprosencefalia." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/61/61132/tde-12112013-150520/.
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Objetivos: Analisar por meio da técnica de sequenciamento direto a presença de alterações moleculares nos genes SHH, SIX3, ZIC2 e TGIF1 em indivíduos com diagnóstico clínico de HPE. Analisar por meio da técnica de CGH-array a presença de alterações moleculares em indivíduos com diagnóstico clínico de HPE previamente submetidos à análise por sequenciamento direto. Local: Laboratório de Genética e Citogenética Humana HRAC/USP, Bauru-SP. Casuística e metodologia: Foram selecionados 50 indivíduos, de ambos os sexos com idades entre 03 meses a 50 anos com diagnóstico clínico para HPE. Todos foram analisados por meio da técnica de sequenciamento direto para os genes SHH e TGIF1 completamente e para os genes ZIC2 e SIX3 parcialmente. Dentre os indivíduos que não apresentaram alterações na técnica de sequenciamento oito indivíduos com fenótipo mais grave foram selecionados para a análise por CGH-array. Resultados e discussão: Foram analisados 50 indivíduos por meio da técnica de sequenciamento direto dos gene SHH e TGIF1, foram encontradas duas variantes patogênicas na análise do gene SHH, no caso 1 a variante p.24G>P foi identificada, e no caso 2 foi identificada a variante c.1031del C. No gene TGIF1 foram encontrados cinco polimorfismos já descritos na literatura. Foi identificada uma nova variante silenciosa no éxon 1 do gene ZIC2 p.Q46Q (c. 431 G>A) e um polimorfismo já descrito na literatura em dois indivíduos no gene SIX3. A análise por CGH-array revelou a presença de uma microdeleção no caso 37, de 1,5Mb no cromossomo 17p12 entre as posições genômicas 14,052,279-15,102,307. A mesma deleção foi encontrada na mãe, sendo que esta região nunca foi associada a HPE. Conclusão: A técnica de sequenciamento direto é uma ferramenta muito importante no diagnóstico molecular da HPE, a padronização do sequenciamento direto para os genes ZIC2 e SIX3 poderá auxiliar em diagnósticos mais precisos em estudos futuros dentro do HRAC/USP. O emprego de novas técnicas como CGH-array pode indicar novas relações entre regiões cromossômicas e os múltiplos fatores envolvidos na formação da HPE.Objective: Analyze through direct sequencing technique the presence of molecular changes on the genes SHH, SIX3, ZIC2 and TGIF1 on individuals with clinical diagnosis of HPE. Analyze through array-CGH technique the presence of molecular changes on individuals with clinical diagnosis of HPE previously submitted to the direct sequencing analyzes. Local: Genetics and Human Cytogenetics Laboratory, HRAC/USP, Bauru-SP. Methods: Were selected 50 individuals from both genders with ages between 03 months and 50 years clinically diagnosed with HPE. Everyone was analyzed through the direct sequencing technique for the genes SHH and TGIF1 completely and for the genes ZIC2 and SIX3 partially. From those individuals which did not have shown changes on the direct sequencing technique, eight individuals with more severe phenotype were selected to the analysis through array-CGH. Results an Discussion: Were analyzed 50 individuals through the technique of direct sequencing of the genes SHH and TGIF1, were found two pathogenic variants in the analysis of SHH gene, in the case 1, the variant p.G24P was identified, and in the case 2 was identified the variant c.1031delC. On the TGIF1 gene were found five polymorphisms already described on the literature. Was identified a new silent variant on the exon 1 of the ZIC2 gene p. Q46Q(c.431G>A) and a polymorphism already described in the literature in two individuals on the gene SIX3. The analysis through array-CGH revealed the presence of one microdeletion in the case 37, of 1,5 Mb on the region 17p12 between the genomic positions 14,052,279-15,102,307. The same deletion was detected in the mother, though this region was never associated to the HPE. Conclusion: The direct sequencing technique is a very important tool for the molecular diagnosis of the HPE, and the direct sequencing standardization for the genes ZIC2 and SIX3 might help in more precise diagnostics on HRAC/USP future studies. The employ of new techniques such as array-CGH may indicate new relations between chromosomal regions and the multiple hit involved in the development of HPE.
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Castells, Sarret Neus. "Array CGH com a primera opció per al diagnòstic genètic postnatal." Doctoral thesis, Universitat Autònoma de Barcelona, 2015. http://hdl.handle.net/10803/325159.
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La citogenètica convencional detecta un 3-5% dels pacients amb retard global del desenvolupament / discapacitat intel·lectual (RGD / DI) i / o malformacions congènites (MC). L'amplificació de sondes múltiples dependents de lligació (MLPA) permet incrementar la taxa diagnòstica entre 2,4-5,8%. Actualment els arrays d'hibridació genòmica comparada (aCGH) constitueixen l'eina diagnòstica amb major rendiment en pacients amb RGD / DI, MC i trastorns de l'espectre autista (TEA).
L'objectiu del present treball ha estat avaluar l'eficiència de l'ús dels aCGH com a tècnica de primera opció diagnòstica en aquestes i altres indicacions (epilèpsia, talla baixa).
Per assolir aquest objectiu, s'han estudiat 1.000 pacients afectats de les patologies abans esmentades mitjançant la tècnica de aCGH, utilitzant una estratègia d'hibridació pacient versus pacient i afegint el suport de la tècnica de MLPA en el 50% dels pacients estudiats.
En primer lloc es va validar la tècnica i es va escollir la plataforma d’oligoarrays. Per tal de minimitzar costos i incrementar la eficiència, es va utilitzar l’estratègia d’hibridació de pacient versus pacient amb MLPA confirmatòria i es van establir criteris de diagnòstic per optimitzar la detecció de desequilibris patogènics. Per facilitar la interpretació dels resultats es va dissenyar un programa informàtic EasyArray.
Es van detectar desequilibris d'efecte patogènic en un 14% dels pacients (140 / 1.000). En funció del fenotip es van diagnosticar un 18,9% dels pacients afectats de RGD / DI; un 13,7% de les MC; un 9,75% de les patologies psiquiàtriques, 1 7,01% dels casos amb epilèpsia i un 13,3% dels pacients amb talla baixa. Dins de les MC destaquen les del sistema nerviós central amb un 14,9% i les cardiopaties congènites amb un 10,6% de diagnòstics. Dins de les patologies psiquiàtriques, destaquen els pacients amb TEA amb un 8.9% de diagnòstics.
Podem concloure que la tècnica d’arrayCGH té un rendiment diagnòstic molt superior al del cariotip amb bandes G. La seva utilització com a eina diagnòstica de primera opció juntament amb el disseny d’estratègies d’hibridació no estàndards, suposa una reducció considerable de costos.
Els nostres resultats demostren l'efectivitat i eficiència de la utilització de l’arrayCGH com a primera opció en el diagnòstic genètic dels pacients amb sospita de desequilibris genòmics. Tot això avala la seva inclusió dins del Sistema Nacional de Salut.Conventional cytogenetics diagnoses 3-5% of patients with unexplained developmental delay / intellectual disability (DD / ID) and / or multiple congenital Anomalies (MCA). Multiplex ligation probes Amplification (MLPA) increases diagnostic rate between 2.4 to 5.8%. Currently the array comparative genomic Hybridization (CGH) is the highest performing diagnostic tool in patients with DD / ID, MC and autism spectrum disorders. Our aim was to evaluate the efficiency of the use of aCGH as first-line test replacing the karyotype and MLPA in these and other pathological indications (epilepsy, short stature). A total of 1000 patients referred by one or more of the above mentioned disorders were analysed by aCGH using a methodology / strategy hybrid alternative patient versus patients adding support MLPA technique in 50% of patients studied. Following a validation period, an oligoarray platform was chosen. In order to minimize costs and increase efficiency, a patient versus patient hybridization strategy plus MLPA confirmation was used, and analysis criteria were set to optimise detection of pathogenic imbalances. In order to facilitate interpretation of results, a database application named Easy Array was designed. Pathogenic genomic imbalances were detected in 14% of the cases (140/1000), with a variable distribution of diagnosis according to the phenotypes: 18.9% of patients with DD / ID, 13.7% of MCAS, 9.75% of Psychiatric pathologies, 7.01% of patients with Epilepsy and 13.3% of patients with short Stature. Within the MCA, central nervous system abnormalities and congenital heart diseases accounted for 14.9% and 10.6% of diagnosis respectively. Among the Psychiatric disorders, patients with ASD accounted for 8.9% of diagnosis. We can conclude that Array-CGH provides a substantially higher diagnostic yield tan G-banded chromosomes analysis. Its use as first line test and the development of non-standard hybridization strategies reduces consumable costs considerably. Our results demonstrate the effectiveness and efficiency of the use of arrayCGH as the first line test in genetic diagnosis of patients suspected of genomic imbalances, supporting its inclusion within the National Health System.
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Kim, Mee Hye. "Optimisation and application of comparative genomic hybridisation (CGH) in cancer cytogenetics." Thesis, University of Glasgow, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.272858.
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Zhang, Yunyu. "Hidden Markov Model inference copy number change in array-CGH data." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/33086.
Full textAbstract:
Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2005.Includes bibliographical references (p. 56-57).
Cancer development and progression typically features genomic instability frequently resulting in genomic changes involving DNA copy number gains or losses. Identifying the genomic location of these regional alterations provides important opportunities for the discovery of potential novel oncogenes and tumor suppressors. Recently, array based competitive genomic hybridization (array-CGH) has become available as a powerful approach for genome-wide detection of DNA copy number changes. Array-CGH assesses DNA copy number in tumor samples through competitive hybridization on microarrays containing probes for thousands of genes. The datasets generated are complex and require statistical methods to accurately define discrete and uniform copy number from the data and to identify transitions between genomic regions with altered copy number. Several approaches based on different statistical frameworks have been developed. However, a fundamental informatic issue in array-CGH analysis remains unsolved by these methods. In particular, sample-specific data compression, a result of tumor cells being commonly admixed with normal cells in many tumor types, must be accounted for in each sample analyzed. Additionally, in order to accurately assess deviations from normal copy number, the copy number readout must be shifted to faithfully represent the baseline copy number in each tumor sample. Failure to appropriately address these issues reduces the accuracy of the data in hard-threshold based high-level analysis.
(cont.) By using the natural framework Hidden Markov Models (HMM) to model the distribution of array-CGH signals, a method infer the absolute copy number and identify change points has been developed to address the above problems. This method has been validated on independent dataset and its utility in inference on array-CGH data is demonstrated here.
by Yunyu Zhang.
S.M.
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Jaillard-Herrebrecht, Sylvie. "Place de la CGH-array dans l'étude des anomalies du développement." Rennes 1, 2010. http://www.theses.fr/2010REN1B141.
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Larré, Stéphane. "Anomalies cytogénétiques impliquées dans la carcinogénèse des tumeurs urothéliales et application clinique." Thesis, Paris Est, 2010. http://www.theses.fr/2010PEST0046.
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Les carcinomes urothéliaux représentent la 4ème cause de cancer chez l'homme après les cancers de la prostate, du colon et du poumon. Leur incidence est en augmentation de plus de 50% depuis 25 ans. Ce cancer présente principalement deux formes, une superficielle (70% des cas) de bon pronostic et une invasive (30%) de mauvais pronostic. Les formes superficielles nécessitent une surveillance active rapprochée afin d'identifier les récidives fréquentes et l'évolution vers un stade invasif. Cette surveillance fait principalement appel à la cystoscopie et engendre morbidité et cout importants. Une alternative à la cystoscopie est possible à l'aide de tests de détection urinaire des cellules cancéreuses, mais leur sensibilité jusqu'à présent n'est pas suffisante pour une utilisation en pratique courante. Notre but a été de développer un outil de détection urinaire des tumeurs urothéliales.Matériel, Méthode et RésultatsLes tumeurs urothéliales étant très instables sur le plan génétique, le travail a initialement consisté à faire la synthèse des anomalies cytogénétiques retrouvées dans la littérature. Les anomalies les plus pertinentes ont été sélectionnées et une puce de CGH en a été développée comprenant 341 clones (BAC) répartis sur l'ensemble des chromosomes. Cette puce intitulée BCA-1 a été développée en collaboration avec la société ArrayGenomics (Voisins Le Bretonneux, France). La validité de ce test a été confirmée sur 10 lignées cellulaires tumorales et bénignes.Notre travail a ensuite consisté à étudier la valeur ajoutée de cette puce en pratique clinique. Pour ce faire, une cohorte de 163 patients porteurs de tumeurs urothéliales et de témoins a été constituée. Les urines ont été prélevées et analysées en utilisant la puce BCA-1. Un logiciel a été développé sous filemaker pro afin de permettre une saisie uniforme et détaillée des données cliniques et de prendre en considération le caractère complexe de la prise en charge de ces tumeurs.Le test urinaire utilisant la puce de CGH a montré une excellente performance diagnostique avec une sensibilité de 96% et une spécificité de 98% dans les tumeurs vésicale, et une sensibilité de 100% tumeurs du haut appareil urinaire.Enfin, le test a aussi permit de caractériser le caractère agressif ou non agressif des tumeurs sur le plan cytogénétique. Cette caractérisation est fortement corrélée avec le stade anatomopathologique et un troisième aspect de notre travail a montré que la détermination cytogénétique de l'agressivité des tumeurs prédisait l'évolution défavorable des tumeurs du haut appareil urinaire. Notre travail a permis le développement et l'analyse d'un nouveau test de dépistage urinaire des tumeurs urothéliales permettant le diagnostic urinaire de ces tumeurs et la caractérisation de leur caractère agressif éventuel, ainsi que le développement d'un logiciel de saisie et d'analyse des données cliniquesUrothelial carcinomas are the 4th cause of cancer in men, following prostate, colon and lung cancer. An increase of 50% in its incidence was observed on the last 25 years. This cancer presents two types, a superficial type (70% of the cases) of good prognosis and an invasive type (30% of the cases) of bad prognosis. Superficial type require an active monitoring to identify recurrences and evolution to an invasive stage. This follow up is performed using cystoscopy and leads to some level of morbidity and a high cost. An alternative to cystoscopy is possible using urine test to detect cancer cells, but they are lacking of sensitivity to be used instead of cystoscopy in clinical practice. Our goal was to develop a urine detection tool of urothélial carcinomas.Material and MethodsUrothelial carcinoma usually present with a high level of genetic instability. We first analyse literature so to identify most relevant cytogenetic abnormalities that occur in urothélial carcinomas. A CGH array chip was designed using 341 clones (BAC) that were selected according to initial analysis. This chip called BCA-1 covers the whole genome and was developed in collaboration with ArrayGenomics (Voisins Le Bretonneux, France).ResultsThis test has shown a good efficacy on a preliminary study of cytogenetic analysis on 10 cancerous and benign bladder cell lines. The Chip was then assessed in clinical practice on a series of 163 patients diagnosed with or without urothelial cancer. Urines were collected and analysed using the BCA-1 chip. A software was designed to favour homogeneous and detailed clinical data collection and take into consideration the complex management of the tumours.The test using the CGH chip as shown an excellent diagnosis performance with a sensitivity of 96% and a specificity of 98% for bladder cancer detection, and a sensitivity of 100% on upper urinary tract detection.Finaly, the test was able to define the grade of the tumour according to cytogenetic loci affected. This grade was strongly correlated with the pathology score and could be used to predict outcomes in upper urinary tract carcinomas. Our work lead to the developpement and the analysis of a new urothélial carcinoma urinary detection test, to the identification of the agressivity of the tumour, and to the development of an analysis and data entry software for clinical details
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Grzesiuk, Juliana Dourado. "Caracterização Citogenética Molecular de Rearranjos Cromossômicos Aparentemente Equilibrados Associados ao Fenótipo de Infertilidade." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-22042013-151132/.
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A translocação recíproca é o rearranjo equilibrado mais comum em humanos. Frequentemente, indivíduos com rearranjos equilibrados não apresentam manifestações clínicas, entretanto, na meiose, o pareamento entre cromossomos translocados forma uma figura quadrivalente em forma de cruz que torna a disjunção cromossômica incerta e dependendo do rearranjo, o individuo pode vir a ser infértil, apresentar um risco aumentado de abortamento espontâneo e/ou da prole apresentar alterações fenotípicas. Neste projeto, investigamos duas famílias de pacientes inférteis, portadores de translocações cromossômicas. O objetivo foi caracterizar as alterações citogenéticas e citogenômicas relacionadas à infertilidade masculina em pacientes portadores de rearranjos aparentemente equilibrados, associando técnicas de citogenética clássica (bandeamento GTG), citogenética molecular (FISH) e citogenômica (array-CGH). Foram estudados sete indivíduos da família 1, sendo diagnosticados três portadores da translocação (X;22), sendo um deles azoospérmico. Nesta família foram ainda detectados dois casos de mosaicismo para síndrome de Turner. A família 2 foi composta por dois irmãos oligozoospérmicos, portadores de translocação (8;13). Com a aplicação da técnica de FISH, definimos o cariótipo final dos portadores dos rearranjos como 46,XX ou 46,XY,t(X;22)(p22.3;q11.2) para a família 1 e 46,XY,t(8;13)(q13;q14)para a família 2. A técnica de array-CGH (plataforma 2x400K, Agilent) detectou alterações no número de cópias de alguns genes candidatos relacionados ao fenótipo de infertilidade, sendo a sequência 132 de piRNAs, os genes DDX11, Jagged 2 e ADAM18 na família 1 e os genes candidatos ADAM18 e POTE nos pacientes da família 2.Reciprocal translocations are the most common balanced rearrangement in humans. Often individuals with balanced rearrangements show no clinical findings. However, in meiosis, the pairing between translocated chromosomes forms a quadrivalent cross-shaped figure which has the effect of making chromosome disjunction uncertain and, depending on the rearrangement, and on the segregation of the unbalanced chromosomes, the individual can be infertile, can present with an increased risk of spontaneous abortions or can have an offspring with abnormal phenotype. We have studied two families of infertile patients, who were carriers of chromosomal translocations. The objective was to characterize the cytogenetic and cytogenomic alterations related to male infertility in patients with apparently balanced rearrangements using classical cytogenetic techniques (GTG banding), molecular cytogenetics (FISH) and cytogenomics (array-CGH). Seven subjects of the family 1 were studied, including three carriers of translocation (X;22), one azoospermic. Two cases of mosaicism for Turner syndrome were detected in this family. The second family consisted of two oligozoospermic brothers with translocation (8;13). FISH was used to characterize the karyotypes as 46, XX or 46,XY, t(X;22)(p22.3;q11.2) for the members of the family 1 and 46,XY,t(8;13)(q13;q14) for family 2. Array-CGH was also performed using the Agilent platform 2x400K, to detect associated copy number variations of some of the candidate genes that could be related to infertility. In the family 1 the candidate genes were 132 piRNAs sequences and DDX11,Jagged 2 and ADAM18 genes. The candidate genes for the family 2 were ADAM18 and POT.
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Picard, Franck. "Segmentation/classification de processus. Application a l'analyse de donnees de microarrays CGH." Phd thesis, Université Paris Sud - Paris XI, 2005. http://tel.archives-ouvertes.fr/tel-00116025.
Full textAbstract:
Dans cette thèse nous proposons un nouveau modèle statistique pour l'analyse des problèmes de segmentation/classification dont l'objectif est de partitionner des données en zones homogènes, et de regrouper ces zones en un nombre fini de classes. Les problèmes de segmentation/classification sont traditionnellement étudiés à l'aide
des modèles de chaînes de Markov cachées. Nous proposons un modèle alternatif qui combine un modèle de segmentation et un modèle de mélange.
Nous construisons notre modèle dans le cas gaussien et nous proposons une généralisation à des variables discrètes dépendantes. Les paramètres de ce modèle sont estimés par maximum de vraisemblance à l'aide d'un algorithme hybride fondé sur la programmation dynamique et sur l'algorithme EM. Nous abordons un nouveau problème de sélection de modèle qui est la sélection simultanée du nombre de groupes et du nombre de segments et proposons une heuristique pour ce choix.
Notre modèle est appliqué à l'analyse de données issues d'une nouvelle technologie, les microarrays CGH (Comparative Genomic Hybridization). Cette technique permet de compter le nombre de milliers de gènes le long du génome en une seule expérience. L'application de notre méthode à ces données permet de localiser des zones délétées ou amplifiées le long des chromosomes. Nous proposons également une application à l'analyse des séquences d'ADN pour l'identification de régions homogènes en terme de composition en nucléotides.
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Glentis, S. "Whole genome amplification for PGD and PND : molecular and a-CGH diagnosis." Thesis, University College London (University of London), 2009. http://discovery.ucl.ac.uk/18554/.
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Whole genome amplification amplifies the entire genome in a few hours from samples of minimal DNA quantities, even from single cells. This may have many applications, especially in prenatal diagnosis, PGD and PGS. The hypothesis for chapter 3 was: Can multiple displacement amplification (MDA) be used as a universal step prior to molecular analysis for PGD? WGA using MDA (Qiagen) was used on single cells in order to overcome the problem of limited DNA in PGD. MDA allows the diagnosis through haplotyping or a combination of direct and indirect mutation analysis. Different cell types, including buccal cells, lymphocytes, fibroblasts and blastomeres were examined. A modification on the cell lysis buffer was also tested in order to achieve more accurate results. PGD seems to benefit from MDA when multiple tests are performed for direct and indirect analysis. The modified lysis buffer (exclusion of DTT) produced better results than the other lysis buffers and buccal cells do not produce as accurate results as other cell types. The hypothesis was met as the amount of DNA produced by MDA can be used for direct and indirect testing and haplotyping. The hypothesis for chapter 4 was: Is it possible to accurately assess the chromosomes of a single cell by a-CGH? WGA was achieved by MDA and GenomePlex (Sigma) on single lymphocytes, fibroblasts and blastomeres prior to a-CGH analysis. The difficulty of this technique was the high background noise that was produced by WGA that makes interpretation difficult. Different lysis buffers, modifications of the WGA reaction and analysis software were examined for better results. A-CGH slides from different companies and institutions were used. The results showed that GenomePlex produced less background noise compared to MDA but the amplification efficiency of the technique was less reliable. The BlueGnome Cytochip arrays produced the best compared to arrays from any other companies or institutions. More experiments would be necessary to determine if the hypothesis was met as a number of chromosomal abnormalities detected were not always confirmed by other experiments. The hypothesis for chapter 5 was: Can aneuploidy be detected in coelomic fluid using a-CGH? The possibility of using WGA and a-CGH on coelomic fluid was tested as this could be used as an early form of prenatal diagnosis. Coelomic fluid was collected between the 5th and 11th week of pregnancy from women undergoing termination of pregnancy. MDA and GenomePlex were used to amplify the DNA prior to a-CGH analysis. Both genomic (high resolution) and constitutional (low resolution) arrays were tested. The results showed that aneuploidy can be detected by a-CGH. BlueGnome Cytochip slides produced the best results. A triploid sample was detected as normal. The hypothesis was met and even higher resolution could be achieved with the use of GenomePlex and BlueGnome Cytochip arrays. WGA may be very important for downstream genetic tests when the DNA is from very low quality and quantity. Further optimisation of the technique is needed in order to achieve similar results to those of good quality genomic DNA. Arrays from different companies or institutions may produce very different results. In conclusion, the results showed that WGA can benefit PGD and PND, and a-CGH gives great potential to PGS and coelomic fluid diagnosis.
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Picard, Franck. "Segmentation-classification de processus : application à l'analyse des données de microarrays CGH." Paris 11, 2005. http://www.theses.fr/2005PA112186.
Full textAbstract:
Dans cette thèse nous proposons un nouveau modèle statistique pour l'analyse des problèmes de segmentation/classification dont l'objectif est de partitionner des données en zones homogènes, et de regrouper ces zones en un nombre fini de classes. Les problèmes de segmentation/classification sont traditionnellement étudiés à l'aide des modèles de chaînes de Markov cachées. Nous proposons un modèle alternatif qui combine un modèle de segmentation et un modèle de mélange. Nous construisons notre modèle dans le cas gaussien et nous proposons une généralisation à des variables discrètes dépendantes. Les paramètres de ce modèle sont estimés par maximum de vraisemblance à l'aide d'un algorithme hybride fondé sur la programmation dynamique et sur l'algorithme EM. Nous abordons un nouveau problème de sélection de modèle qui est la sélection simultanée du nombre de groupes et du nombre de segments et proposons une heuristique pour ce choix. Notre modèle est appliqué à l'analyse de données issues d'une nouvelle technologie, les microarrays CGH (Comparative Genomic Hybridization). Cette technique permet de compter le nombre de milliers de gènes le long du génome en une seule expérience. L'application de notre méthode à ces données permet de localiser des zones délétées ou amplifiées le long des chromosomes. Nous proposons également une application à l'analyse des séquences d'ADN pour l'identification de régions homogènes en terme de composition en nucléotidesThis thesis is devoted to the development of a new statistical model for segmentation/clustering problems. The objective is to partition the data into homogeneous regions and to cluster these regions into a finite number of groups. Segmentation/clustering problems are traditionally studied with hidden Markov models. We propose an alternative model which combines segmentation models and mixture models. We construct our model in the Gaussian case and we propose a generalization to discrete dependent variables. The parameters of the model are estimated by maximum likelihood with a hybrid algorithm based on dynamic programming and on the EM algorithm. We study a new model selection problem which is the simultaneous selection of the number of clusters and of the number of segments. We propose a heuristic for this choice. Our model is applied to the analysis of CGH microarray data (Comparative Genomic Hybridization). This technique is used to measure the number of thousands of genes on the genome in one experiment. Our method allows us to localize deleted or amplified regions along chromosomes. We also propose an application to the analysis of DNA sequences for the identification of homogeneous regions in terms of nucleotide composition
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Fuhrmann, Christine. "Entwicklung der Array-CGH zur hochauflösenden, genomweiten Untersuchung von DNA-Veränderungen einzelner Tumorzellen." Diss., lmu, 2008. http://nbn-resolving.de/urn:nbn:de:bvb:19-89535.
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Davey, Robert Paul. "Refinement and validation of algorithms for deduction of gene content from CGH microarrays." Thesis, University of East Anglia, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.429607.
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Morris, J. A. "A bioinformatics framework for management and analysis of high throughput CGH microarray projects." Thesis, University College London (University of London), 2012. http://discovery.ucl.ac.uk/1364856/.
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High throughput experimental techniques have revolutionised biological research; these techniques enable researchers, in an unbiased fashion to survey entire biological systems such as all the somatic mutations in a tumour in a single experiment. Due to the often complex informatics demands of these techniques, robust computational solutions are required to ensure high quality reproducible results are generated. The challenge of this thesis was to develop such a computational solution for the management and analysis of high throughput microarray Comparative Genomic Hybridisation (aCGH) projects. This task also provided an opportunity to test the hypothesis that agile software development approaches are well suited for bioinformatics projects and that formalised development practices produce better quality software. This is an important question as formalised software development practices have been underused so far in the eld of bioinformatics. This thesis describes the development and application of a bioinformatics framework for the management and analysis of microarray CGH projects. The framework includes: a Laboratory Information Management System (LIMS) that manages and records all aspects of microarray CGH experimentation; a set of easy to use visualisation tools for aCGH experimental data; and a suite of object oriented Perl modules providing a exible way to construct data pipelines quickly using the statistical programming language R for quality control, normalisation and analysis. In order to test the framework, it was successfully applied in the aCGH pro ling of 94 ovarian tumour samples. Subsequent analysis of these data identi ed 4 well supported genomic regions which appear to in uence patient survival. The evaluation of agile practices implemented in this thesis has demonstrated that they are well suited to the development of bioinformatics solutions as they enable developers to react to the changes of this rapidly evolving eld, to create successful software solutions such as the bioinformatics framework presented here.
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Fuhrmann, Christine. "Entwicklung der Array-CGH zur hochauflösenden, genomweiten Untersuchung von DNA-Veränderungen einzelner Tumorzellen." kostenfrei, 2008. http://edoc.ub.uni-muenchen.de/8953/.
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Richard, Frank. "Chromosomale Imbalancen invasiv duktaler und invasiv lobulärer Mammakarzinome detektiert mittels komparativer genomischer Hybridisierung (CGH)." [S.l.] : [s.n.], 1999. http://deposit.ddb.de/cgi-bin/dokserv?idn=96200166X.
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Richard, Frank. "Chromosomale Imbalancen invasiv duktaler und invasiv lobulärer Mammakarzinome detektiert mittels komparativer genomischer Hybridisierung (CGH)." Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 1999. http://dx.doi.org/10.18452/14599.
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Das Ziel der vorliegenden Arbeit bestand in der molekularzytogenetischen Charakterisierung von invasiv duktalen und invasiv lobulären Mammakarzinomen sowie der Identifizierung unterschiedlicher genetischer Alterationsmuster in Tumorsubgruppen der invasiv duktalen Mammakarzinome. Mit Hilfe der komparativen genomischen Hybridisierung (CGH) wurden 30 invasiv duktale und 20 invasiv lobuläre Mammakarzinome auf genetische Veränderungen untersucht. In beiden Tumorarten überwiegen DNA-Deletionen gegenüber DNA-Gewinnen, daher scheint die Inaktivierung tumorsupprimierender Gene einen größeren Einfluß auf das maligne Wachstumsverhalten auszuüben. Invasiv duktale Mammakarzinome zeichnen sich durch eine im Mittel größere Anzahl an Alterationen pro Tumorfall aus als invasiv lobuläre Karzinome (14,9 vs. 8,9). Neben einer größeren Anzahl an DNA-Verlusten ist auch die Anzahl der DNA-Überrepräsentierungen deutlich höher verglichen mit invasiv lobulären Mammakarzinomen (6,2 pro Tumorfall vs. 2,7 pro Tumorfall). DNA-Gewinne auf Chromosom 1q und DNA-Verluste auf den Chromosomen 6q, 11q22- qter und 13q fanden sich in >=40% der Fälle in beiden histologischen Tumortypen. In invasiv duktalen Mammakarzinomen traten DNA-Gewinne mit größerer Frequenz auf den Chromosomen 6p, 8q, 11q13, 16p, 17q, 19p/q und 20q auf. Ebenfalls häufiger waren DNA-Deletionen auf den Chromosomen 2q, 3p, 4p/q, 5q, 7p, 8p, 9q, 10q und 15q zu finden. DNA-Verluste auf den Chromosomen 16q, 17p, 18q und 22q wurden dagegen vermehrt in invasiv lobulären Karzinomen detektiert. Gut (G1) und schlecht (G3) differenzierte invasiv duktale Mammakarzinome zeichnen sich durch ein unterschiedliches genetisches Muster aus. Während gut differenzierte Tumore durch DNA-Gewinne auf 1q, 11q11-13, 16p und 20q gekennzeichnet sind, weisen die schlecht differenzierten Tumore zusätzlich DNA-Deletionen im Bereich der Chromosomen 5q, 18q und 21q21 auf. Außerdem läßt sich ein unterschiedliches genetisches Muster bei Östrogenrezeptor- positiven und Östrogenrezeptor-negativen invasiv duktalen Mammakarzinomen feststellen. Die Östrogenrezeptor-negativen Tumore zeigen eine größere Anzahl an Alterationen, dazu gehören zusätzliche DNA-Überrepräsentierungen auf 1p, 6p und 22q und DNA-Verluste der Chromosomen 5q, 7p, 8p und 12q. Somit läßt sich feststellen, daß sich invasiv duktale und invasiv lobuläre Mammakarzinome durch ein wiederkehrendes Muster chromosomaler Veränderungen charakterisieren lassen.The aim of the study was to analyze invasive ductal and invasive lobular breast carcinomas regarding to molecular DNA imbalances as well as different DNA imbalances in tumor subgroups of the invasive ductal carcinomas. Comparative genomic hybridization (CGH) was applied to analyze 30 invasive ductal and 20 invasive lobular breast carcinomas to carry out genetic alterations. In both tumor subgroups, DNA losses showed a higher incidence compared to DNA gains, suggesting a higher influence of inactivation of tumor suppressor genes in tumor progression. Invasive ductal carcinomas showed a higher incidence of alterations per case compared to invasive lobular carcinomas (14,9 vs. 8,9). Besides a higher incidence of DNA losses, particularly DNA gains were statistically significant in invasive ductal carcinomas (6,2 per tumorcase vs. 2,7 per tumorcase). DNA gains on chromosome 1q and DNA losses on chromosomes 6q, 11q22-qter and 13q were investigated in >=40% of all tumor cases. DNA gains were observed with a higher frequency in invasive ductal carcinomas on 6p, 8q, 11q13, 16p, 17q, 19p/q and 20q. Additionally, DNA losses showed a higher incidence on 2q, 3p, 4p/q, 5q, 7p, 8p, 9q, 10q and 15q compared to invasive lobular carcinomas. In contrast, DNA losses on 16q, 17p, 18q and 22q reached statistical significance in invasive lubular carcinomas. Well-differentiated (G1) and poorly differentiated (G3) invasive ductal carcinomas reflected different genetic imbalances. Well-differentiated carcinomas are associated with DNA gains on 1q, 11q11-13, 16p and 20q, whereas poorly differentiated tumors showed additional DNA losses on 5q, 18q and 21q21. Furthermore, the investigation indicated that the average number of alterations is correlated also to the estrogen receptor content of the invasive ductal carcinomas. Tumors with estrogen receptor negative content showed a higher incidence of alterations on the following regions, i.e., DNA gains on 1p, 6p and 22q and DNA losses on 5q, 7p, 8p and 12q. Consequently, invasive ductal and invasive lobular carcinomas are characterized by distinct patterns of chromosomal alterations.
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Goeze, Almut. "Charakterisierung chromosomaler Imbalancen in Adenokarzinomen der Lunge mit Hilfe der Comparativen genomischen Hybridisierung (CGH)." Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 2000. http://dx.doi.org/10.18452/14568.
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Das Adenokarzinom ist weltweit das häufigste nicht-kleinzellige Lungenkarzinom mit ansteigender Inzidenz insbesondere bei Frauen. Zur genetischen Analyse dieses Tumortyps haben wir 60 Fälle mittels der Comparativen Genomische Hybridisierung (CGH) untersucht, dabei wurden 60 Primärtumoren und von 10 Fällen zusätzlich 23 Metastasen (pro Primärtumor max. 4 korrespondierende Metastasen) analysiert. Bei den 60 Primärtumoren wurden folgende Veränderungen in über 50% der Fälle beobachtet: Deletionen auf den Chromosomen 3p, 4p, 4q, 5q, 6q, 8p, 9p, 9q, 13q, 15q und 18q sowie Überrepräsentationen auf den Chromosomen 1q, 5p, 8q, 11q. 17q. 19q und 20q. Häufigste Veränderung war die Überrepräsentation auf Chromosom 1q22-q23 (73,3%), gefolgt von Überrepräsentationen auf den Chromosomen 20q11.2-q13.2 (66,7%) und 8q23-q24.1 (61,7%) und Deletionen auf 3p22-p21 (61,7% ), 4q26-q28 (63,3%), 6q16 (60,0%), 6q22 (60,0%), 9p13-p21 (63,3%), 13q21 (68,3%) und 13q31 (68,3%). Beim statistischen Vergleich mittels c2-Test von 24 nicht-metastasierten Primärtumoren mit der Gruppe von 23 metastasierten Primärtumoren und 10 Metastasen waren folgende Veränderungen statistisch signifikant mit Metastasierung verbunden: Deletionen von 3p22-p25, 4p13-p15.1 und 17p12-p13 sowie Überrepräsentationen von 1q21, 11q12-13, 14q11.1-q13, 15q24 und 20q12-13.1. Statistisch signifikant häufiger mit dem nicht-metastasierten Phänotyp assoziiert waren dagegen folgende Veränderungen: Deletion von 19p13.1-p13.3 und Überrepräsentationen von 3p12-p14 , 4q26-q28 und 5p14. Die Analyse der Primärtumoren und ihrer korrespondierenden Metastasen konnten in jedem Fall einen klonalen Zusammenhang aufzeigen. Zusammenfassend sind Adenokarzinome der Lunge durch wiederkehrende Muster chromosomaler Veränderungen charakterisiert, die eine Korrelation zwischen Tumor-Genotyp und -Phänotyp ermöglichen.Adenocarcinomas are the most common non small cell lung carcinomas worldwide with increasing incidence especially in women. For the genetic analysis of this tumor type we screened 60 primary tumors and additionally 23 metastases from 10 cases (4 corresponding metastases per primary tumor as maximum) by Comparative Genomic Hybridization (CGH). The following alterations were found in over 50% of the 60 primary tumors: Deletions on chromosomes 3p, 4p, 4q, 5q, 6q, 8p, 9p, 9q, 13q, 15q, and 18q as well as overrepresentations on chromosomes 1q, 5p, 8q, 11q. 17q. 19q und 20q. The most frequent alteration was the overrepresentation on chromosome 1q22-q23 (73,3%), followed by overrepresentations on chromosomes 20q11.2-q13.2 (66,7%), and 8q23-q24.1 (61,7%), and deletions on 3p22-p21 (61,7% ), 4q26-q28 (63,3%), 6q16 (60,0%), 6q22 (60,0%), 9p13-p21 (63,3%), 13q21 (68,3%), and 13q31 (68,3%). At the comparison between 24 non metastasizing primary tumors versus 23 metastasizing tumors and 10 metastases the following changes were statistically significant (c2 test) associated with the metastasizing phenotype: deletions on chromosomes 3p22-p25, 4p13-p15.1, and 17p12-p13, as well as overrepresentations on 1q21, 11q12-13, 14q11.1-q13, 15q24, and 20q12-13.1 whereas the deletion on chromosome 19p13.1-p13.3 and overrepresentations on chromosomes 3p12-p14 , 4q26-q28, and 5p14 were associated with the non metastasizing phenotype. A clonal relationship could be shown in every case with primary tumor and corresponding metastases. In summary, adenocarcinomas of the lung are characterized by recurrent patterns of chromosomal imbalances allowing a correlation between tumor genotype and tumor phenotype.
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Rooney, Patrick Hugh. "A genomic approach to the study of chemoresistance." Thesis, University of Aberdeen, 2000. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU602009.
Full textAbstract:
This study evaluated comparative genomic hybridisation (CGH) as a tool to detect candidate regions of the genome associated with chemoresistance. Using a variation on conventional CGH, DNA from three cell lines that were resistant to thymidylate synthase (TS) inhibitors (tomudex [TDX] or 5-fluorouracil [5-FU]) and their sensitive parent cells were evaluated. In MCF-7 and H630, cells that were resistant to TDX, a specific TS inhibitor with no other known cytotoxic potential, only a single region of change (18p gain) was apparent. The third cell line H630R10, which was resistant to 5-FU, had changes in several genomic regions following the acquisition of resistance, including 18p. Gain in the chromosomal region containing the TS gene (18pll.32) was detected by CGH in all three resistant cell lines. However, additional novel regions of interest were identified in the cells that were resistant to 5-FU, a cytotoxic agent known to have several other modes of cytotoxicity besides TS inhibition. These results suggested that CGH is of potential use in the detection of regions of the genome involved in chemoresistance. Having shown the potential of CGH as a tool for assessing chemoresistance at the genomic level, steps toward clinical application of this technique were evaluated. A prerequisite for study in archival pathology samples was successful DNA extraction and universal amplification of tumour DNA from paraffin-embedded tumour sections for CGH analysis. Degenerate oligonucleotide primed - polymerase chain reaction (DOP-PCR) was performed on minute quantities (50ngs) of fresh cell line DNA (H630R10) and tumour DNA (osteosarcoma), as well as paraffin-embedded DNA from the same case. The results of these DOP-PCR CGH reactions were compared with conventional CGH using l|0.g quantities of fresh DNA from both H630R10 cell line and osteosarcoma. The CGH profiles of the conventional CGH and DOP-PCR CGH did not show a high level of concordance, only 55% of the gains and 83.3% of losses detected by conventional CGH were detected by DOP-PCR CGH The use of universal amplification by DOP-PCR in paraffin-embedded sections was not taken forward into clinical evaluation. A study of colorectal cancer (CRC) was initiated which involved the microdissection of 29 Dukes' C CRC tumours from fresh frozen material for CGH analysis. This conventional CGH analysis of CRC tumours involved assessing each tumour twice by reversal of fluorochromes. Only genomic regions that were detected as changed in both forward and reverse profiles were accepted. This approach detected several regions of genome as changed across the 29 tumours. In all, 108 gains (a mean number of 3.7 aberrations per tumour, range 1-12) and 85 losses (a mean number of 2.9 aberrations per tumour, range 0-11) were detected in the 29 tumours. CGH analyses identified certain chromosomal regions as more likely to be changed than others. The most frequent aberrations detected across the 29 tumours was a loss of chromosomal arm 18q, seen in 31% of the tumours assessed. Gain was also common at some sites throughout the genome, for example, gain of chromosomal arms, 13q and 20q was seen in 27.6% of cases. Mann-Whitney U tests investigating the association between specific chromosomal aberrations such as gain of 20q or loss of 18q and known markers of CRC tumourigenesis (p53, p27, p21, Rb, cyclin Dl, PCNA, P-catenin, e-cadherin, c-erbB-2, bcl2, EGFR and c-erbB-2) assessed by immunohistochemistry (IHC) in 29 tumours found no association. Testing of the total number of genomic aberrations detected (loss + gain = genetic grade) rather than the frequency of aberration at specific chromosomal loci also found no association with the CRC tumour markers. Finally, the association between the chromosomal aberrations detected by CGH was investigated in relation to patient survival. This thesis has demonstrated the value of a global approach to the study of chemoresistance and tumourigenesis through the application of powerful technology such as CGH.
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Piard, Juliette. "Déficience intellectuelle : identification de nouveaux gènes par une approche multicentrique." Thesis, Bourgogne Franche-Comté, 2018. http://www.theses.fr/2018UBFCE005.
Full textAbstract:
La déficience intellectuelle (DI) touche 1 à 3% de la population générale avec un excès de sujets de sexe masculin. Cette affection est caractérisée par une extrême hétérogénéité clinique et génétique rendant son élucidation complexe. La révolution technologique des outils permettant l’analyse du génome intervenue depuis les années 2000 avec l’analyse chromosomique sur microréseau et singulièrement depuis 2010 avec les applications du séquençage à haut débit a considérablement facilité l’identification de nouveaux gènes. Nous avons tiré avantage de ce phénomène pour identifier trois affections neurologiques à caractère familial Nous avons procédé selon une méthodologie structurée pour conduire, grâce à la mise en place d’un réseau de collaborations, à la découverte ou à la confirmation de l’existence de nouvelles formes de DI. 1.Séquençage de l'exome couplé à la recherche de variations du nombre de copies 2. Mise à jour d’une altération de séquence génique potentiellement causale retrouvée chez le cas index et chez les autres sujets atteints de la famille 3.Extension des résultats à d’autres familles par la constitution d’une cohorte de réplication 4.Élaboration d’une série d’études fonctionnelles venant conforter l’hypothèse de causalité par la création d’un modèle animal et/ou la réalisation d’études biochimiques spécifiquesL’application de cette méthodologie nous a permis de conduire à terme trois projets : L’individualisation d’une forme syndromique de DI récessive autosomique associée à une malformation du rachis cervical et liée aux mutations bi-alléliques de CDK10. La caractérisation d’une encéphalopathie récessive autosomique létale associée à une hypertonie sévère et à une arthrogrypose distale liée aux mutations bi-alléliques d’ATAD1. L’implication de FRMPD4 dans une nouvelle forme de DI non syndromique liée à l’XIntellectual disability (ID) impacts 1 to 3% of the general population with an excess of affected males. This condition is characterized by an extreme clinical and genetic heterogeneity making the deciphering of its causes more complex. The technological revolution that took place in the study of the genome over the last two decades has provided a useful tool for identification of new genetic entities. This is particularly true for chromosomal micro-array analysis since early 2000s and for next generation sequencing since 2011. We took advantage of this by identifying the molecular basis of three singular conditions. We applied a structured methodology and created a network of collaborations to define or confirm these new ID syndromes. 1. Whole exome sequencing alongside with array-CGH 2.Identification of a candidate gene sequence alteration in the index case and other affected patients of the family 3.Constitution and study of a replication cohort 4.Biochemical studies and/or animal models in order to support the assumption of causalityBased on this research strategy, we were able to complete the following projects : Discovery of a syndromic form of autosomal recessive ID associated with cervical spine defects due to bi-allelic CDK10 mutations. Identification of an ATAD1-related profound and lethal autosomal recessive encephalopathy with stiffness and distal arthrogryposis. Characterization of a FRMPD4-related X-linked non-syndromic ID
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Delahaye-Duriez, Andrée. "Identification de nouveaux gènes impliqués dans des maladies ophtalmologiques rares en utilisant la CGH-array." Paris 7, 2011. http://www.theses.fr/2011PA077066.
Full textAbstract:
L'objectif de ce travail était de caractériser par CGH (Comparative Genomic Hybridization) array des régions chromosomiques impliquées dans des maladies ophtalmologiques rares, pour identifier de nouveaux gènes. Dans le premier volet de ma thèse, 65 patients présentant une malformation oculaire syndromique ont été explorés par CGH-array. Une anomalie probablement causale a été identifiée chez 15% d'entre eux. Quatre patients ont une délétion emportant un gène déjà connu dans le développement de l'œil (FOXC1 ou OTX2) et 4 autres patients, une délétion pathogénique non classiquement associée à une atteinte oculaire : del(17)(p!3. 3pl3. 3), del(10)(pl4p!5. 3) et del(16)(pll. 2pll. 2). En collaboration avec d'autres équipes nous avons rassemblé des patients pour étudier les corrélations génotype-phénotype des délétions 6p25 et 17pl3. 3. La deuxième partie de ce travail s'est centrée sur l'étude d'un gène candidat : ARHGEF26. L'étude de la ségrégation dans la famille index et le séquençage de ce gène chez des patients à phénotype commun ne nous ont pas permis de conclure à l'implication d'ARHGEF26 dans ce phénotype. Cette deuxième partie souligne les difficultés et les limites de la stratégie d'identification de nouveaux gènes par CGH-array. Au total, ces résultats montrent que l'analyse chromosomique par CGH-array au-delà de son intérêt diagnostique et pour le conseil génétique, permet d'établir de nouvelles corrélations génotype-phénotype et d'identifier de nouvelles régions potentiellement impliquées dans des pathologies ophtalmologiques raresThe karyotype detects a chromosomal anomaly in 7. 7% to 10% of neonates with ocular birth defect. The introduction of microarray technology showed a very high rate of rearrangements below the resolution of karyotyping. My objectives in this work were to characterize using comparative genome hybridisation-based microarray analysis (array-CGH) chromosomal regions involved in rare ophthalmologic disorders, and then to identify new genes. In the first part of my work, we performed array-CGH in 65 patients presenting syndromal ocular developmental anomalies. A causal or potentially causal anomaly was found for 15% of them. Four had a pathogenic deletion involving a gene known to be involved in ocular anomalies (FOXC1 or OTX2}, while 4 others had a pathogenic deletion not classically associated with ocular malformations: del(17)(pl3. 3p!3. 3), del(10)(pl4p!5. 3) and del(16)(pl 1. 2pl 1. 2). In collaboration with other teams, we gathered patients to study genotype-phenotype correlations for 6p25 and 17pl3. 3 deletions. The second part of my work focused on a candidate gene study: ARHGEF26. Sequencing this gene in other patients with similar phenotype and studying the index patient family segregation, we could not demonstrate the ARHGEF26 involvement in this phenotype. This second part highlights the limits and difficulties of gene identification using array-CGH. These results demonstrate that array-CGH-based chromosomal analysis, beyond its importance for diagnosis and genetic counselling, can help to establish new genotype-phenotype correlations for chromosomal anomalies as well as identify potential new regions involved in rare ophthalmologic disorders
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RASSU, STEFANIA. "Utilità clinica dell’array-CGH nello studio di pazienti in età pediatrica con Leucemia Linfatica Acuta." Doctoral thesis, Università degli Studi di Cagliari, 2016. http://hdl.handle.net/11584/266634.
Full textAbstract:
Acute leukemia represent the most common malignancy in children, with the 80% of
cases of lymphoblastic type. Most patients with acute lymphocytic leukemia are
reported to have acquired chromosomal abnormalities in their leukemic bone marrow
cells. Multiple chromosome rearrangements have been described, and their
associations with specific clinical, biologic, and prognostic features are well defined.
Conventional cytogenetic analysis is critical in the diagnosis of LLA, identifying
characteristic chromosomal abnormalities associated with a given prognosis, therein
facilitating optimized treatment.
We investigated the utility of array comparative genomic hybridization (array-CGH)
for detection of chromosomal abnormalities compared to standard clinical evaluation
with karyotype and fluorescent in-situ hybridization (FISH). In the present study 19
LLA pediatric bone marrows were analyzed, 12 diagnosis and 7 relapse sample.
Array-CGH detected unbalanced chromosome rearrangements in all cases except
testicular relapses. The most recurrently altered chromosome regions were 9p (
deletion of CDKN2A/B, JAK2, PAX5 genes) and 21q (amplification of RUNX1
gene). The complementary use of microarray and conventional cytogenetics would
allow for more sensitive, comprehensive, and accurate analysis of the underlying
genetic profile, with concomitant improvement in prognosis and treatment for
pediatric LLA.
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Kreuz, Markus. "Entwicklung und Implementierung von Auswertungswerkzeugen für Hochdurchsatz-DNA-Kopienzahl-Analysen und deren Anwendung auf Lymphomdaten." Doctoral thesis, Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-161664.
Full textAbstract:
Aberrationen in der DNA-Kopienzahl sind häufige genetische Veränderungen bei malignen Lymphomerkrankungen. Zugewinne sowie Deletionen stellen dabei Mechanismen zur Onkogen-Aktivierung sowie Tumorsuppressorgen-Inaktivierung dar und tragen somit zur Pathogenese der Erkrankung bei. Array-CGH und SNP-Array sind Messplattformen, die die genomweite Bestimmung von Kopienzahlaberrationen in einem Experiment ermöglichen. Die bei der Analyse entstehenden Datensätze sind komplex und erfordern automatische Methoden zur Unterstützung der Analyse und Interpretation der Messergebnisse.
In dieser Promotionsarbeit wurden Methoden entwickelt, welche die Analyse von Array-CGH- und SNP-Array-Messungen ermöglichen. Diese Methoden wurden für die Auswertung umfangreicher Datensätze von malignen Non-Hodgkin-Lymphomen verwendet. Dabei wurden Lymphome der Entitäten Burkitt-Lymphom, diffus großzelliges B-Zell-Lymphom, Mantelzelllymphom, primäres ZNS-Lymphom und peripheres T-Zell-Lymphom – nicht anderweitig spezifiziert – analysiert. Für die untersuchten Lymphom-Entitäten konnten hierbei zahlreiche neue rekurrente Kopienzahlaberrationen sowie uniparentale Disomien gezeigt werden, die neue Einblicke in die Pathogenese der jeweiligen Erkrankungen erlauben.
Darüber hinaus erfolgte ein Vergleich beider Messplattformen anhand eines Datensatzes mit gepaarten Array-CGH- und SNP-Array-Daten. Für die eingesetzten Plattformen (2800k-BAC-Array vs. Affymetrix 250k-Sty-SNP-Array) konnte eine circa zwölffach höhere effektive Auflösung der SNP-Array-Plattform gezeigt werden. Die wesentlichen Ergebnisse dieser Arbeit sind in sieben Publikationen eingeflossen.
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Armengol, Rosell Gemma. "Detecció de guanys i pèrdues de material genètic en tumors sòlids." Doctoral thesis, Universitat Autònoma de Barcelona, 2000. http://hdl.handle.net/10803/3685.
Full textAbstract:
Durant molts anys la citogenètica ha estat l'únic mètode disponible per a analitzar els canvis genètics en els tumors. Malgrat això, els estudis cariotípics estan sovint obstaculitzats per problemes tècnics i metodològics. L'any 1992 es va descriure una nova estratègia, que es coneix com hibridació genòmica comparada (CGH), i que identifica en un sol experiment aquelles regions que s'hagin amplificat (indicadores d'oncogens), així com regions delecionades (indicadores de gens supressors de tumors). En aquesta tesi s'han estudiat 37 mostres de tumors de la família Ewing (ET), vuit xenografts de tumors pancreàtics i set metàstasis de tumors pancreàtics originades en els ratolins. En totes les mostres s'ha aplicat la CGH. En els ET s'han detectat guanys recurrents del braç llarg del cromosoma 1 (mínima regió comuna 1q21-q22), i guanys dels cromosomes 8 i 12, així com guany de 7q i 6p2,1-pter i pèrdua de 16q. Aquestes regions podrien contenir gens importants en el desenvolupament i/o progressió dels ET. Mitjançant Southern blot s'ha detectat l'amplificació de dos gens, FLG i SPRR 3, localitzats a 1q21. A més, mitjançant una anàlisi estadística s'ha observat que els guanys de 6p estaven associats a un pitjor pronòstic. També s'ha desenvolupat una nova estratègia, la CGH amb mescles de DNAs de diferents mostres del mateix tipus tumoral. Aquesta tècnica permet detectar en un únic experiment les alteracions presents a la majoria de les mostres. En el present estudi s'ha demostrat l'eficàcia d'aquest mètode amb nombroses mostres (14-28) de sis tipus tumorals diferents, que prèviament s'havien estudiat individualment. En els tumors pancreàtics s'han detectat guanys en els cromosomes 8 (8q24),15 (15q25-q26),16, 20q i 19q, i pèrdues en els cromosomes 18 (18q21), 6 (6q21 i 6q24-qter), 13 (13q21) i 10 (10q 14-pter), en ordre decreixent de freqüència. Els estudis de pèrdues al·lèliques a 10p14-pter no han permès una delimitació més exacta de la regió afectada, ja que tots els casos amb pèrdua per CGH han mostrat pèrdues al·lèliques per a tots els loci informatius. Les regions cromosòmiques 8q24 i 15q25-qter s'han estudiat amb més detall per hibridació in situ fluorescent i Southern blot. L'estudi dels oncogens MYC a 8q24 i FES i IGF1R a 15q25-qter ha mostrat, en general, un baix nivell d'amplificació. Podria ésser que solament unes poques còpies extra d'aquests gens fossin suficients per a tenir efectes en la tumorogènesi pancreàtica o bé que fossin altres gens localitzats en aquestes regions els que realment estarien amplificats i els quals jugarien un paper important en la carcinogènesi pancreàtica. D'altra banda, s'ha observat una forta relació clonal entre les metàstasis estudiades i els tumors originaris implantats en els ratolins. Totes les metàstasis tenien les mateixes alteracions que els implants i, a més, noves alteracions que podrien contenir gens relacionats amb la progressió metastàtica del carcinoma de pàncreas. La majoria d'aquestes alteracions addicionals ja estaven presents en els subclons de l'implant, però no en proporció suficient com per a ser detectades per CGH.
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Coe, Bradley P. "The role of specific genomic alterations in small cell lung cancer aggressiveness." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/2283.
Full textAbstract:
Small Cell Lung Cancer (SCLC) is a very aggressive neuroendocrine tumour of the lung, which demonstrates a 5 year survival of only 10% for extensive stage disease (20-30% for limited stage), with only modest improvement over the last few decades. Identification of new molecular diagnostic and therapeutic targets is thus imperative. Previous efforts in identifying molecular changes in SCLC by gene expression profiling using microarrays have facilitated disease classification but yielded very limited information on SCLC biology. Previous DNA studies have been successful in identifying several loci important to SCLC. However the low resolution of conventional chromosomal Comparative Genomic Hybridization (CGH) has limited the findings to large chromosomal regions with only a few specific candidate genes discovered to date. Thus, to further understand the biological behaviour of SCLC, better methods for studying the genomic alterations in SCLC are necessary.
This thesis highlights the development of array CGH technology for the high resolution dissection of aneuploidy in cancer genomes and the application of this new technology to the study of SCLC. I present the development of the first whole genome CGH array which offered unprecedented resolution in the profiling of cancer genomes allowing fine mapping of genes in a single experiment. Through application of DNA based analysis in conjunction with integrated expression analysis and comparison of SCLC to less aggressive non-small cell lung tumours I have identified novel patterns of pathway disruption specific to SCLC. This included alteration to Wnt pathway members and striking patterns of cell cycle activation through predominantly downstream disruption of signalling pathways including direct activation of the E2F transcription factors, which are normally repressed by the Rb gene.
Analysis of targets of the E2F/Rb pathway identified EZH2 as being specifically hyper-activated in SCLC, compared to NSCLC. EZH2 is a polycomb group gene involved in the control of many cellular functions including targeted DNA methylation and escape from senescence in hematopoietic stem cells.
Taken together these results suggest that in SCLC, downstream disruption may replace multiple upstream alterations leading to activation independent of a specific mitogenic pathway, and that EZH2 represents a potentially important therapeutic target.
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Móz, Luis Eduardo Silva. "Caracterização genômica do Edema de Reinke." Botucatu, 2017. http://hdl.handle.net/11449/149913.
Full textAbstract:
Orientador: Patrícia Pintor dos ReisResumo: Introdução: o Edema de Reinke (ER) é uma lesão laríngea considerada benigna relacionada ao tabagismo. Dados em literatura relatam associações entre o ER e a detecção de diferentes graus de displasia e carcinoma in situ, bem como alterações na imunoexpressão de proteínas tumorais como a p53. Alguns autores classificam o ER entre as lesões pré-malignas, com risco de transformação e progressão para carcinoma de laringe. Não havendo consenso na literatura, torna-se necessária a realização de estudos moleculares. Objetivos: caracterizar o perfil genômico global de alterações no número de cópias do DNA em amostras de pacientes com ER. Métodos: oito amostras removidas por microcirurgia foram submetidas à extração do DNA. Os perfis de alteração no número de cópias genômicas e os genes candidatos associados foram analisados pela metodologia da hibridação genômica comparativa (CGH array), utilizando-se a plataforma de 4x180K (Agilent Technologies). Os dados de microarranjos foram analisados utilizando o programa CytoGenomics v4.0.2.21 (Agilent Technologies). As alterações no número de cópias (CNAs) obtidas foram comparadas com o banco de dados Database of Genomic Variants (DGV). A classificação dos genes selecionados para análise foi realizada baseada em dados descritos no National Center for Biotechnology Information (NCBI). Resultados: Foram encontrados perdas, ganhos ou deleções em 54 genes, um RNA não codificador longo intergênico (lincRNA), seis sequências hipotéticas e 10 microRN... (Resumo completo, clicar acesso eletrônico abaixo)
Doutor
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Lohan, Silke [Verfasser]. "Analyse von genomischen Aberrationen mit hochauflösender Array-CGH bei Patienten mit Fehlbildungen der Extremitäten / Silke Lohan." Berlin : Freie Universität Berlin, 2013. http://d-nb.info/1031190546/34.
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Machado, Isabela Nelly. "Detecção de instabilidade genômica por hibridização genômica comparativa baseada em microarranjos (array CGH) em fetos dismórficos." [s.n.], 2010. http://repositorio.unicamp.br/jspui/handle/REPOSIP/311739.
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Orientador: Ricardo BariniTese (doutorado) - Universidade Estadual de Campinas. Faculdade de Ciências Médicas
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Resumo: Introdução: Para uma parcela significativa de fetos com defeitos congênitos o diagnóstico sindrômico permanece indefinido, dificultando a abordagem perinatal, o estabelecimento de prognóstico e o aconselhamento genético. A incapacidade de detecção de pequenas instabilidades genômicas, atualmente apontadas como provável fator causal nestas condições dismórficas, é a principal limitação do estudo cromossômico microscópico pelo bandamento G (cariótipo convencional). A hibridização genômica comparativa (comparative genomic hybridization-CGH) é capaz de identificar perdas e ganhos de material genômico com alta resolução, sem envolver o cultivo celular e o conhecimento prévio da região genômica envolvida. Objetivo: Avaliar a aplicabilidade da técnica de array CGH em sangue fetal para o diagnóstico de perdas e ganhos genômicos em um grupo de fetos dismórficos. Sujeitos/Método: Foi realizado um estudo prospectivo descritivo a partir de amostras sanguíneas de fetos dismórficos e com cromossomos numericamente normais ao bandamento G, admitidos no Setor de Medicina Fetal do Centro de Atenção Integral à Saúde da Mulher (CAISM) da Universidade Estadual de Campinas (Unicamp). Foi realizada a caracterização da amostra estudada e uma análise descritiva dos achados moleculares através da técnica de array CGH. Resultados: Foram incluídos no estudo 50 fetos, dos quais 49 preencheram os critérios de qualidade da técnica. A taxa de detecção de alterações cromossômicas pela técnica de array CGH não detectadas pelo cariótipo convencional foi de 93,7% (45 fetos), e 27% foram consideradas significativas dos pontos de vista citogenético e clínico. Entre os fetos com alterações do número de cópias, 87% apresentaram pelo menos um clone para o qual já estão descritas variações do número de cópias (CNV) em indivíduos fenotipicamente normais. Adicionalmente, a técnica mostrou-se eficaz para o esclarecimento diagnóstico da origem, exata localização e dimensionamento do material adicional encontrado em um feto com anomalia cromossômica estrutural. Conclusões: A caracterização do perfil genômico por array CGH de fetos com defeitos congênitos permitiu complementar o diagnóstico citogenético convencional, aumentando a definição diagnóstica e a identificação de regiões cromossômicas associadas a algumas anomalias congênitas
Abstract: Introduction: A great number of fetuses with congenital defects remain without definitive diagnosis, making difficult the perinatal management, the prognosis establishment and the genetic counseling. The incapacity of detection of short sequence copy number changes, pointed as a probable etiology factor for some congenital defects, is the main limitation of routine G-banding. The Comparative Genomic Hybridization (CGH) overcome this limitation, and also does not require cellular culture or prior knowledge of the involved genomic region. Objective: To evaluate the applicability of the CGH method on fetal material for genomic gains and losses in a group of malformed fetuses. Methods: On a prospective descriptive study, fetal blood samples were collected from malformed fetuses with numerically normal chromosomes at G-banded karyotype, at the Fetal Medicine Unit of the Centro de Atenção Integral à Saúde da Mulher (CAISM) of the Universidade Estadual de Campinas (UNICAMP). Sample characterization and a descriptive analysis of the CGH-based technique results were accomplished. Results: Fifty fetuses were included in this study and 49 were considered optimal according to adopted quality control criteria. The detection rate of fetuses with copy number imbalances not detected by the G-banded karyotype was 93.7% (45 fetuses), with 27% of cytogenetic and clinical significance. Among fetuses with copy number imbalances, 87% presented at least one abnormal clone encompassing CNVs described for phenotipically normal individuals. Additionally, the array CGH showed to be effective for the identification of the additional genetic material origin, with its precise location and size, presented in one fetus with structural chromosomal anomaly. Conclusions: The genomic profile characterization of malformed fetuses through array CGH allowed complementing the conventional cytogenetic diagnosis, obtaining a higher precise diagnosis and the identification of chromosomal regions associated with some congenital anomalies
Doutorado
Tocoginecologia
Doutor em Tocoginecologia
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Pinato, Claudia. "ARRAY-CGH COME ESAME DI PRIMO LIVELLO NELLA DIAGNOSI MOLECOLARE DI RITARDO MENTALE E ANOMALIE CONGENITE." Doctoral thesis, Università degli studi di Padova, 2015. http://hdl.handle.net/11577/3424644.
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The array-CGH technique has emerged in recent years as a powerful tool for the identification of molecular causes underlying complex phenotypes characterized by intellectual disability, autism, epilepsy, psychiatric disorders and multiple congenital anomalies. Over the past 10 years, it has become clear that the conventional cytogenetic analysis is unable to detect rearrangements less than 5-10Mb which can be responsible for these clinical phenotypes. This limit has been exceeded with array-CGH technique which has increased by 15-20% the detection rate of cryptic chromosomal imbalances (deletions or duplications).
The possibility to have a genome wide technique with a high resolution led to the proposal, in 2010, by the International Standard Cytogenomic Array (ISCA) Consortium, to use this technique as the first-line test in individuals with intellectual disabilities and congenital anomalies.
From studies with microarray technology it has become clear that there are chromosomal regions in which aberrant recombination are particularly frequent, due to the presence of segments with elevated sequence homology, that cause a high degree of genomic instability.
Moreover the use of the array-CGH showed the presence in the genome of a large number of structural variations, larger than 1Kb, defined copy number variation or CNVs, that does not always represent a direct cause of disease because they have also been identified in healthy individuals. This complexity in the interpretation of pathogenic CNVs is even more relevant in prenatal diagnosis because it leads to uncertainty in terms of prognosis for the fetal health. For this reason, despite the advantages of the technique, the array-CGH analysis in prenatal diagnosis is considered as a second-line test to be used in association to conventional cytogenetics analysis.
In this study were evaluated with array-CGH analysis, 1051 patients with mental and / or developmental disabilities, autism, multiple congenital anomalies and dimorphisms. The main purpose was to verify the presence of cryptic chromosomal rearrangements in order to demonstrate the utility of genomic microarray as first-line test for the characterization of the molecular causes underlying the phenotype of individuals.
Then the mechanisms of formation of anomalies were hypothesized by the analysis of the breakpoints, to verify the presence of regions of homology that may have predisposed to the rearrangement. So it was examined whether the mechanism of formation and the clinical significance of the identified CNVs could be related to the pattern of inheritance, the type or the size of the imbalance.
The results show that 15.8% of the patients has at least one pathological anomaly or VOUS (variant of uncertain significance) that is likely pathological, and that these are more frequently deletions and CNVs arisen de novo. It was also highlighted that both the clinical significance of CNVs and their mechanism of formation may be related to the size of the imbalance.
It was later analyzed the distribution of CNVs in different chromosomes and it was found that in some of them the density of anomalies is greater than the others.
The application of the array-CGH in a high number of patients has also allowed to estimate the sensitivity to detect mosaicism, although they have a frequency less than 1% in individuals with learning disabilities. It was observed that the technique is able to detect anomalies present in up to 10% of cells.
Finally some fetal samples of chorionic villi and amniotic fluid were analyzed to evaluate the possible use of genomic microarray in prenatal diagnosis. The small number of analyzed samples did not allow us to draw conclusions, but the difficulties in the interpretation of the clinical significance of CNVs, make it a second-line test to be used in association with standard karyotype.La tecnica di array-CGH si è affermata negli ultimi anni come un potente strumento per l’identificazione delle cause molecolari alla base di fenotipi complessi caratterizzati da disabilità intellettive, autismo, epilessia, disordini psichiatrici e anomalie congenite multiple. Negli ultimi 10 anni, infatti, è emerso sempre più chiaramente che l’analisi citogenetica convenzionale non è in grado di rilevare riarrangiamenti inferiori alle 5-10 Mb che possono essere responsabili di tali fenotipi clinici. Questo limite è stato superato dall’array-CGH che ha aumentato del 15-20% la detection rate di sbilanciamenti cromosomici criptici (delezioni o duplicazioni). La possibilità di avere una tecnica di tipo genome wide ad elevata risoluzione ha portato alla proposta, nel 2010, da parte dell’International Standard Cytogenomic Array (ISCA) Consortium, dell’utilizzo di tale tecnica come esame di primo livello in individui con disabilità intellettive e anomalie congenite. Dagli studi effettuati con tecnologia microarray è risultato evidente che esistono regioni cromosomiche in cui sono particolarmente frequenti ricombinazioni aberranti, dovute alla presenza di segmenti con un’elevata omologia di sequenza che causano un alto grado di instabilità genomica. L’utilizzo dell’array-CGH ha inoltre rivelato la presenza nel genoma di un elevato numero di variazioni strutturali, di dimensioni maggiori di 1Kb, chiamate copy number variations (CNVs), le quali, essendo state identificate anche in individui sani, non sempre rappresentano una causa diretta di malattia. Questa difficoltà nell’interpretazione della patogenicità delle CNVs è ancora più rilevante in diagnosi prenatale poiché si traduce in una incertezza in termini prognostici sulla salute del feto. Per questo motivo, nonostante i vantaggi dati dalla tecnica, l’array-CGH in diagnosi prenatale viene, al momento, considerato un test di secondo livello da utilizzare in associazione all’analisi citogenetica convenzionale. In questo studio sono stati valutati, mediante array-CGH, 1051 pazienti che presentano ritardo mentale e/o dello sviluppo, autismo, anomalie congenite multiple e dimorfismi. L’obiettivo principale è stato quello di verificare la presenza di riarrangiamenti cromosomici criptici in modo da dimostrare l’utilità dell’impiego di microarray genomici come esame di primo livello per la caratterizzazione delle cause molecolari alla base del fenotipo patologico degli individui. Sono stati poi ipotizzati i meccanismi di formazione delle anomalie verificando, mediante l’analisi dei breakpoints, la presenza di regioni di omologia che possano aver predisposto al riarrangiamento. Quindi è stato valutato se il meccanismo di formazione e il significato clinico delle CNVs identificate possano essere correlati al pattern di ereditarietà, al tipo o alle dimensioni dello sbilanciamento. I risultati ottenuti mostrano che il 15.8% dei casi analizzati è portatore di una anomalia patologica o VOUS (variant of uncertain significance) verosimilmente patologica, e che queste sono più frequentemente delezioni e CNVs insorte de novo. È stato inoltre evidenziato che sia il significato clinico delle CNVs sia il loro meccanismo di formazione possano essere correlati alle dimensioni degli sbilanciamenti. È stata successivamente analizzata la distribuzione delle CNVs nei diversi cromosomi ed è emerso che in alcuni di essi la densità di anomalie riscontrate è maggiore rispetto agli altri. L’applicazione dell’array-CGH in un elevato numero di pazienti ha permesso, inoltre, di stimarne la sensibilità nell’identificazione di mosaicismi, sebbene abbiano una frequenza inferiore all’1% in individui con disabilità intellettive. È stato osservato che la tecnica è in grado di rilevare anomalie che coinvolgono anche un numero limitato di cellule, fino al 10%. Infine sono stati analizzati alcuni campioni fetali di villi coriali e liquido amniotico per valutare il possibile utilizzo dei microarray genomici in diagnosi prenatale. Il numero esiguo di campioni analizzati non ci ha permesso di trarre delle conclusioni, tuttavia, per le difficoltà che si riscontrano nell’interpretazione del significato clinico delle CNVs, è da ritenere al momento un test di secondo livello da utilizzare in associazione al cariotipo standard.
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Ribeiro, Cintia Marques. "Estudo de genes candidatos aos Transtornos do Espectro Autista." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-06092013-153442/.
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Os transtornos do espectro autista (TEA) são condições neuropsiquiátricas caracterizadas por padrões comportamentais estereotipados, ausência ou limitação de comunicação verbal e de interação social recíproca. Diversos estudos têm mostrado que esses transtornos possuem etiologia genética complexa e heterogênea, o que dificulta a identificação dos fatores causais. Estima-se que cerca de 70% dos casos de TEA são idiopáticos. Portanto, com o objetivo de identificar mecanismos etiológicos associados aos TEA, utilizamos as seguintes estratégias: customização de uma lâmina de microarray CGH que possibilite a detecção não só de grandes CNVs, mas também de alterações menores do que 10 kbp, em exons e regiões UTR de genes potencialmente candidatos; a comparação entre os tipos de rearranjos detectados em pacientes sindrômicos e em não sindrômicos e, ainda, a investigação mais detalhada de uma família com indivíduos portadores de transtorno autista e síndrome de Asperger. Foram avaliados 103 portadores de TEA não sindrômicos e 18 sindrômicos, sendo as taxas de detecção de alterações potencialmente patogênicas, respectivamente, de 11,6% e 38,9%. Dentre as alterações detectadas 44,4% são menores do que 10 Kbp. Portanto, a estratégia de usar uma lâmina customizada, com alta densidade de sondas complementares aos exons e regiões não codificantes de genes potencialmente envolvidos na etiologia dos TEA, capaz de detectar tanto alterações grandes quanto pequenas, parece ser relevante na tentativa de elucidar o maior número de casos possíveis e melhor compreender esses transtornos. Além disso, essa lâmina também pode ser utilizada como uma ferramenta para auxiliar o diagnóstico clínico e o aconselhamento genético com um custo mais acessível em comparação a outras comerciais ou ao sequenciamento de última geração. Cerca de 33,3% das CNVs observadas afetam região UTR, sugerindo que mutações nessas regiões podem explicar uma proporção significativa dos casos nos quais não são detectadas alterações através de outros testes genômicos, visto que a maioria desses ainda não exploram adequadamente regiões não codificantes. Entre os pacientes autistas não sindrômicos verificou-se que a maioria dos genes afetados por CNVs estão envolvidos em duas principais funções biológicas - sinapses glutamatérgicas e orientação axonal, sugerindo que TEA não sindrômico pode ser causado por disfunção em genes diferentes envolvidos em processos fisiológicos comuns. Diferente do que observamos entre pacientes não sindrômicos, detectamos mais de uma alteração em um mesmo indivíduo ou alterações que englobam mais de um gene entre os pacientes sindrômicos, reforçando o modelo oligogênico para alguns casos de TEA. Por fim, os dados obtidos no estudo da família com portadores de síndrome de Asperger e transtorno autista sugere que a gravidade do quadro clínico possa estar relacionada ao número de mutações e possivelmente por duas mutações diferentes em ambos os alelos de um mesmo gene. Nossos resultados, além de apoiar o envolvimento dos genes MDGA2, FHIT, HTR2A, SHANK2, GRIA3, ZNF778, PRKCα, CDH15, DIAPH3, GCH1, GRM5, MARK1, SLC17A6, IMMP2L, BZRAP1, SYNGAP1, ANK3, MAP1A, GABRR2 e LAMC3 nos TEA também sugere novos genes candidatos: LRRC7, LRRIQ3, CADPS1, NUFIP, SEMA3A, SNAP29, MBD2, GAD2, DGKH e PARD3The autism spectrum disorders (ASD) are neuropsychiatric conditions typically characterized by social deficits, communication difficulties, stereotyped or repetitive behaviors and interests. Several studies have shown that these disorders have a complex and heterogeneous genetic etiology, which makes difficult to identify the causal factors. Approximately 70% of cases are idiopathic. In order to identify etiological mechanisms associated with ASD, we have used the following strategies: customized a microarray CGH platform that allows detection not only of large CNVs, but also alterations smaller than 10 kbp in exons and UTR regions of potential candidate genes, the comparison between the types of rearrangements detected in syndromic and non-syndromic patients and further, more detailed investigation of a family segregating both autistic disorder and Asperger syndrome. We evaluated 103 nonsyndromic and 18 syndromic patients by the custom-designed array and the detection rate of possibly pathogenic alterations were, respectively, 11.6% and 38.9%. Among these CNVs, 44.4% are smaller than 10 kbp. Therefore, the strategy of using a custom-designed array, enriched with probes targeted to genes potentially involved in the ASD etiology and able to detect both large and small CNVs, seems to be relevant in an attempt to elucidate the largest number of cases and to better understand these disorders. Furthermore, this platform can also be used as a tool to support the clinical diagnosis and genetic counseling with a more affordable cost compared to conventional other or next-generation sequencing. Approximately 33.3% of the observed CNVs affect UTR region, suggesting that mutations in non-coding regions might explain a significant proportion of ASD cases negative for most genomic screenings, which still do not explore adequately these regions. Among nonsyndromic autistic patients we found that most of the genes affected by CNVs are involved in two main biological functions - glutamatergic synapses and axonal guidance, suggesting that nonsyndromic ASD can be caused by dysfunction in different genes of a few common physiological processes. In contrast to our findings in nonsyndromic patients, we detected more than one alteration in a single individual or alterations that involve more than one gene among the syndromic patients, reinforcing the oligogenic model for some cases of ASD. Finally, the data obtained in the study of the family segregating both Asperger syndrome and autistic disorder suggests that the severity of ASD seems to be modulated by the number of hits and possibly by hits in both alleles of the same gene. Our results support the involvement of genes MDGA2, FHIT, HTR2A, SHANK2, GRIA3, ZNF778, PRKCα, CDH15, DIAPH3, GCH1, GRM5, MARK1, SLC17A6, IMMP2L, BZRAP1, SYNGAP1, ANK3, MAP1A, GABRR2 and LAMC3 in ASD etiology and also suggests new candidates: LRRC7, LRRIQ3, CADPS1, NUFIP, SEMA3A, SNAP29, MBD2, GAD2, DGKH and PARD3
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Dimassi, Sarra. "Identification de gènes responsables d'épilepsies de l'enfant." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSE1114.
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L'épilepsie est une affection neurologique chronique qui se définit par la répétition de crises épileptiques, signe de l'hyperactivité paroxystique d'un groupe de neurones corticaux. Ces dernières années, plusieurs gènes responsables d'épilepsies monogéniques ont été mis en évidence. Notre travail avait pour objectif l'identification d'anomalies génétiques responsables ou favorisants certaines formes d'épilepsies de l'enfant. Ce travail est composé de quatre études complémentaires. La première était l'exploration pangénomique d'une cohorte de 47 patients porteurs d'épilepsie à paroxysme rolandique (EPR) par CGH array, à la recherche de variations de nombre de copies (CNV) récurrentes. Nous avons ainsi pu mettre en évidence plusieurs CNVs emportant des gènes impliqués dans l'épilepsie, dont PRRT2 et GRIN2A. La deuxième reposait sur la même approche appliquée à une cohorte de 8 patients tunisiens présentant des spasmes infantiles. Elle a permis d'identifier une délétion 9q34.3 emportant le gène EHMT1, responsable du syndrome de Kleefstra et une duplication 15q13.1, région impliquée dans des troubles du neurodéveloppement. Pour la troisième étude, nous avons comparé deux techniques de capture pour séquençage à haut débit d'un panel de gènes impliqués dans les épilepsies de l'enfant, à partir des échantillons de 24 patients épileptiques. Cette approche nous a permis de mettre au point un logiciel d'analyse de couverture, que nous avons nommé DeCovA. Lors de la dernière étude, nous avons appliqué une stratégie de séquençage d'exome en trio pour explorer 10 patients porteurs des spasmes infantiles. Nous avons ainsi pu mettre en évidence des variants pathogènes de novo chez quatre patients,impliquant les gènes KCNQ2, SCN1A, NR2F1 et ALG13. Nos résultats confirment ainsi la place importante de la génétique et l'intérêt majeur des nouvelles technologies dans l'exploration étiologique des épilepsies de l'enfantEpilepsy is a chronic neurological disorder characterized by repeated epileptic seizures, a sign of cortical neurons paroxysmal hyperactivity. In recent years, several monogenic genes involved in epilepsy have been identified. The aim of our work is to identify new genetic abnormalities responsible for childhood epilepsies. This work is divided into four complementary studies. First, we searched copy number variation (CNV) by pangenomic exploration of a cohort of 47 patients with Rolandic epilepsy (RE) using CGH array. We identified several CNVs carrying genes involved in epilepsy, including PRRT2 and GRIN2A (genes). Secondly, the same approach was applied to a cohort of 8 Tunisian patients with infantile spasms. It allowed the identification of a 9q34.3 deletion includingEHMT1, implicated in Kleefstra syndrome and a 15q13.1 duplication, known to be involved in neurodevelopment disorders. For the third study, we compared two library-building methods for a gene-targeted panel for the diagnosis of Monogenic childhood epilepsies, in a cohort of 24 epileptic patients. This approach allowed us to develop a coverage analysis software, which we named DeCovA. In the last study, we used a trio-based exome-sequencing approach to look for de novo mutations in 10 patients with infantile spasms. We found de novo pathogenic variants in four patients, involving KCNQ2, SCN1A, NR2F1, and ALG13. Our results confirm the increasing role of genetics and the major interest of new technologies in the etiological exploration of childhood epilepsy
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Vogazianou, Artemis P. "Analysis of chromosome 1 status in human oligodendrocytic, oligoastrocytic and astrocytic gliomas, using tiling-path CGH-microarray." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614682.
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Baker, Serena F. "Assessment of aCGH Clustering Methodologies." BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2644.
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Array comparative genomic hybridization (aCGH) is a technique for identifying duplications and deletions of DNA at specific locations across a genome. Potential objectives of aCGH analysis are the identification of (1) altered regions for a given subject, (2) altered regions across a set of individuals, and (3) clinically relevant clusters of hybridizations. aCGH analysis can be particularly useful when it identifies previously unknown clusters with clinical relevance. This project focuses on the assessment of existing aCGH clustering methodologies. Three methodologies are considered: hierarchical clustering, weighted clustering of called aCGH data, and clustering based on probabilistic recurrent regions of alteration within subsets of individuals. Assessment is conducted first through the analysis of aCGH data obtained from patients with ovarian cancer and then through simulations. Performance assessment for the data analysis is based on cluster assignment correlation with clinical outcomes (e.g., survival). For each method, 1,000 simulations are summarized with Cohen's kappa coefficient, interpreted as the proportion of correct cluster assignments beyond random chance. Both the data analysis and the simulation results suggest that hierarchical clustering tends to find more clinically relevant clusters when compared to the other methods. Additionally, these clusters are composed of more patients who belong in the clusters to which they are assigned.
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Oliveira, Jakeline Santos. "Determinação das alterações genômicas em pacientes com malformações congênitas." Botucatu, 2018. http://hdl.handle.net/11449/180587.
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Orientador: Danilo Moretti-FerreiraResumo: As ACs são alterações visíveis nos cromossomos, classificadas como numéricas e estruturais. Atualmente o grande desafio da genética clínica é classificar e associar a relevância clínica dos desequilíbrios genéticos ao fenótipo dos portadores. O trabalho tem como objetivo principal caracterizar desequilíbrio genômico sem diagnóstico sindrômico previamente descritos pelas técnicas de citogenética clássica, molecular visando apurar os pontos de quebras e genes inseridos na região cromossômica alterada por meio da citogenômica em estudos de casos. Foram feitas análises por citogenética (bandamento GTG), citogenética molecular (FISH) e citogenômica (array-CGH) em três pacientes com malformações congênitas não-sindrômicas para definição diagnóstica e maior conhecimento sobre a correlação genótipo-fenótipo. Foram redigidos estudos de casos de três pacientes portadores de MCs, atraso do desenvolvimento e deficiência intelectual. O primeiro copilado de caso trata-se de paciente do sexo feminino com anomalias esqueléticas, deficiência intelectual e atraso do desenvolvimento. O cariótipo da paciente é 46,XX[11]/47,XX,+mar[9]. A análise de array-CGH revelou dois ganhos/duplicações nas bandas cromossômicas 6p11.2q12 (10.335 Mb de tamanho) e 6q14.1q14.3 (10.765 Mb de tamanho). Por meio da técnica da FISH e os resultados do array-CGH a região duplicada 6q14.1q14.3 encontra-se inserida em um cromossomo marcador, oriundo do cromossomo 6. Os sinais clínicos descritos na paciente foram semelhan... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The ACs are visible changes in the chromosomes, classified as numerical and structural. Currently the great challenge of clinical genetics is to classify and associate the clinical relevance of genetic imbalances with the phenotype of the carriers. The main objective of this work is to characterize genomic imbalance without syndromic diagnosis previously described by the classical and molecular cytogenetic techniques, in order to determine the breakpoints and genes inserted in the chromosomal region altered by cytogenetics in case studies. Cytogenetics (GTG banding), molecular cytogenetics (FISH) and cytogenetics (array-CGH) were performed in three patients with non-syndromic congenital malformations for diagnostic definition and greater knowledge on genotype-phenotype correlation. Case studies of three patients with MCs, developmental delay and intellectual disability were written. The first case file is a female patient with skeletal anomalies, intellectual disability and developmental delay. The patient's karyotype is 46, XX [11] / 47, XX, + sea [9]. The array-CGH analysis revealed two gains / doublings in the chromosomal bands 6p11.2q12 (10,335 Mb in size) and 6q14.1q14.3 (10,765 Mb in size). Through the FISH technique and the results of the array-CGH the duplicate region 6q14.1q14.3 is inserted in a chromosome marker, coming from chromosome 6. The clinical signs described in the patient were similar to other patients with duplication of the region 6q14. The genes PGM3, M... (Complete abstract click electronic access below)
Mestre
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Morice-Picard, Fanny. "Etude clinique et génétique de l’albinisme oculocutané : développement d’outils de diagnostic moléculaire et recherche de nouveaux gènes." Thesis, Bordeaux 2, 2013. http://www.theses.fr/2013BOR22101/document.
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Notre travail s’est intéressé à l’albinisme oculocutané en étudiant ses aspects clinico- moléculaires. Malgré l’analyse approfondie des gènes connus d’albinisme oculocutané, 15 % des patients restent sans mutation identifiée indiquant que les mutations sont situées dans des régions géniques non analysées par les techniques classiques de diagnostic moléculaire, ou qu’il existe d’autres gènes d’albinisme oculocutané. Nous avons établi une base de données clinico- biologiques décrivant les caractéristiques de plus de 400 patients analysés. Des outils de diagnostic moléculaire ont été développés à la recherche de mutations situées dans les introns et les régions régulatrices et de réarrangements géniques. Différentes stratégies ont également été utilisées pour rechercher des gènes candidats. La puce à façon a permis l’identification de grands réarrangements dans les gènes TYR, OCA2 et SLC45A2 et un réarrangement complexe du gène OCA2 chez 2 patients non apparentés. L'analyse de gènes candidats nous a permis d'identifier, chez 5 patients non apparentés présentant un albinisme oculocutané non syndromique, des mutations dans le gène SLC24A5, très récemment associé à l’AOC6. Le séquençage d’exome de 6 patients a mis en évidence des gènes candidats pour lesquels des analyses complémentaires sont poursuivies afin de confirmer leur implication dans la pathogenèse de l’AOC.Les résultats de ce travail permettent de redéfinir les aspects cliniques et moléculaires de l’AOC, d’identifier de nouveaux mécanismes moléculaires à l’origine de l’AOC ainsi que des gènes candidats dont la fonction dans le développement pigmentaire reste à élucider. L’identification de nouveaux gènes impliqués dans l’AOC pourrait permettre de mieux comprendre et de mieux prendre en charge les patients avec un AOCOur work focused on oculocutaneous albinism (OCA) by studying its clinical and molecular aspects. Despite a thorough analysis of the known genes involved in oculocutaneous albinism, 15% of patients remain without diagnostic at the molecular level indicating that mutations are located in unexplored regions and are undetected by standard techniques or that other genes are involved in albinism. We established a clinicomolecular database describing more than 400 patients and developped molecular tools in order to improve molecular diagnostic including a custom high resolution array-CGH dedicated to the four OCA genes (TYR, OCA2, TYRP1 and SLC45A2). We also used different strategies to identify new genes. Array-CGH allows us to detect large deletion in TYR, OCA2 and SLC45A2 and a complexe rearrangement in OCA2 in 2 unrelated patients. We identified, in 5 patients presenting with a non syndromic OCA, mutations in SLC24A5, recently associated with OCA6. Exome sequencing of 6 different patients allows us to identify candidate genes, for which further studies are required to confirm their involvement in OCA pathogenesis. The results of this work allowed us to delineate clinical and genetics aspects of more than 400 OCA patients and to identify new molecular mechanisms leading to OCA and candidates genes for which exact nature of their functions has to be understood. Giving the complexity of pigmentary system development and its regulation, identification of new genes leading to OCA could help to better understand OCA and take care of patients
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Birnbaum, David. "Altérations moléculaires dans l'adénocarcinome du pancréas." Thesis, Aix-Marseille, 2014. http://www.theses.fr/2014AIXM5088.
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Le cancer du pancréas est un problème majeur de santé publique. Le mauvais pronostic de l'adénocarcinome du pancréas est lié à un diagnostic tardif, une progression rapide, et à une mauvaise réponse aux traitements médicaux disponibles. Une caractérisation complète des altérations génétiques moléculaires sont aujourd'hui nécessaires pour permettre une détection plus précoce et identifier/élaborer de nouvelles thérapies ciblées dans le traitement de l'ADK du pancréas. En utilisant la technique d'hybridation génomique comparative, nous avons étudié les altérations du génome de 39 ADK. Plusieurs pertes récurrentes ont été observées, ainsi que des gains de matériel génétique. A partir de ces résultats, nous avons voulu aller plus loin en identifiant les gènes qui pourraient avoir des conséquences au niveau transcriptomique. A partir de données publiques, nous avons comparé les profils d'expression d'ADK (n=419) et de pancréas normal (n=105). Parmi les gènes trouvés amplifiés et/ou gagnés par aCGH, 170 (48%) étaient surexprimés dans les ADK par rapport au tissus normal. Les principales voies de signalisation impliquées touchaient la régulation du cycle cellulaire, les voies TP53 et TGFß. Parmi les gènes délétés en aCGH, 141 (41%) étaient sous exprimés dans les ADK du pancréas par rapport au tissus normal et étaient essentiellement liés au « métabolome » de la cellule pancréatique. Enfin, nous avons identifié une dizaine de gènes dont l'expression pourrait être liée à la survie des patients. Certains de ces gènes pourraient être des candidats à tester en tant que biomarqueurs pronostic ou cibles pour le développement de nouvelles thérapeutiquesPancreatic adenocarcinoma (PDCA) is a major public health problem in France and worldwide. The inoperability and the poor prognosis of the PDCA are due to late diagnosis, rapid tumor progression (>80% of patients displayed metastases at diagnosis), early recurrences after resection, and poor response to available therapies. Innovative approaches and a comprehensive characterization of molecular genetic alterations are dearly needed to help develop techniques of early detection, identify new molecular targets and devise novel targeted-therapies (Hidalgo, 2010). Using high-resolution array-comparative genomic hybridization (aCGH), we studied the genome alterations of 39 fine-needle aspirations from PDCA. Recurrent losses were observed and comprised several known tumor suppressor genes. We identified frequent genetic gains. With this study, we decided to go one step further by identifying genes that might also be deregulated at the transcriptomic level. We started our analysis with a population of PDCA (n=419) versus normal pancreas (n = 105). Among the 352 genes found amplified and/or gained by aCGH, 170 (48%) were up regulated at the transcriptional level in PDCA compared to normal pancreatic tissues. Major pathways involved were cell cycle, TP53 and TGFß. Among the genes located in regions of losses, 141 (41%) were down regulated in PDCA compared to normal tissues. Furthermore, some genes were found related to a patients' survival With this study, we highlighted novels genes associated to PDCA oncogenesis. Some of those candidates should be further investigated as prognosis markers or as potential targets for new therapeutic approaches
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Joaquim, Tatiana Mozer. "Correlação cariótipo-genótipo-fenótipo de rearranjo cromossômico estrutural familiar envolvendo as regiões 4p e 12q." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-04012017-114707/.
Full textAbstract:
Rearranjos cromossômicos estruturais estão potencialmente associados ao desenvolvimento de doenças genéticas devido à disrupção, inativação ou alteração da dosagem gênica. O objetivo deste projeto foi realizar a caracterização genômica de duas pacientes e seus familiares portadores de rearranjo cromossômico estrutural envolvendo o braço curto do cromossomo 4 e o braço longo do cromossomo 12, associando técnicas de citogenética clássica (bandamento GTG), citogenética molecular (FISH) e citogenômica (array-CGH), para definição diagnóstica e maior conhecimento sobre os fatores envolvidos na correlação cariótipo-genótipo-fenótipo. Foram avaliados seis indivíduos, duas pacientes, primas em primeiro grau que apresentavam alterações fenotípicas, assim como seus familiares, portadores de translocação aparentemente equilibrada e fenótipo normal. Apesar das duas pacientes apresentarem alteração cromossômica comum, derivativo do cromossomo 4 [der(4)], foram observados achados fenotípicos distintos. A investigação permitiu a definição do diagnóstico de deleção 4p16 e trissomia 12qter para as duas pacientes com fenótipo alterado e cariótipo 46,XX,der(4)t(4;12)(p16;q24.3), a definição precisa dos pontos de quebra em 4p16.3 e 12q24.31->q24.33, assim como a determinação da origem parental do rearranjo e a definição do diagnóstico citogenético final de quatro portadores de translocação aparentemente equilibrada e cariótipo t(4;12)(4pter->4p16.3::2q24.31->12qter;12qter->12q24.31::4p16.3->4pter),direcionando o aconselhamento genético para a família. Nas duas pacientes, a técnica de array-CGH (Plataforma 2x400K, Agilent®) detectou uma diferença sutil de tamanho entre as perdas e ganhos referentes aos cromossomos envolvidos no rearranjo, sendo diagnosticado em P1 uma perda de 2.707.221 pb na citobanda 4p16.3, além de um ganho de 12.405.205 pb em 12q24.31->q24.33. A paciente 2 apresentou uma perda de 2.710.969 pb em 4p16.3 e um ganho de 12.393.885 pb em 12q24.31->q24.33. Ambas as regiões de desequilíbrio genômico incluem genes que podem ser relevantes para manifestação fenotípica observada nas pacientes, entre eles: WHSC1, NELFA, LETM1, FGFRL1 e SPON2. Os resultados da investigação citogenômica indicaram, ainda, a presença de translocação equilibrada nos quatro indivíduos portadores, não sendo detectadas perdas e/ou ganhos genômicos nas regiões dos pontos de quebra cromossômica. Os resultados obtidos na investigação do padrão de metilação dos genes FGFRL1 e SPON2 não permitiram afirmar que uma provável repressão da expressão gênica devido ao imprinting materno e paterno esteja associada às características fenotípicas distintas observadas nas duas pacientes. Embora tenha sido possível a indicação de genes correlacionados ao fenótipo das pacientes, a correlação entre a alteração genética e o fenótipo das mesmas pode depender da ação sinérgica dos mais de 190 genes envolvidos neste rearranjo cromossômico estrutural familiar.Structural chromosomal rearrangements are potentially associated with the development of genetic disorders due to disruption, inactivation or gene dosage alterations. The objective of this project was to perform the genomic characterization of a familial structural chromosomal rearrangement involving the short arm of chromosome 4 and the long arm of chromosome 12 in two patients and carriers. The experimental approach involved using a combination of classical cytogenetic techniques (GTG banding), molecular cytogenetics (FISH) and cytogenomics (array-CGH), to provide a diagnostic definition and a better understanding of how changes in the karyotype and genotype may be associated with the phenotype. Six individuals were evaluated, two patients with phenotypic abnormalities, as well as the carriers of an apparently balanced 4p;12q translocation with normal phenotypes. Although the two patients showed a common chromosomal abnormality, the derivative chromosome 4 [der (4)], they presented distinct phenotypic findings. The investigation provided a definition of the diagnosis of 4p16 deletion and trisomy 12qter for the two patients with abnormal phenotypes and a karyotype 46,XX,der(4)t(4;12)(p16;q24.3). In addition a precise definition of the breakpoints at 4p16.3 and 12q24.31->q24.33, and the parental origin of the rearrangement was determined. A precise definition of the cytogenetic diagnosis of four carriers with an apparently balanced translocation and karyotype t(4;12)(4pter->4p16.3::2q24.31->12qter; 12qter 12q24.31->4pter::4p16.3), facilitated the genetic counseling for the family. In both patients, the array-CGH technique (2x400K Platform, Agilent®) detected a subtle difference in size between losses and gains in the chromosomal regions involved in the rearrangement. Patient 1 presented a loss of 2,707,221 bp in the cytoband 4p16.3, and a gain of 12,405,205 bp in 12q24.31->q24.33. Patient 2 had a loss of 2,710,969 bp in 4p16.3 and a gain of 12,393,885 bp in 12q24.31 -> q24.33. Both regions of genomic imbalance included genes that may be relevant to phenotypic findings observed in our patients, including: WHSC1, NELFA, LETM1, FGFRL1 and SPON2. Genomic findings also confirmed the presence of a balanced translocation in four carriers, with no genomic losses and/or gains in the regions of chromosome breakpoints. The results of the investigation of the methylation pattern of FGFRL1 and SPON2 genes could not demonstrate that repression of gene expression due to maternal and paternal imprinting was associated with the distinct phenotypes observed in the two patients. Although it has been possible to indicate genes related to the phenotype of the patients, the correlation between the genetic alteration and phenotype may depend on the synergistic action of multiple genes from more than the 190 involved in this familial chromosomal rearrangement.
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Grzesiuk, Juliana Dourado. "Investigação genômica de pacientes inférteis com oligozoospermia." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-30032017-162247/.
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A infertilidade afeta aproximadamente 15% dos casais, sendo atualmente reconhecido o envolvimento de fatores masculinos em metade dos casos. Alterações nas análises seminais são detectadas na maioria dos homens inférteis e a mais frequente é a baixa concentração de espermatozoides no ejaculado, conhecida como oligozoospermia. Vários estudos mostram uma forte relação entre fatores genéticos e a infertilidade, incluindo alterações cromossômicas e microdeleções do cromossomo Y, porém as causas da oligozoospermia ainda permanecem obscuras. O desenvolvimento de novas tecnologias de investigação vem possibilitando a detecção de alterações a nível genômico, como mutações e variações no número de cópias (CNVs). O presente trabalho teve por objetivo a caracterização genômica de homens com oligozoospermia sem causa definida, visando estabelecer correlação entre alterações no número de cópias e perdas de heterozigosidade (LOHs) e o fenótipo de infertilidade. Foram selecionados 18 pacientes após rigorosa avaliação clínica e investigação do histórico reprodutivo, sendo excluídos pacientes portadores de alterações cromossômicas e portadores de microdeleções do cromossomo Y. Seis homens comprovadamente férteis foram selecionados para o grupo controle. A investigação genômica de ambos os grupos, amostral e controle, foi realizada pela técnica de hibridação genômica comparativa em microarranjos (aCGH) utilizando a plataforma de resolução 180K (Agilent®,US), analisada pelo software Nexus 8.0. Foram detectadas alterações possivelmente patogênicas no cromossomo Y, no cromossomo X e em autossomos. Um ganho na região de AZFc envolvendo apenas os genes DAZ1 e DAZ4 foi detectado em nove pacientes e em quatro controles, sendo classificado como alteração benigna. Porém, alterações na região de AZFc possivelmente relacionadas ao fenótipo de oligozoospermia foram detectadas em três pacientes e incluíram extensas duplicações e deleções envolvendo, entre outros genes, as quatro cópias do gene DAZ. Após comparação de regiões selecionadas com a literatura e com diferentes bancos de dados genéticos, sugerimos que os genes PLEC, SPATC1, COL1A1, MOV10L1, SYCE3 e ODF3B possam estar associados a alterações na produção espermática. Adicionalmente, entre os doze miRNAs presentes em regiões de LOH possivelmente relacionadas ao fenótipo de infertilidade, dez têm como alvo genes com funções relacionadas à espermatogênese e reprodução humana. Estudos adicionais a nível de expressão e sequenciamento gênico são necessários para confirmar a correlação entre o genótipo e o fenótipo de oligozoospermia.Infertility affects about 15% of the couples, and it is currently recognized, that male factors are involved in about 50% of cases. Changes in seminal parameters are detected in most infertile men and the most common alteration, known as oligozoospermia, is a low concentration of sperm in the ejaculate. Several studies show a strong relationship between genetic factors and infertility, including chromosomal abnormalities and microdeletions of Y chromosome, however, the causes of oligozoospermia remain unclear. The development of new research technologies has allowed the detection of changes at genomic levels, such as mutations and copy number variations (CNVs). This study aimed to perform a genomic characterization of patients with idiopathic oligozoospermia to determine whether there is a correlation between changes of copy number and losses of heterozygosity (LOHs) in relation to the phenotype of infertility. Eighteen patients were selected for the cases after rigorous clinical examination and investigation of their reproductive history. Patients with chromosomal abnormalities or microdeletions of the Y chromosome were excluded. Six proven fertile men comprised the control group. Genomic investigation of both groups was performed by microarray comparative genomic hybridization (aCGH) using 4X180K platform (Agilent, US) analysed by Nexus 8.0 software. Potential pathogenic changes were detected on Y chromosome, as well as on the X and autosome chromosomes. A gain in AZFc region involving only DAZ1 and DAZ4 genes was detected in nine patients and four controls, and was considered as benign. However, changes in AZFc region, that could be related to the oligozoospermia phenotype were detected in three patients. These changes included extensive duplications and deletions involving the four copies of the DAZ gene together with copy number changes affecting other genes. After comparing the selected regions with the literature and with different databases, we suggest that changes such as LOH affecting PLEC, SPATC1, COL1A1, MOV10L1, SYCE3 and ODF3B genes may influence sperm production. Our analysis indicates that, ten out of the twelve miRNAs present in LOH regions could be involved in the infertility phenotype and could have target genes with functions related to spermatogenesis and human reproduction. Additional studies involving gene sequencing and expression analysis are needed to confirm the the correlation between the genotype and oligozoospermia phenotype.
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Bockmühl, Ulrike. "Molekularzytogenetische Charakterisierung von Plattenepithelkarzinomen des Kopf-Hals-Bereiches." Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 1999. http://dx.doi.org/10.18452/13706.
Full textAbstract:
Ziel der Habilarbeit war die molekulargenetische und -zytogenetische Charakterisierung von Kopf-Hals-Karzinomen, um das biologische Verhalten dieser Tumoren besser einschätzen zu können als mit Hilfe der bekannten klinisch-pathologischen Tumorklassifikation. Dazu wurden 100 primäre Plattenepithelkarzinome des Kopf-Hals-Bereiches, 27 Fälle syn- oder metachroner Metastasen und 10 Fälle von Zweitkarzinomen mit Hilfe der Comparativen Genomischen Hybridisierung (CGH) analysiert. Alle untersuchten Tumoren stammten von Patienten, die primär im Zeitraum zwischen 1994 und 1998 in der HNO-Klinik der Charité operiert wurden. Die Auswertung der analysierten Tumoren brachte die nachfolgenden wesentlichen Ergebnisse: Plattenepithelkarzinome des Kopf-Hals-Bereiches sind durch Deletionen der Chromosomen 3p, 4p/q, 5q, 6q, 8p, 9p, 11p/q, 13q, 18q und 21q sowie DNA-Gewinne im Bereich von 1p, 3q, 5p, 8q, 9q, 11q13, 16p, 17q, 19, 20q und 22q. Gut differenzierte Tumoren sind durch Deletionen auf Chromosom 3p und 9p kombiniert mit einem DNA-Gewinn auf 3q gekennzeichnet. Die schlecht differenzierten Malignome zeigen zusätzlich die Deletionen von Chromosom 4, 5q, 8p, 11, 13q, 18q sowie 21q und die DNA-Gewinne von 8q, 11q13 sowie 20q.Der metastatische Phänotyp ist bei Kopf-Hals-Karzinomen durch Deletionen im Bereich der Chromosomen 10q und 11 charakterisiert.Als wichtigstes Ergebnis konnten zwei unabhängige genetische Prognosemarker für Kopf-Hals-Karzinome charakterisiert werden - die 11q13- und 3q-Amplifikation. In der multivariaten Cox-Regression zeigte sich, daß der Einfluß beider Parameter, besonders aber der 11q13-Amplifikation für die Einschätzung des rezidiv- und metastasenfreien sowie des Gesamtüberlebens der Patienten größer ist als der aller klinisch-pathologischen Parameter, insbesondere der TNM-Klassifikation.Comparative Genomic Hybridization (CGH) was performed on 100 primary head and neck squamous cell carcinomas, 27 cases of lymph node metastases and 10 second primaries. The main results are summarized as follows: The entity of head and neck squamous cell carcinomas is characterized by a pattern of chromosomal alterations involving deletions chromosomes 3p, 4p/q, 5q, 6q, 8p, 9p, 11p/q, 13q, 18q and 21q combined with overrepresentations of chromosomes 1p, 3q, 5p, 8q, 9q, 11q13, 16p, 17q, 19, 20q and 22q.Well differentiated carcinomas (G1) carry deletions on chromosomes 3p and 9p together with the overrepresentation of 3q indicating early tumor development. Accordingly, the undifferentiated tumors (G3) were charaterized by addtional deletions on chromosomes 4, 5q, 8p, 11, 13q, 18q, 21q and overrepresentations on 8q, 11q13 and 20q suggesting that these changes are preferentially associated with tumor progression.The metastatic phenotype of head and neck suqamous cell carcinomas is significantly associated with deletions of chromosomes 10q and 11.The overall survival time as well as the recurrence free survival time were significantly lower in patients who's tumors showed amplifications of the chromosomal region 11q13 and/or overrepresentations of chromosome 3q (tested for significance by the log rank test p=0.0008 / p=0.0299). Multivariate analysis (Cox's proportional hazards model) revealed both chromosomal alterations as most important independent prognostic factors in HNSCC prior to the established TNM staging system.
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Rousseau, Audrey. "Approche diagnostique et pronostique dans les tumeurs gliales : de l'immunohistochimie à l'hybridation génomique comparative." Paris 6, 2007. http://www.theses.fr/2007PA066256.
Full textAbstract:
Les 2 principaux types de tumeurs gliales sont les gliomes diffus et les épendymomes. L’étude immunohistochimique de l’expression de marqueurs de lignage astrocytaire (GFAP, YKL-40, ApoE) et oligodendroglial (Olig2, Sox10, ASCL1, NKX2-2) a porté sur 55 gliomes diffus. Les molécules GFAP, YKL-40, ApoE, ASCL1 et NKX2-2 permettaient de distinguer les oligodendrogliomes des astrocytomes et représentent donc des marqueurs tumoraux prometteurs. Les anomalies les plus fréquentes détectées en CGH array dans 45 épendymomes étaient un gain des chromosomes (chr) 7, 9, 12, 15, et une perte du chr22. L’association de ces 5 altérations était corrélée aux épendymomes médullaires tandis que les formes myxopapillaires du cône présentaient un profil génomique caractéristique, associant un gain des chr5, 7, 9, 16 et 18. L’identification d’altérations génomiques spécifiques d’un siège tumoral donné suggère que les épendymomes issus de régions différentes représentent des maladies génétiquement distinctes