<p>OVARIAN cancer research focuses on answering important questions related to the disease, determining whether new approaches are feasible to contribute towards improving current treatments or discovering new ones. This study focused on the transcriptional regulation of genes that have been implicated in ovarian cancer, based on the occurrences of single nucleotide polymorphisms (SNPs) within transcription factor binding sites (TFBSs). Through the application of several in silico tools, databases and custom programs, this research aimed to contribute toward the identification of potentially bio-medically important genes or SNPs for pre-diagnosis and subsequent treatment planning of ovarian cancer. A total of 379 candidate genes that have been experimentally associated with ovarian cancer were analyzed. This led to the identification of 121 SNPs that were found to coincide with putative TFBSs potentially influencing a total of 57 transcription factors that would normally bind to these TFBSs. These SNPs with potential phenotypic effect were then evaluated among several population groups, defined by the International HapMap consortium resulting in the identification of three SNPs present in five or more of the eleven population groups that have been sampled.</p>

<p>OVARIAN cancer research focuses on answering important questions related to the disease, determining whether new approaches are feasible to contribute towards improving current treatments or discovering new ones. This study focused on the transcriptional regulation of genes that have been implicated in ovarian cancer, based on the occurrences of single nucleotide polymorphisms (SNPs) within transcription factor binding sites (TFBSs). Through the application of several in silico tools, databases and custom programs, this research aimed to contribute toward the identification of potentially bio-medically important genes or SNPs for pre-diagnosis and subsequent treatment planning of ovarian cancer. A total of 379 candidate genes that have been experimentally associated with ovarian cancer were analyzed. This led to the identification of 121 SNPs that were found to coincide with putative TFBSs potentially influencing a total of 57 transcription factors that would normally bind to these TFBSs. These SNPs with potential phenotypic effect were then evaluated among several population groups, defined by the International HapMap consortium resulting in the identification of three SNPs present in five or more of the eleven population groups that have been sampled.</p>

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.

Après 25 ans de recherche intensive, aucun vaccin ou traitement définitif contre le SIDA n'existe, et les mécanismes moléculaires de pathogenèse de l'infection VIH-1 ne sont pas clairement élucidés. Les avancées technologiques permettent de comparer des sujets malades avec des sujets contrôles sur tout le génome. Il est ainsi possible d’identifier sans a priori des gènes potentiellement impliqués dans le développement de la maladie avec pour conséquence le développement rationnel de nouvelles stratégies diagnostiques ou thérapeutiques. Durant ma thèse, j’ai réalisé deux études d’association ‘génome entier’ dans le SIDA, en comparant les 275 non-progresseurs à long terme ou les 85 progresseurs rapides de la cohorte GRIV avec une cohorte de contrôles séronégatifs. J’ai réalisé une troisième analyse en exploitant les données issues de trois études ‘génome entier’ internationales dont la nôtre (France, Pays-Bas, USA), ciblant plus particulièrement les SNPs de fréquence faible (fréquence de l’allèle mineur, MAF<5%). Ces approches ‘génome entier’ ont réaffirmé le rôle central du HLA dans la progression vers le SIDA, mais aussi dévoilé de nouveaux gènes candidats très pertinents donnant une nouvelle lumière sur les mécanismes moléculaires de la maladie. / After 25 years of intensive research, no vaccine or cure exists against AIDS, and the molecular mechanisms of pathogenesis of HIV-1 infection are not clearly understood. Technological progress has made possible to compare cases versus controls over the whole genome. It is thus possible to identify genes potentially involved in disease development with no a priori, and consequently develop rationally new diagnostic or therapeutic strategies. During my PhD, I have completed two genome-wide association studies (GWAS) in AIDS, comparing 275 long term non-progressors or the 85 rapid progressors from the GRIV cohort with a cohort of seronegative controls. I have also completed a third analysis exploiting data from three international GWAS including ours (France, Netherlands, USA), targeting particularly low frequency SNPs (minor allele frequency, MAF <5%). These GWAS approaches have reaffirmed the central role of HLA for progression towards AIDS, but also revealed new relevant candidate genes, shedding a new light on the molecular mechanisms of disease progression.

Magister Scientiae - MSc / OVARIAN cancer research focuses on answering important questions related to the disease, determining whether new approaches are feasible to contribute towards improving current treatments or discovering new ones. This study focused on the transcriptional regulation of genes that have been implicated in ovarian cancer, based on the occurrences of single nucleotide polymorphisms (SNPs) within transcription factor binding sites (TFBSs). Through the application of several in silico tools, databases and custom programs, this research aimed to contribute toward the identification of potentially bio-medically important genes or SNPs for pre-diagnosis and subsequent treatment planning of ovarian cancer. A total of 379 candidate genes that have been experimentally associated with ovarian cancer were analyzed. This led to the identification of 121 SNPs that were found to coincide with putative TFBSs potentially influencing a total of 57 transcription factors that would normally bind to these TFBSs. These SNPs with potential phenotypic effect were then evaluated among several population groups, defined by the International HapMap consortium resulting in the identification of three SNPs present in five or more of the eleven population groups that have been sampled. / South Africa

Mycobacterium bovis, agent étiologique de la tuberculose bovine (bTB), affecte principalement les bovins mais évolue également dans des systèmes multi-hôtes. La France possède le statut UE indemne de bTB depuis 2000, mais la prévalence de la maladie a augmenté régulièrement ces cinq dernières années. Son contrôle passe par la connaissance des nouveaux facteurs de risque. Pour les déceler, nous avons étudié l’évolution spatio-temporelle de la bTB via la caractérisation des souches isolées de foyers français depuis 1978. A partir de plus de 2.000 souches, environ 600 profils génétiques ont été définis par spoligotypage et typage MLVA. Les groupes majoritairement identifiés, SB0120, SB0134, SB0121 et la «famille F4», sont différenciés plus finement par le MLVA qui augmente la puissance des études d’épidémiologie moléculaire. La diminution de la variabilité génétique et des changements de la distribution géographique des souches s’explique par des modifications dans les pratiques d’élevages et par la prolifération de certains génotypes évoluant dans des systèmes multi-hôtes. L’identification des groupes clonaux existants en France est confirmée par l’étude de mutations SNP effectuée suite au séquençage total de 82 génomes sélectionnés. De nouveaux outils de typage visant à affiner l’identification des souches, définir des profils de transmission méconnus et établir des liens épidémiologiques entre animaux sauvages et de rente sont envisagés. / Myobacterium bovis is the causative agent of bovine tuberculosis (bTB), principally affecting cattle but also evolving in multi-host livestock-wildlife systems. Prevalence is regularly increasing in France, an EU bTB-free state since 2000’s, after a 50 year collective fighting-campaign. To control the disease, it is necessary to acknowledge new risk factors. For identifying them, we have studied the spatial-temporary evolution of the disease by characterizing M. bovis strains causative of French outbreaks since 1978. Within more than 2,000 strains, around 600 profiles could be defined by spoligotyping and MLVA. SB0120, SB0134, SB0121 and the « F4 family » are the major spoligotypes isolated. In these groups, the refinement of differentiation can be increased by MLVA typing for powerful molecular epidemiological studies. Decreases in genetically and geographical variability could be explained by changes in husbandry practices and by the proliferation of unique genotypes in multi-host systems. Identification of clonal groups coexisting in France is confirmed by the study of SNPs mutations deduced from the whole genome sequencing of 82 representative strains. New typing tools for refining strains identification and disclosing unknown transmission patterns between livestock and wildlife are foreseeable

Les technologies actuelles permettent d'explorer le génome entier pour identifier des variants génétiques associés à des phénotypes particuliers, notamment de maladies. C’est le rôle de la bioinformatique de répondre à cette problématique. Dans le cadre de cette thèse, un nouvel outil logiciel a été développé qui permet de mesurer avec une bonne précision le nombre de marqueurs génétiques effectivement indépendants correspondant à un ensemble de marqueurs génotypés dans une population donnée. Cet algorithme repose sur la mesure de l’entropie de Shannon contenue au sein de ces marqueurs, ainsi que des niveaux d’information mutuelle calculés sur les paires de SNPs choisis au sein d’une fenêtre de SNPs consécutifs, dont la taille est un paramètre du programme. Il a été montré que ce nombre de marqueurs indépendants devient constant dès que la population est homogène avec une taille suffisante (N > 60 individus) et que l'on utilise une fenêtre assez grande (taille > 100 SNPs). Ce calcul peut avoir de nombreuses applications pour l'exploitation des données.Une analyse génome-entier a été réalisée sur le photo-vieillissement. Elle a porté sur 502 femmes caucasiennes pour lesquelles un grade de photo-vieillissement a été évalué selon une technologie bien établie. Les femmes ont été génotypées sur des puces Illumina OmniOne (1M SNPs), et deux gènes ont été identifiés (STXBP5L et FBX040) associés à un SNP passant le seuil de Bonferroni, dont l'implication dans le photo-vieillissement était jusqu'alors inconnue. De plus, cette association a aussi été retrouvé dans deux autres phénotypes suggérant un mécanisme moléculaire commun possible entre le relâchement cutané et les rides. On n'observe pas de réplication au niveau du critère lentigines, la troisième composante étudiée du photo-vieillissement.Ces travaux sont en cours de publication dans des revues scientifiques internationales à comité de lecture. / New technologies allow the exploration of the whole genome to identify genetic variants associated with various phenotypes, in particular diseases. Bioinformatics aims at helping to answer these questions. In the context of my PhD thesis, I have first developed a new software allowing to measure with a good precision the number of really independent genetic markers present in a set of markers genotyped in a given population. This algorithm relies on the Shannon's entropy contained within these markers and on the levels of mutual information computed from the pairs of SNPs chosen in a given window of consecutive SNPs, the window size is a parameter of the program. I have shown that the number of really independent markers become stable as soon as the population is homogeneous and large enough (N > 60) and as soon as the window size is large enough (size > 100 SNPs). This computation may have several applications, in particular the diminution of the Bonferroni threshold by a factor that may reach sometimes 4, the latter having little impact in practice.I have also completed a genome-wide association study on photo-ageing. This study was performed on 502 Caucasian women characterized by their grade of photo-ageing, as measured by a well-established technology. In this study, the women were genotyped with OmniOne Illumina chips (1M SNPs), and I have identified two genes (STXBP5L et FBX040) associated with a SNP that passes the Bonferroni threshold, whose implication in photo-ageing was not suspected until now. Interestingly, this association has been highlighted with two other phenotypes which suggest a possible common molecular mechanism between sagging and wrinkling. There was no replication for the lentigin criteria, the third component studied of photo ageing.These studies are on the process to be published in international peer-reviewed scientific journals.

L'Indonésie a été l'objet de la dispersion Austronésienne qui a débuté il y a environ 5000 ans depuis Taiwan, se propager à travers les Philippines et l'Indonésie, puis toucher l'Océanie à l'est, et à Madagascar à l'ouest. Malgré de nombreuses recherches en génétique sur la dispersion Austronésienne vers l'est, il y a très peu de données sur la dispersion vers l'ouest, laissant sans réponse de nombreuses questions, liées notamment au peuplement de Madagascar. Reposant sur l'analyse des données culturelles et biologiques, les populations d'Indonésie semblent avoir joué un rôle majeur dans la colonisation de Madagascar, le premier millénaire de notre ère. Cependant, le peu de populations Indonésiennes étudiées à ce jour n'a pas permis jusqu'à présent d'identifier la population indonésienne source. Dans ce présent travail, j'ai réalisé des études en génétique des populations de 12 populations Indonésiennes, qui à priori devraient éclairer l'histoire des migrations austronésiennes dans l'Océan Indien. Parmi elles sont inclus le Ma'anyan du sud-est de Bornéo qui sont les plus proches linguistiquement des Malgaches. En utilisant différents marqueurs génétiques, ma recherche a amélioré nos connaissances de la diversité génétique Indonésienne, et du lien génétique entre l'Indonésie et Madagascar. Résultats L'analyse des marqueurs uniparentaux (chr-Y et ADNmt) suggère que les Malgaches proviennent de plusieurs régions d'Indonésie, avec un lien privilégié avec le sud-est de Bornéo, le sud de Sulawesi et les îles de la Sonde. Etonnamment, les Ma'anyan partagent un nombre limité de lignées paternelles et maternelles avec les Malgaches, malgré leur proximité linguistique. Par ailleurs, en combinant l'analyse de fréquences des SNPs et l'analyse haplotypique à partir des données autosomales, il a été confirmé que la diversité génétique des Ma'anyan ne correspond pas à l'ancestralité asiatique des Malgaches. Cependant, en centrant l'analyse sur les populations du sud-est de Bornéo, l'origine de l'ancestralité asiatique des Malgaches est ancrée dans la population Banjar, un mélange de population Ma'anyan et Malaise, résultat des activités commerciales de l'empire Malais dans le sud-est de Bornéo, qui se sont poursuivies à travers l'océan Indien. Par ailleurs nos résultats ont aussi permis d'accroitre notre compréhension de la diversité génétique de l'Indonésie en identifiant (1) une nouvelle composante génétique austronésienne présente chez les Ma'anyan, et retrouvée à faible fréquence à travers l'Asie du Sud-Est, suggérant une plus grande complexité du modèle d'expansion austronésien dans la région et (2) le rôle joué par les nomades de la mer dans la structuration de la diversité génétique et les échanges entre populations dans l'Indonésie, soulignant l'histoire génétique complexe de populations suivant un mode de vie nomade. / Indonesia hosts a wide range of linguistic, ethnic and genetic diversity, comprising ~600 ethnic groups and 700 living languages. Indonesia has facilitated the last substantial wave of human migration was the Austronesian dispersal ~5,000 years ago, which is thought to have originated in Taiwan. Its influence spread through Philippines and Indonesia, ultimately impacting a wide geographical area, from Remote Oceania in the east and to Madagascar in the west. Despite considerable genetic research on the eastward Austronesian expansion, there is little equivalent research on the western edge, leaving major issues unresolved regarding the settlement of Madagascar. Based on cultural and biological studies, it has been suggested that Indonesian peoples played a major role in the colonization of Madagascar from around the mid-first millennium CE (Current Era). However, poor geographical coverage of Indonesian populations has prevented the Indonesian source populations from being identified. Here, I performed human population genetic studies on 12 new Indonesian populations, which were a priori expected to shed light on the westward migration of Austronesians across the Indian Ocean. This includes the Ma'anyan ethnic group from Southeast Borneo, who are the closest linguistic siblings to modern Malagasy. Using different genetic markers (Y-chromosome SNPs, mitochondrial DNA and genome-wide SNPs), my research has improved the description of Indonesian genetic diversity, and investigated the genetic links between Indonesia and Madagascar. Results Uniparental markers (Y-chromosome and mtDNA) analyses suggest that Malagasy derive from multiple regional sources in Indonesia, with a focus on southeastern Borneo, southern Sulawesi and the Lesser Sunda islands. Interestingly, the Ma'anyan share limited paternal and maternal lineages with the Malagasy, despite their linguistic connection. Furthermore, combining SNP frequency and haplotype-based analyses from autosomal genome-wide data, it was confirmed that the genetic diversity of the Ma'anyan does not match the Asian ancestry of the Malagasy. However, by focusing on Southeast Borneo populations, strong support was found for an origin of the Asian ancestry of Malagasy among the people of Banjar, an admixed population of Ma'anyan and Malay, likely resulting from trading activities by the Malay Empire in Southeast Borneo, and later continuing across the Indian Ocean arena. These results increase our understanding of genetic diversity across Indonesia by 1) identifying the unique and undiscovered Austronesian genetic component carried by the Ma'anyan, which occurs at low levels across Island Southeast Asia and suggests a more complex model for the Austronesian expansion in this region, and 2) describing the role played by sea-nomads in structuring genetic diversity and exchanges in central Indonesia, thus revealing the complex genetic history of populations living this rare nomadic lifestyle.

O uso de marcadores do tipo STR e SNP tem se revelado de grande importância na discriminação entre indivíduos de uma mesma população, assim como para estudos evolutivos. A utilização de um conjunto de 17 STRs e 46 SNPs específicos de cromossomo Y permitiu a caracterização de um conjunto de amostras representativas das populações do Rio de Janeiro e do oeste africano, com uma avaliação mais ampla sobre a ancestralidade de origem paterna. Na primeira parte deste estudo foram analisados 605 indivíduos do sexo masculino do estado do Rio de Janeiro. Como resultado, não foram observadas diferenças significativas entre as populações do sudeste e do Rio de Janeiro, que apresentou uma alta diversidade de haplótipos (0,9999 0,0001) e de haplogrupos (0,7589 0,0171). A comparação da população miscigenada do Rio de Janeiro com diferentes grupos étnicos ou populacionais mostrou que a frequência de indivíduos com marcadores tipicamente Europeus é de 77%, africanos é de 14,87% e em ameríndios é de 2,31%. A segunda parte do estudo revelou uma grande diversidade haplotípica (1,0000 0,0018) numa amostra do Oeste africano. Quanto ao valor da diversidade de haplogrupos (0,6895 0,0200), este foi similar aos observados em populações de origem Bantu do oeste e centro africanos, principalmente de Benin, Nigéria e Costa do Marfim. A terceira parte deste estudo mostrou que não existem diferenças significativas entre o componente africano da amostra do Rio de Janeiro e as populações africanas do sudeste, oeste e centro oeste. Por outro lado, observamos diferenças significativas quando comparamos o componente africano do Rio de Janeiro e o oeste africano com populações de Uganda, Quênia e África do Sul. A ampliação de estudos genéticos nas populações da África se fazem necessários para o entendimento da diversidade genética no mundo. Este trabalho contribuiu para fornecer mais alguns dados genéticos, que podem ser somados aos estudos mundiais que estão sendo realizados, ampliando os nossos conhecimentos sobre a formação das populações que também foram influenciadas pelo fenômeno da Diáspora Africana. / The use of STR and SNP markers has proved to be of great importance to discriminate individuals of the same population as well as for evolutionary studies. The use of a set of 17 STRs and 46 SNPs specific from the Y chromosome allowed the characterization of a group of samples representative of the Rio de Janeiro and the West African populations, with a deep assessment of the paternal ancestry. The first part of this study focused in the analysis of 605 males of the state of Rio de Janeiro. The results showed no significant differences between the Brazilian southeastern populations and Rio de Janeiro, which showed high values of haplotype (0.9999 0.0001) and haplogroup (0.7589 0.0171) diversities. The second part of the study revealed a high haplotype diversity (1.0000 0.0018) in a sample from West Africa. The value of haplogroup diversity (0.6895 0.0200) was similar to those previously seen in the West and Center African Bantu populations, mainly from Benin, Nigeria and Ivory Coast. The third part of this study showed no significant differences between the African component of our sample from Rio de Janeiro and the Southeastern, Western and Midwestern African populations. On the other hand, significant differences were observed when comparing the samples of the African component in Rio de Janeiro and of West Africa with population samples from Uganda, Kenya and South Africa. The increase of genetic studies in African populations is important for a better understanding of world genetic diversity. This work provided new genetic data, which can be added to those already available, expanding our knowledge about the formation of other populations also influenced by the African Diaspora.

O uso de marcadores do tipo STR e SNP tem se revelado de grande importância na discriminação entre indivíduos de uma mesma população, assim como para estudos evolutivos. A utilização de um conjunto de 17 STRs e 46 SNPs específicos de cromossomo Y permitiu a caracterização de um conjunto de amostras representativas das populações do Rio de Janeiro e do oeste africano, com uma avaliação mais ampla sobre a ancestralidade de origem paterna. Na primeira parte deste estudo foram analisados 605 indivíduos do sexo masculino do estado do Rio de Janeiro. Como resultado, não foram observadas diferenças significativas entre as populações do sudeste e do Rio de Janeiro, que apresentou uma alta diversidade de haplótipos (0,9999 0,0001) e de haplogrupos (0,7589 0,0171). A comparação da população miscigenada do Rio de Janeiro com diferentes grupos étnicos ou populacionais mostrou que a frequência de indivíduos com marcadores tipicamente Europeus é de 77%, africanos é de 14,87% e em ameríndios é de 2,31%. A segunda parte do estudo revelou uma grande diversidade haplotípica (1,0000 0,0018) numa amostra do Oeste africano. Quanto ao valor da diversidade de haplogrupos (0,6895 0,0200), este foi similar aos observados em populações de origem Bantu do oeste e centro africanos, principalmente de Benin, Nigéria e Costa do Marfim. A terceira parte deste estudo mostrou que não existem diferenças significativas entre o componente africano da amostra do Rio de Janeiro e as populações africanas do sudeste, oeste e centro oeste. Por outro lado, observamos diferenças significativas quando comparamos o componente africano do Rio de Janeiro e o oeste africano com populações de Uganda, Quênia e África do Sul. A ampliação de estudos genéticos nas populações da África se fazem necessários para o entendimento da diversidade genética no mundo. Este trabalho contribuiu para fornecer mais alguns dados genéticos, que podem ser somados aos estudos mundiais que estão sendo realizados, ampliando os nossos conhecimentos sobre a formação das populações que também foram influenciadas pelo fenômeno da Diáspora Africana. / The use of STR and SNP markers has proved to be of great importance to discriminate individuals of the same population as well as for evolutionary studies. The use of a set of 17 STRs and 46 SNPs specific from the Y chromosome allowed the characterization of a group of samples representative of the Rio de Janeiro and the West African populations, with a deep assessment of the paternal ancestry. The first part of this study focused in the analysis of 605 males of the state of Rio de Janeiro. The results showed no significant differences between the Brazilian southeastern populations and Rio de Janeiro, which showed high values of haplotype (0.9999 0.0001) and haplogroup (0.7589 0.0171) diversities. The second part of the study revealed a high haplotype diversity (1.0000 0.0018) in a sample from West Africa. The value of haplogroup diversity (0.6895 0.0200) was similar to those previously seen in the West and Center African Bantu populations, mainly from Benin, Nigeria and Ivory Coast. The third part of this study showed no significant differences between the African component of our sample from Rio de Janeiro and the Southeastern, Western and Midwestern African populations. On the other hand, significant differences were observed when comparing the samples of the African component in Rio de Janeiro and of West Africa with population samples from Uganda, Kenya and South Africa. The increase of genetic studies in African populations is important for a better understanding of world genetic diversity. This work provided new genetic data, which can be added to those already available, expanding our knowledge about the formation of other populations also influenced by the African Diaspora.