Das Ziel der vorliegenden Arbeit war die Quantifizierung JAK2 p.V617F mutierter Allele zur Verlaufskontrolle von Patienten mit JAK2 p.V617F positiven MPN nach allogener Stammzelltransplantation (SCT). Dabei sollte insbesondere untersucht werden, ob sich frühzeitig nach SCT ein höheres Rezidivrisiko der MPN vorhersagen lässt und zu welchen Zeitpunkten molekulare Untersuchungen nach SCT sinnvoll sind. Wir analysierten retrospektiv den Krankheitsverlauf von 30 Patienten. Dafür verwendeten wir die ARMS-QPCR und WTB-AS QPCR als zwei allel-spezifische Amplifikationsmethoden und untersuchten 142 Proben der ersten Kohorte (n=14) und 32 Proben einer zweiten Kohorte (n=16) im direkten Vergleich. Aus unseren Ergebnissen konnten folgende Rückschlüsse gezogen werden: 1. Die beiden allel-spezifischen Amplifikationsmethoden ARMS-QPCR und WTB-AS QPCR zur Quantifizierung der JAK2 p.V617F Mutation sind vergleichbar. 2. Als Ausgangsmaterial sind antikoaguliertes Vollblut oder auch Beckenkammbiopsien gleichermaßen geeignet. 3. Der Nachweis von > 1% JAK2 p.V617F Allele 28 Tage nach allogener SCT ist assoziiert mit einem signifikant höheren Rezidivrisiko einer JAK2 positiven MPN und einem schlechteren Gesamtüberleben.

Pediatric acute lymphoblastic leukemia (ALL) is the most common malignancy in children, which results from the malignant transformation of progenitor cells in the bone marrow into leukemic cells. The precise mechanisms for this transformation are not well defined, however recent studies suggest that aberrant regulation of gene expression or DNA methylation may play an important role. Hence, the aim of this thesis was to use novel methods to investigate genome-wide gene expression and DNA methylation patterns in a large collection of primary ALL cells from pediatric patients. With these studies, we aimed to increase the understanding of factors that regulate gene expression and DNA methylation in ALL. In the first study of the thesis we found that data obtained from genome-wide digital gene expression analysis enabled excellent cytogenetic subtype-specific classification of ALL cells and revealed new features of gene expression within the disease, such as prevalent antisense transcription and alternative polyadenylation. In the second study we used technology developed for large-scale single nucleotide polymorphism (SNP) genotyping for quantitative analysis of allele-specific gene expression (ASE), revealing widespread ASE in ALL cells. Analysis of DNA methylation in promoter regions of the genes displaying ASE using DNA-microarrays revealed frequent regulation of gene expression by DNA methylation. In the third study, using the same DNA methylation array, we identified differences in the DNA methylation patterns in ALL cells at diagnosis compared to healthy mononuclear cells from the bone marrow of the same children at remission. In the fourth study we measured the DNA methylation of >450,000 CpG sites across the genome in a large collection of ALL samples and non-leukemic control cells. We found that ALL cells displayed highly divergent DNA methylation patterns depending on their cytogenetic subtype and widespread regions of differential methylation were enriched for repressive histone marks. DNA methylation levels at distinct regions in the genome were substantially increased at relapse compared to matched cells from diagnosis. Collectively, the results presented in this thesis provide new insights into the patterns of gene expression and epigenetic changes in ALL and further increase our understanding of the development and progression of the disease, which will hopefully lead to better treatment options in the future.

In traditional forensic DNA casework, the inclusion or exclusion of individuals who may have contributed to an item of evidence may be dependent upon the assumption on the number of individuals from which the evidence arose. Typically, the determination of the minimum number of contributors (NOC) to a mixture is achieved by counting the number of alleles observed above a given analytical threshold (AT); this technique is known as maximum allele count (MAC). However, advances in polymerase chain reaction (PCR) chemistries and improvements in analytical sensitivities have led to an increase in the detection of complex, low template DNA (LtDNA) mixtures for which MAC is an inadequate means of determining the actual NOC. Despite the addition of highly polymorphic loci to multiplexed PCR kits and the advent of interpretation softwares which deconvolve DNA mixtures, a gap remains in the DNA analysis pipeline, where an effective method of determining the NOC needs to be established. The emergence of NOCIt -- a computational tool which provides the probability distribution on the NOC, may serve as a promising alternative to traditional, threshold- based methods. Utilizing user-provided calibration data consisting of single source samples of known genotype, NOCIt calculates the a posteriori probability (APP) that an evidentiary sample arose from 0 to 5 contributors. The software models baseline noise, reverse and forward stutter proportions, stutter and allele dropout rates, and allele heights. This information is then utilized to determine whether the evidentiary profile originated from one or many contributors. In short, NOCIt provides information not only on the likely NOC, but whether more than one value may be deemed probable. In the latter case, it may be necessary to modify downstream interpretation steps such that multiple values for the NOC are considered or the conclusion that most favors the defense is adopted. Phase I of this study focused on establishing the minimum number of single source samples needed to calibrate NOCIt. Once determined, the performance of NOCIt was evaluated and compared to that of two other methods: the maximum likelihood estimator (MLE) -- accessed via the forensim R package, and MAC. Fifty (50) single source samples proved to be sufficient to calibrate NOCIt, and results indicate NOCIt was the most accurate method of the three. Phase II of this study explored the effects of template mass and sample complexity on the accuracy of NOCIt. Data showed that the accuracy decreased as the NOC increased: for 1- and 5-contributor samples, the accuracy was 100% and 20%, respectively. The minimum template mass from any one contributor required to consistently estimate the true NOC was 0.07 ng -- the equivalent of approximately 10 cells' worth of DNA. Phase III further explored NOCIt and was designed to assess its robustness. Because the efficacy of determining the NOC may be affected by the PCR kit utilized, the results obtained from NOCIt analysis of 1-, 2-, 3-, 4-, and 5-contributor mixtures amplified with AmpFlstr® Identifiler® Plus and PowerPlex® 16 HS were compared. A positive correlation was observed for all NOCIt outputs between kits. Additionally, NOCIt was found to result in increased accuracies when analyzed with 1-, 3-, and 4-contributor samples amplified with Identifiler® Plus and with 5-contributor samples amplified with PowerPlex® 16 HS. The accuracy rates obtained for 2-contributor samples were equivalent between kits; therefore, the effect of amplification kit type on the ability to determine the NOC was not substantive. Cumulatively, the data indicate that NOCIt is an improvement to traditional methods of determining the NOC and results in high accuracy rates with samples containing sufficient quantities of DNA. Further, the results of investigations into the effect of template mass on the ability to determine the NOC may serve as a caution that forensic DNA samples containing low-target quantities may need to be interpreted using multiple or different assumptions on the number of contributors, as the assumption on the number of contributors is known to affect the conclusion in certain casework scenarios. As a significant degree of inaccuracy was observed for all methods of determining the NOC at severe low template amounts, the data presented also challenge the notion that any DNA sample can be utilized for comparison purposes. This suggests that the ability to detect extremely complex, LtDNA mixtures may not be commensurate with the ability to accurately interpret such mixtures, despite critical advances in software-based analysis. In addition to the availability of advanced comparison algorithms, limitations on the interpretability of complex, LtDNA mixtures may also be dependent on the amount of biological material present on an evidentiary substrate.

Made available in DSpace on 2015-04-01T14:16:04Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 1809210 bytes, checksum: e118d10e8ea156df56a7871608a59d7b (MD5) Previous issue date: 2014-02-26 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Human identification is based on analyzing DNA through present throughout the genome molecular markers. These markers are transmitted from parents to offspring by heredity. STR markers are currently the most commonly used genetic markers in Forensic Genetics due to their high polymorphism, high reproducibility, possibility of being amplified by PCR in multiple copies in a single reaction, and minute quantities of DNA (1ng). The DNA test that allows individualization of the people is essential tool to the solution of forensic human identification cases, sex crimes, crime scenes (including or excluding suspects), mass disasters, and its result is presented in statistical calculations that consider allele frequency of markers used. So it is important to know the allele frequencies presented in the regional population so that the results are the most reliable possible. In this study , 15 autossomal markers (loci) STR or microsatellite (CSF1PO, D13S317, D16S539, D18S51, D19S433, D21S11, D2S1338, D3S1358, D5S818, D7S820, D8S1179, FGA, TH01, and VWA TPOX) were studied in 766 unrelated individuals paraibanos, demonstrating a tri population - hybrid formed Africans (25.86 %), Amerindian (6.81 %) and Europeans (67.33 %). The most informative were D21S11 and FGA, and were less informative TPOX, D7S820 and D13S317. The results are important for a database with allele frequencies found in Paraiba population can serve as a useful basis for calculating forensic practice in the State of Paraíba. / A identificação humana está baseada na análise do DNA através de marcadores moleculares presente em todo o genoma. Estes marcadores são transmitidos de pais para filhos por hereditariedade. Atualmente os marcadores STR são os marcadores genéticos mais utilizados em Genética Forense devido ao seu elevado polimorfismo, alta reprodutibilidade, possibilidade de serem amplificados por PCR em inúmeras cópias numa só reação e em mínimas quantidades de DNA (1ng). O exame de DNA que permite a individualização das pessoas é ferramenta indispensável à solução de casos forenses de identificação humana, crimes sexuais, locais de crime (incluindo ou excluindo suspeitos), desastres em massa, e tem seu resultado apresentado em cálculos estatísticos que consideram a frequência alélica dos marcadores usados. Por isso é importante o conhecimento das frequências alélicas apresentadas na população regional de forma que os resultados sejam os mais fidedignos possíveis. Neste trabalho, 15 marcadores autossômicos (loci) STR ou microssatélites (CSF1PO, D13S317, D16S539, D18S51, D19S433, D21S11, D2S1338, D3S1358, D5S818, D7S820, D8S1179, FGA, TH01, TPOX e vWA) foram estudados em 766 indivíduos paraibanos não aparentados, demonstrando uma população tri - hibrida, formada de africanos (25,86%), ameríndios (6,81%) e europeus (67,33%). Os mais informativos foram D21S11 e FGA, e os menos informativos foram TPOX, D7S820 e D13S317. Os resultados são importantes para que um banco de dados com as frequências alélicas encontradas na população paraibana possa servir de base de cálculo útil para prática forense no Estado da Paraíba.

Entre as muitas aplicações das tecnologias de identificação biológica humana, estão as finalidades forenses. O objetivo desta pesquisa foi verificar frequências alélicas de Short Tandem Repeat (STR) e os parâmetros estatísticos de interesse em genética de populações e forense para desenvolver o primeiro banco de dados populacional de DNA na Faculdade de Odontologia de Bauru, Universidade de São Paulo, (FOB/USP) para futuros usos forenses. Frequências alélicas de 15 locos autossômicos e do marcador de gênero amelogenina foram determinadas utilizando amostras de 200 μL de saliva doados por 296 alunos de graduação da FOB/USP, com idade ≥ 18 anos, após aprovação ética. Os testes laboratoriais foram feitos com kits comerciais. Resultados e parâmetros estatísticos foram obtidos por meio de programas clássicos: GeneMapper-ID-X, MS Excel 2002 versão 10.6871.6870, GenAlEx 6.5 e Arlequin 3.5, comparando quatro populações (brasileira, portuguesa, norte-americana e a população deste estudo). Os locos mais polimórficos foram D18S51 (17 alelos) e FGA (15 alelos), seguidos pelo D21S11 (13 alelos) e os menos polimórficos foram D16S539 e TH01 (7 alelos cada). A análise comparativa com amostra da população brasileira proveniente de estudos anteriores (n > 100.000) pelo teste goodness of fit X2 index não mostrou diferenças significativas entre estes grupos (p = 0,9999). Outros parâmetros estatísticos foram calculados comparando as populações: local (deste estudo), portuguesa e norte-americana. A análise de variância molecular (AMOVA) entre as três populações, entre as pessoas da mesma população e para cada pessoa de cada população mostrou que existe uma elevada variância individual (99%), que esta variância é mantida uniformemente entre as pessoas da mesma amostra/região (1%) e entre as três populações estudadas (0%). O estudo confirmou o elevado grau de polimorfismo e a alta heterozigosidade (96,5%) da população. Houve diferença significativa quanto ao gênero (79,7% mulheres) quando comparado à população brasileira em geral (50,4%), explicada pelas características do corpo discente da FOB/USP composto por 80,6% de pessoas do gênero feminino. Interessante foi a observação de uma microvariante alélica no loco D18S51, fora da escada padrão e da escala de abrangência do kit, correspondente ao alelo 29, ainda não definida na base de dados internacional (STRBase, atualizada em 07/08/2015). Esta microvariante deverá ser confirmada por testes familiares e sequenciamento de DNA para verificar a possibilidade de outra ocorrência familiar ou duplicação de nucleotídeos. No futuro, os dados obtidos neste estudo devem ser incorporados ao banco de dados da população brasileira e podem ser considerados como referência genética da população regional, ajudando a elucidar casos forenses. Após a confirmação, a potencial nova microvariante alélica contribuirá para a base de dados internacional STRBase. / There are many ways of applying biological human identification technologies, among these are forensic applications. The objective of this study was to verify allele frequencies for 15 autosomal short tandem repeat (STR) loci and develop the first human DNA population database at the Bauru School of Dentistry, University of São Paulo (FOB/USP), for future forensic uses. Allele frequencies for these STR loci and an amelogenin gender marker were determined using 200 μL samples of saliva donated by 296 undergraduates from FOB/USP who were ≥ 18 years old at the time of the sample collect after signing a consent form with ethical approval. For laboratory tests, commercial kits were used. Results and statistical parameters were obtained using the following software: GeneMapper IDX (version 1.5), MS Excel 2002 (version 10.6871.6870), GenAlEx (version 6.5) and Arlequin (version 3.5) to compare four populations (Brazil, Portugal, U.S. and this study population). Results indicated that the most polymorphic loci were D18S51 (17 alleles) and FGA (15 alleles), followed by D21S11 (13 alleles); the least polymorphic loci were D16S539 and TH01 (7 alleles each). Various Brazilian populations (n > 100,000) from other studies were compared with this studys Brazilian population using a goodness-of-fit chi-squared test, and no significant differences in these frequencies were observed between these two population groups (p = 0.9999). Other forensic and population genetic statistical parameters were calculated comparing this studys population with Portugal and U.S. populations. For example, an analysis of molecular variance (AMOVA) among all populations, among people of the same population and for each person for each population, showed that people have high individual variance (99%) and that this variance is maintained evenly between people of the same sample/region (1%) and among the three populations studied (0%). This study reinforced the conclusion of other allele frequency population studies for the 15 autosomal STR loci tested, confirming high polymorphic grade and high heterozygosity (96.5%). There were significantly more women in the study (79.7%) when compared to the general Brazilian population (50.4%) since the student body of FOB/USP is 80.6% female. Interestingly, an off-ladder D18S51 allele micro-variance corresponding to the allele 29, not yet identified, was found which should be confirmed using paternity and sequencing tests to verify the possibility of either familial occurrence or nucleotide duplication. In the future, due to the small differences found, the parameters obtained in this study should be incorporated into the Brazilian population database and be considered for a regional population genetic prototype database potentially aiding forensic cases with comparisons and calculations. After confirmation, the potentially new micro variant allele found could be included in the international STRBase.

Philosophiae Doctor - PhD / Solute carrier transporters belonging to the major facilitator family of membrane transporter are increasingly being recognized as a possible mechanism to explain inter-individual variation in drug efficacy and response. Genetic factors are estimated to be responsible for approximately 15-30% of inter-individual variation in drug disposition and response. The aims of this study were to determine the minor allele frequencies of 78 previously identified single nucleotide polymorphisms in the pharmacogenomically relevant SLC22A1-3 and SLCO1B1 genes in the Admixed population of South Africa. Thereafter, to determine whether allele and genotype frequencies for these SNP were different from that reported for other African, Caucasian, and Asian populations. The inferred haplotypes from the genetic information possessed the potential to subsequently be used in future to design and interpret results of pharmacogenomic association studies involving these genes and their substrate drugs. Furthermore, to determine whether the Cape Admixed population harbour novel SNPs in the proximal promoter regions of SLC22A1- 3 and SLCO1B1-3 genes, that encodes hOCT1-3 and hOATP1 and hOATP3, respectively. SNaPshot™ multiplex single base mini-sequencing systems were developed and optimized for each of SLC22A1, SLC22A2, SLC22A3, and SLCO1B1 genes covering the previously identified 78 SNPs. These systems were then used to genotype the alleles of 130 healthy Cape Admixed subjects residing in Cape Town, South Africa. In addition, the proximal promoter regions of the SLC22A1-3 and SLCO1B1-3 genes of 96 of the participants were screened for novel SNPs by direct sequencing. The Cape Admixed subjects investigated displayed a lack of variation and were monomorphic for 78% of the SNPs screened. None of the SLC22A3 SNPs investigated was observed in this study. Sequencing of the proximal promoter regions of the SLC22 and SLCO genes did not reveal any novel SNPs in the 96 Cape Admixed subjects that were screened. This study highlights the fact that African populations do not have the same allele frequencies for SNPs in harmacogenomically relevant genes. Furthermore, the Cape Admixed and other African populations do not share all reduced-function variants of the SLC22A1-3 and SLCO1B1-3 genes with Caucasian and Asian populations. In addition, previously identified novel regulatory variants in SLC22A2 did not exhibit a significant effect on the ability of the promoter to drive transcription. However, it must be noted that these results were observed at 95% confidence interval, and that a 99% confidence interval the significance may increase theoretically. Additionally, it should be noted that more intensive studies are required to determine the potential effect these novel variants may well cause. This study lays the foundation for the design and interpretation of future pharmacogenomic association studies between the variant alleles of the SLC22A and SLCO genes in the Cape Admixed population, as well as optimizations for future expression, and more importantly, drug transport assays with respect to drug disposition and efficacy. / National Research Foundation (NRF) and the Medical Research Council (MRC)

Les cancers de l’ovaire constituent la cinquième cause de cancer chez la femme et la principale cause de décès pour cancer gynécologique. Ce mauvais pronostique est lié à un diagnostic tardif de la maladie et à l’acquisition de la résistance au sel de platine. L’individualisation thérapeutique est nécessaire compte tenu de l’évolution très clinique hétérogène malgré une histologie et un stade similaire. Les facteurs pronostiques classiques comme l’âge, le stade FIGO, le type histologique, le grade et le résultat chirurgical, ne sont pas suffisants pour prédire la réponse thérapeutique et le pronostique. Cette hétérogénéité clinique est probablement expliqué par l’existence des formes biologiques différentes. La réponse clinique initiale à la chimiothérapie chez la plupart des patientes suivi d’une récidive dans plus de la moitié des cas suggère l’existence d’une subpopulation des cellules qui développe des mécanismes de résistance et survivent. Le TGCA a retrouvé des mutations au niveau de TP53 dans plus de 95% des patientes avec un cancer séreux de l’ovaire à haut grade. Ils ont trouvé une prévalence élevé de mutations somatiques mais peu récurrentes, avec un nombre important des variations du nombre de copies. La recombinaison homologue est défectueuse dans la moitié des tumeurs analysées et les voies de signalisation NOTCH et FOXM1 sont également impliqués. La mutation TP53 et les défets de réparation d’ADN provoquent une instabilité génétique et favorisent une diversité génétique. Il y a des données dans la littérature sur l’hétérogénéité existante entre différentes localisations des cancers de l’ovaire en fonction du moment de la maladie chez la même patiente et chez des patientes différentes avec la même histologie. Nous avons centré notre étude sur la caractérisation de l´expression génique des métastases péritonéales sur une série de patientes avec un cancer sereux de haut grade de l’ovaire en carcinose péritonéale. Nous avons montré des profils géniques différents entre les localisations péritonéales et la tumeur primitive. Nous avons mis en évidence que les gènes présentant des variations d’expression génique les plus marquées au niveau du péritoine codaient pour des protéines impliquées dans les voies de signalisation des principales cytokines intervenant dans l’oncogenèse dont la voie JAK/STAT. Ces voies de signalisation sont probablement impliquées dans la réponse des tumeurs à leur microenvironnement au niveau du péritoine (J Translational medicine 2012). Nous avons réalisé une deuxième étude pour combiner le séquençage génomique et transcriptomique au niveau des prelevements multi-site des patientes avec un cancer de haut grade de l´ovaire afin d’évaluer s’il existe des différences d’expression allélique. 43 gènes montrent des variants alléliques communs à tous les patients. La majorité des gènes presentent une expresión preferentielle par site mais les voies de sigalisation sont similaires pour les localisations peritoneales et pour les tumeurs primitives. Ces produits codent des protéines impliquées dans les voies de signalisation impliquées dans l’adhésion, la migration cellulaire, la réparation de l’ADN ou la croissance cellulaire et peuvent être des cibles thérapeutiques éventuelles (PLOS Genetics under final review). / Ovarian cancer is the fifth most common cause of cancer in women and the leading cause of death in gynaecological cancer. This low survival rate is due to the frequent diagnosis of epithelial ovarian cancer at an advanced stage, and to intrinsic and acquired resistance to platinum-based chemotherapy. Individualisation of treatment is necessary since EOC is a heterogeneous disease. Patients with morphologically similar, advanced-stage tumours display a broad range of clinical outcomes. Prognostic features, including patient’s age, performance status, FIGO stage, histological tumour grade and subtype, and initial surgery results, are insufficient to capture the important individual variations in response to chemotherapy and survival. This heterogeneous outcome suggests the existence of biologically different forms. The Cancer Genome Atlas (TCGA) found that TP53 mutations are present in more than 95% of HGSOC. They found a high prevalence of somatic mutations, but there is a low prevalence of recur¬rent mutations; and there are large-scale copy number aberrations. Initial analyses also suggest that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in ovarian cancer pathogenesis. However, TP53 mutation and frequent germline and somatic DNA repair defects lead to genetic instability with the potential to generate genetic diversity. Indeed, genetic heterogeneity by different mutational profiles throughout time among different tumor localisations within the same patient, and between patients have been reported.We have focused our research on the charecterisation of peritoneal gene expression profiles compared to primary ovarian lesions. High-density gene expression arrays demonstrate significant different gene expression profiles compared to theirs matched ovarian primary tumors. Differentially expressed genes are enriched in specific pathways, including cell adhésion, cytokine signaling and specifically JAK-STAT pathway. Underlying copy number variation significantly affect gene expression, and patients with copy number alterations displayed greater gene expression différences between their peritoneal and matched primary ovarian lesions (J Translational medicine 2012). In a second study, we performed a combined genome and transcriptome analysis form multi-site samples form ovarian cancer patients to identify preferentially expressed alleles. 43 genes shared across all patients presented significant allele variants. Patients clustered together but every sample and site clustered independently at the variant level. Most genes seemed site-specific but there were similar pathways in the primary and metastatic sites. Preferentially expressed alleles could act as cancer drivers and therefore they can constitute a new therapeutic target (PLOS Genetics under final review).

No description available.

No description available.

In the last years, Genome-Wide Associations Studies (GWAS) found many variants associated with complex diseases. However, the biological and molecular links between these variants and phenotypes are still mostly unknown. Also, even if sample sizes are constantly increasing, the associated variants do not explain all the heritability estimated for many traits. Many hypotheses have been proposed to explain the problem: from variant-variant interactions, the effect of rare and ultra-rare coding variants and also technical biases related to sequencing or statistic on sexual chromosomes. In this thesis, we mainly explore the hypothesis of variant-variant interaction and, briefly, the rare coding variants hypothesis while also considering possible molecular effects like allele-specific expression and the effects of variants on protein interfaces. Some parts of the thesis are also devoted to explore the implementation of efficient computational tools to explore these effects and to perform scalable genotyping of germline single nucleotide polymorphisms (SNPs) in huge datasets. The main part of the thesis regards the development of a new resource to identify putative variant-variant interactions. In particular, we integrated ChIP-seq data from ENCODE, transcription factor binding motifs from several resources and genotype and transcript level data from GTeX and TCGA. This new dataset allows us to formalize new models, to make hypothesis and to find putative novel associations and interactions between (mainly non-coding) germline variants and phenotypes, like cancer-specific phenotypes. In particular, we focused on the characterization of breast cancer and Alzheimer’s Disease GWAS risk variants, looking for putative variants’ interactions. Recently, the study of rare variants has become feasible thanks to the biobanks that made available genotypes and clinical data of thousands of patients. We characterize and explore the possible effects of rare coding inherited polymorphisms on protein interfaces in the UKBioBank trying to understand if the change in structure of protein can be one of the causes of complex diseases. Another part of the thesis explores variants as causal molecular effect for allele-specific expression. In particular, we describe UTRs variants that can alter the post-transcriptional regulation in mRNA leading to a phenomenon where an allele is more expressed than the other. Finally, we show those variants can have prognostic significance in breast cancer. This thesis work introduces results and computational tools that can be useful to a broad community of researcher studying human polymorphisms effects.