Dentre os vários marcadores genéticos existentes, alguns SNPs (Single Nucleotide Polymorphisms) podem estar associados à determinação de uma série de características fenotípicas (cor de pele, olhos e cabelos, estatura, forma do rosto, espessura do fio de cabelo) tendo sua predição um grande valor nas investigações forenses. Dentre os principais genes conhecidos por controlarem a pigmentação humana, através da produção da melanina, o SLC24A5 (solute carrier family 24, member 5) e o MC1R (melanocortin 1-receptor) apresentam um papel fundamental na melanogênese. O advento do sequenciamento de nova geração permitiu o processamento de várias regiões genômicas e indivíduos simultaneamente, aumentando a disponibilidade e precisão de dados de genomas completos, como alcançado em estudos como o 1000 Genomes Project. Nossas análises preliminares demonstraram que os dados de Fase 3 do 1000 Genomes são muito mais confiáveis do que as versões anteriores. Com esses dados, obtidos para 26 populações globais, foram realizadas análises populacionais (diversidade haplotípica, desequilíbrio de ligação, redes de haplótipo e de variância molecular) para os genes MC1R e SLC24A5 a fim de se compreender melhor seus padrões de diversidade, correlacionando-os à prováveis eventos de seleção natural que tenham moldado sua história evolutiva, como por exemplo a intensidade da radiação UV nas diferentes regiões geográficas. Alguns padrões foram encontradas entre os grupos africano, europeu e asiático, de acordo com a história evolutiva já descrita para estes grupos. Apesar disso, foi observado um padrão claro de varredura seletiva para o SLC24A5 nos resultados obtidos, como o alto desequilíbrio de ligação e baixa diversidade haplotípica. As análises da diversidade do SLC24A5 associadas com as zonas de incidência UV, no entanto, não apresentaram uma correlação clara entre a intensidade da radiação UV e a diversidade haplotípica / Among the various existing genetic markers, some SNPs may be associated with the determination of a series of phenotypic characteristics (skin, eyes and hair color, height, face shape, hair thickness) and its prediction could have a great value in forensic investigations. Among the major genes known to control human pigmentation through melanin production, SLC24A5 (solute carrier family 24, member 5) and MC1R (melanocortin-1 receptor) have a major role in melanogenesis. The advent of next-generation sequencing has enabled processing of several individuals and genomic regions simultaneously while increasing the availability and accuracy of whole genomes data, such as 1000 Genomes Project has achieved. Our preliminary analysis showed that Phase 3 data from the 1000 Genomes are far more reliable than previous versions. Using this data, obtained for 26 global populations, several analyzes were performed (haplotype diversity, linkage disequilibrium, haplotype networks and molecular variance) for MC1R and SLC24A5 in order to better understand their diversity patterns, correlating them to natural selection events which may have shaped their evolutionary history, such as UV radiation intensity in different geographical regions. Some patterns were found between African, European and Asian groups, according to the evolutionary history already described for these groups. Nevertheless, a strong pattern of selective sweep was observed for SLC24A5 in our data, such as high linkage disequilibrium and low haplotype diversity. Analysis of SLC24A5 diversity associated to UV, however, did not show a clear correlation between the UV radiation intensity and haplotype diversity

Alloimmunisation becomes a problem when serological discrepancies occur in matching antigens between donors and patients for blood transfusion. The rate of alloimmunisation has been increased especially in multiply transfused patients. Blood group genotyping (BGG) is a DNA-based assay that aids in reducing this situation. Currently, many platforms of BGG have become available, in which every technique has its own advantages and disadvantages. All these platforms lack the ability to identify novel alleles that might have an unknown clinical significance. The advent of next-generation sequencing (NGS) offers identification of the unprecedented alleles due to its basis of sequence-based typing. Moreover, it provides an extreme high-throughput which may be able to screen many donors and patients in a single run. In this project, two approaches have been developed in generating sequencing libraries followed by sequencing on the Ion Torrent Personal Genome MachineTM platform (Ion PGMTM). The first approach was amplicon-based target selection using Ion AmpliseqTM Custom Panel, designated as Human Erythrocyte Antigens and Human Platelet Antigens Panel (HEA and HPA Panel). This panel assay screens 11 blood group systems, as well as 16 human platelet antigens. The outcome was extraordinary, in particular four novel alleles had been identified out of 28 samples, one in the RHCE gene 208C > T (Arg70Trp) in exon 2 and three in the KEL gene. The first SNP was 331G > A (Ala111Thr) in exon 4. The second SNP was 1907C > T (Ala636Val) in exon 17 and the third SNP was 2165T > C (Leu722Pro) in exon 19. However, some issues occurred regarding co-amplification of homologous genes. The second approach was a long-range polymerase chain reaction (LR-PCR) based approach. This method provided a high resolution assay by amplification of entire genes, including the non-coding area, of the Kell and Rh blood group systems. The Kell blood group was initially utilised as a model in order to apply the same approach on the Rh system. Most alleles encoding the antigens of the Kell blood group, especially the high prevalence ones, were identified. The Rh LR-PCR approach was carried out by amplification of the RHD and RHCE genes with seven amplicons. For five RhD-positive samples no mutations were observed within the coding areas. On the other hand, five serotyped weak D samples were genotyped as; two weak D type 1, two weak D type 2 and one DAR3.1 weak partial D 4.0 (RHD*DAR3.01). Regarding the RHCE, the following antigens (C, c, E, c) were predicted properly from the sequencing data. Moreover, the RHCE*ceVS.02 was identified. 64 and 39 intronic SNPs were identified in RHD and RHCE genes, respectively. The intronic SNPs assisted the genotyping process by identifying the haplotype of interest. Interestingly, the novel allele identified in the RHCE gene by the HEA and HPA Panel was confirmed to belong to the RHCE gene by the LR-PCR approach, indicating the panel misaligned it to the RHD gene. In conclusion, NGS paves the way to be an alternative substitution to the previous molecular techniques. It would supplant the conventional serology for typing blood for transfusion.

Breast cancer is the most common cancer in women and research efforts to unravel the underlying mechanisms that drive carcinogenesis are continuous. The emergence of high-throughput sequencing techniques and their constant advancement, in combination with large scale studies of genomic and transcriptomic data, allowed the identification of important genetic changes that take place in the breast cancer genome, including somatic mutations, copy number aberrations and genomic rearrangements.The overall aim of this thesis is to explore the presence of genetic changes that take place in the breast cancer transcriptome and their possible contribution to carcinogenesis. The aim of the first research study was the identification of expressed gene fusions in breast cancer and the study of their association with other genomic events. For achieving this, transcriptome sequencing and Single Nucleotide Polymorphism arrays data for a cohort of 55 tumors and 10 normal breast tissues were combined. Gene fusions were detected in the majority of the samples, with evident differences between breast cancer subtypes, where HER2+ samples had significantly more fusions than the other subtypes. The genome-wide analysis uncovered localization of fusion genes in specific chromosomes like 17, 8 or 20. Additionally, a positive correlation between the number of gene fusions and the number of amplifications was observed, including the association between fusions on chromosome 17 and the amplifications in HER2+ samples, which can be attributed to the highly rearranged genomes of these subtypes. Finally, the absence of highly recurrent fusions across this cohort adds to the notion that gene fusions in breast cancer are most likely private events, with the majority being “passenger” events. In the second research study, the aim was to identify a connection between viral infections and breast cancer by devising five different computational methods for the analysis of both transcriptome and exome data in a cohort of 58 breast tumors. Despite being able to detect viral sequences in our testing dataset, no significantly high numbers of viral sequences were detected in our samples. Specifically, viral sequences (~2-30 reads) were extracted belonging to viruses EBV, HHV6 and Merkel cell polyomavirus. Such low levels of viral expression direct against a viral etiology for breast cancer but one should not exclude possible cases of integrated but silent viruses.In the third research project, we analyzed in silico the transcriptional profiles of human endogenous retroviruses in breast cancer. Despite being scattered across the genome in large numbers, a number of ERVs are actively transcribed, consisting of a small percentage of the total mapped reads. Alongside protein coding genes and lncRNAs, they show distinct expression profiles across the different breast cancer subtypes with luminal and basal-like samples clear separating from each other. Additionally, distinct profiles between ER+ and ER- samples were observed. Tumor specific ERV loci show an association with the immune status of the tumors, indicating that ERVs are reactivated in tumors and could play a role in the activation of the immune response cascade.The results presented in this thesis exhibit only in a small fragment the diversity and heterogeneity of the breast cancer transcriptome. The strength of the sequencing techniques allows the in depth detection of different genomic events. Gene fusions should be considered as part of the breast cancer transcriptome but their low recurrence across samples indicates for a role as passenger events. Under the light of existing results, viral infections do not play a significant role in breast cancer. On the other hand, human endogenous retroviruses, despite originating from exogenous viruses, seems to exhibit transcriptional profiles similar to those of normal genes, indicating that they are part of the genome’s transcriptional machinery. / Doctorat en Sciences biomédicales et pharmaceutiques (Médecine) / info:eu-repo/semantics/nonPublished

The climate in the north is changing over time, which affects the nature in many ways. For instance, some microorganisms that cause infections might become more common. This might have negative consequences for reindeer husbandry. In Sweden, this is an industry that is relatively large. However, even though the reindeer is common in the north the knowledge about its diseases is limited.In this study the prevalence of microorganisms that may cause infection in reindeer was investigated. Comparisons between different sami villages and previous studies were performed to detect differences that could occur due to climate changes. The diseases and microorganisms that were analyzed with PCR were malignant catarrhal fever, herpes infections, Chlamydia sp. and bovine viral diarrhea (BVD). The cause of eye problems in reindeer was also investigated. BVD and bovine leukemia virus where analyzed with ELISA. Next generation sequencing where used for broader screening of samples for microorganisms that might be of interest of future analysis in more detailed follow-up studies.Since not enough samples were available at the time of this study findings could not be linked to changing climate. In the reindeer with eye infection Chlamydia sp., Moraxella sp. and Neisseria sp. can probably be involved causing disease. This should be further investigated to be able to determine whether it is true or not by analyzing samples from individuals without changes in the eyes. The prevalence of reindeers with antibodies against BVD has increased in Sweden since 2012. There will be further studies in this field with reindeers from other northern countries.

Les ataxies cérébelleuses héréditaires sont un ensemble de pathologies neurodégénératives ou neuro-développementales rares responsables d’un handicap fonctionnel important. Nous décrivons la découverte dans deux familles consanguines avec une ataxie cérébelleuse, une épilepsie et un retard mental deux mutations homozygotes dans le gène WWOX à l’aide du séquençage de l’exome d’un des patients de chaque famille. Ce gène était connu comme un gène suppresseur de tumeur. Par une stratégie de capture ciblée de 57 gènes d’ataxies cérébelleuses sur une série de 155 patients, nous avons posé un diagnostic dans 20,6% des cas dont des mutations d’ANO10 et SYNE1. Des études multicentriques ont permis d’étendre les connaissances sur ces maladies et montrer l’existence de phénotypes sévères dans ARCA1.A partir de cette série, nous avons validé en aveugle la pertinence d’un algorithme diagnostique clinico-biologique proposé par l’article de Anheim dans le New England Journal of Medicine en 2012. / Hereditary cerebellar ataxias are a group of neurodegenerative or neurodevelopemental diseases responsible of major disability. We found thanks to exome sequencing mutations in the WWOX gene in two consaguineous families presenting with cerebellar ataxia, epilepsy and mental retardation. This gene was until recently only recognized to be a tumor suppressor.With a 57 ataxia genes targeted capture strategy, next generation sequencing in 155 patients found 20,6% of positive diagnosis, including several new mutations in ANO10 and SYNE1. Multi center studies allow to extend clinical knowledge with severes phenotypes especially in ARCA1.We validate a clinico-biological algorithm for recesssive ataxias diagnosis published by Anheim in the in New England Journal of Medicine, 2012 in a blinded manner.

Contrôler les bactéries altérantes des aliments, notamment les produits carnés crus, est un enjeu majeur pour les industries agroalimentaires. Les conditions de stockage de la viande sous différentes atmosphères exercent une pression de sélection et modifient le comportement et le développement des communautés bactériennes initialement présentes. Des méthodes de séquençage à haut débit, utilisées pour caractériser différents écosystèmes microbiens, ont été appliquées pour étudier la dynamique des communautés bactériennes de la viande de poulet au cours du stockage.Nous avons développé une méthode pour constituer des écosystèmes microbiens standards dont la composition a été déterminée par pyroséquençage du gène de l’ARNr 16S. La présence de Brochothrix thermosphacta et de Pseudomonas parmi les espèces dominantes a été confirmée et nous avons mis en évidence que Shewanella et Carnobacterium étaient sous dominantes. Nous avons sélectionné deux écosystèmes pour effectuer des challenges tests reproductibles sur de la viande de poulet conservée sous 3 atmosphères couramment utilisées. Une analyse métatranscriptomique et métagénomique a été réalisée afin de savoir “Quelles bactéries étaient présentes ?”, “Qu’étaient-elles capables de faire?” et “Qu’exprimaient-elles?” suivant les conditions.Nous avons ainsi pu évaluer l’impact des mélanges gazeux sur la dynamique bactérienne et les fonctions exprimées par les bactéries suivant les contaminants initiaux. Cela nous donne des pistes pour fournir des indications afin d’optimiser la conservation de la viande en contrôlant les écosystèmes microbiens / Controlling spoilage microorganisms, especially in raw meat products, is challenging for the food industry.Storage conditions such as modified atmosphere packaging (MAP) have selective effects on the microbiota dynamics. Thanks to the recent developmentof next generation sequencing methods widely used for characterizing microbes in different ecosystems, we studied bacterial community dynamics during chickenmeat storage.We developed a method to constitute a standard meat microbial ecosystem hosting known bacterial species previously described by 16S rRNA sequencing. Our results confirmed the presence of Brochothrix thermosphacta and Pseudomonas and we also showed the presence of subdominant species as Shewanella and Carnobacterium. We selected 2 bacterial communities enabling reproducible challenge tests on meat during 9 days of storage at 4°C under 3 different atmospheres currently used in the industry.Metatranscriptomic and metagenomic analyses were performed to know “Who is there?”, “What can they do?” and “What are they expressing?” depending on the gaseous mixtures and on the initial microbiota.Consequently, we could evaluate the impact of storage atmosphere on the microbiotas dynamics and on the functions the bacteria expressed, depending on the storage condition and on the nature of the bacterial communities present. This led to indications of optimized storage conditions of poultry meat by managing their ecosystems.

No description available.

Philosophiae Doctor - PhD / Mycobacterium tuberculosis, the causative agent of tuberculosis, is estimated to infect approximately one-third of the world’s population and is responsible for around 2 million deaths per year. The disease is endemic in South Africa which has one of the world’s highest tuberculosis incidence and death rates. The M. tuberculosis Beijing genotype are characterised by having an enhanced virulence capability over other M. tuberculosis strains and are the predominant strain observed in the Western Cape of South Africa. DNA methylation is a largely untapped area of research in M.tuberculosis and has been poorly described in the literature especially given its connection to virulence despite it being well characterised along with its role in virulence in other pathogenic bacteria such as E.coli. The overall aim was to characterise a global DNA methylation profile for two M. tuberculosis Beijing strains, hyper-virulent and hypo-virulent, using single molecule real time sequencing data technology. Moreover, to determine if adenine methylation in promoter regions has a possible functional role. This study identified and characterised the DNA methylation profile at the single nucleotide resolution in these strains using Pacific Biosciences single molecule real time sequencing data. A computational approach was used to discern DNA methylation patterns between the hyper and hypo-virulent strains with a view of understanding virulence in the hyper-virulent strain. Methylated motifs, which belong to known Restriction Modification (RM) systems of the H37Rv referencegenome were also identified. N6-methyladenine (m6A) and N4-methlycytosine (m4C) loci were identified in both strains. m6A were idenitified in both strains occuring within the following sequence motifs CACGCAG (Type II RM system), GATNNNNRTAC/GTAYNNNNATC (Type I RM system), while the CTGGAGGA motif was found to be uniquley methylated in the hyper-virulentstrain.Interestingly, the CACGCAG motif was significantly methylated (p = 9.9 x10 -63) at a higher proportion in intergenic regions (~70%) as opposed to genic regions in both the hyper-virulent and hypo-virulent strains suggesting a role in gene regulation. There appeared to be a higher proportion of m6A occuring in intergenic regions compared to within genes for hyper-virulent (61%) and hypo-virulent (62%) strains. The genic proportion revealed that 35% of total m6A occurred uniquely within genes for the hyper-virulent strain while 27.9% for uniquely methylated genes in hypo-virulent strain.

>Magister Scientiae - MSc / Next generation sequencing (NGS) technology platforms have accelerated ability to produce completed genome assemblies. Recently, collaborators at Tygerberg Medical School outsourced the sequencing of Oryx bacillus, a member of the Mycobacterium tuberculosis complex (MTC). A total of 31,271,059 short reads were generated and required filtering, assembly and annotation using bioinformatics algorithms. In this project, an NGS assembly pipeline was implemented, tailored specifically for SOLiD sequence data. The raw reads were aligned to seven fully sequenced and annotated MTC members, namely, Mycobacterium tuberculosis H37Rv, H37Ra, CDC1551, F11, KZN 1435, Mycobacterium bovis AF2122/97 and Mycobacterium bovis BCG str. Pasteur 1173P2 using NovoalignCS. Depth and breadth of sequence coverage across each base of the reference genome was calculated using BEDTools, and structural variation. Structural variation at the nucleotide level including deletions, insertions and single nucleotidepolymorphisms (SNPs) were called using three tools, GATK, SAMtools and Nesoni. These variations were further filtered using in-house PERL scripts. Putative functional roles for the alterations at the DNA level were extrapolated from the overlap with essential genes present in annotated MTC members. Approximately 20,730,631 short reads (59.78%) out of a total of 31,271,059 reads aligned to the seven reference genomes. The per base sequence coverage calculations revealed an average of 1,243 unaligned regions. These unaligned regions overlapped with mycobacterial regions of difference (RD) and genetic phage elements acquired by the MTC through horizontal gene transfer and are genes prevalent in the clinical isolates of M. tuberculosis. A total of 2,680 genetic variations were identified and categorised into 845 synonymous and 1,724 non-synonymous SNPs together with 44 insertions and 67 deletions. Some of the variant alleles overlapped known genes to be involved in TB drug resistance. While the biological significance of our findings remain to be elucidated, it nonetheless deserves further attention, because SNPs have the potential to impact on strain phenotype by gene disruption. Therefore, any hypotheses generated from these large-scale analyses will be tested by our collaborators at Tygerberg medical school.

The ability of Next-Generation Sequencing (NGS) to produce massive quantities of genomic data inexpensively has allowed to study the structure of viral populations from an infected host at an unprecedented resolution. As a result of a high rate of mutation and recombination events, an RNA virus exists as a heterogeneous "swarm". Virologists and computational epidemiologists are widely using NGS data to study viral populations. However, discerning rare variants is muddled by the presence of errors introduced by the sequencing technology. We develop and implement time- and cost-efficient strategy for NGS of multiple viral samples, and computational methods to analyze large quantities of NGS data and to handle sequencing errors. In particular, we present: (i) combinatorial pooling strategy for massive NGS of viral samples; (ii) kGEM and 2SNV — methods for viral population haplotyping; (iii) ShotMCF — a Multicommodity Flow (MCF) based method for frequency estimation of viral haplotypes; (iv) QUASIM — an agent-based simulator of viral evolution taking in account viral variants and immune response.