Dissertations / Theses on the topic 'Whole-of-population'

Models of whole-brain connectivity are valuable for understanding neurological function. This thesis seeks to develop an optimal framework for extracting models of whole-brain connectivity from clinically acquired diffusion data. We propose new approaches for studying these models. The aim is to develop techniques which can take models of brain connectivity and use them to identify biomarkers or phenotypes of disease. The models of connectivity are extracted using a standard probabilistic tractography algorithm, modified to assess the structural integrity of tracts, through estimates of white matter anisotropy. Connections are traced between 77 regions of interest, automatically extracted by label propagation from multiple brain atlases followed by classifier fusion. The estimates of tissue integrity for each tract are input as indices in 77x77 ”connectivity” matrices, extracted for large populations of clinical data. These are compared in subsequent studies. To date, most whole-brain connectivity studies have characterised population differences using graph theory techniques. However these can be limited in their ability to pinpoint the locations of differences in the underlying neural anatomy. Therefore, this thesis proposes new techniques. These include a spectral clustering approach for comparing population differences in the clustering properties of weighted brain networks. In addition, machine learning approaches are suggested for the first time. These are particularly advantageous as they allow classification of subjects and extraction of features which best represent the differences between groups. One limitation of the proposed approach is that errors propagate from segmentation and registration steps prior to tractography. This can cumulate in the assignment of false positive connections, where the contribution of these factors may vary across populations, causing the appearance of population differences where there are none. The final contribution of this thesis is therefore to develop a common co-ordinate space approach. This combines probabilistic models of voxel-wise diffusion for each subject into a single probabilistic model of diffusion for the population. This allows tractography to be performed only once, ensuring that there is one model of connectivity. Cross-subject differences can then be identified by mapping individual subjects’ anisotropy data to this model. The approach is used to compare populations separated by age and gender.

The revolution in next-generation sequencing has made obtaining both common and rare high-quality sequence variants across the entire genome feasible. Because researchers are now faced with the analytical challenges of handling a massive amount of genetic variant information from sequencing studies, numerous methods have been developed to assess the impact of both common and rare variants on disease traits. In this report, whole genome sequencing data from Genetic Analysis Workshop 18 was used to compare the power of several methods, considering both family-based and population-based designs, to detect association with variants in the MAP4 gene region and on chromosome 3 with blood pressure. To prioritize variants across the genome for testing, variants were first functionally assessed using prediction algorithms and expression quantitative trait loci (eQTLs) data. Four set-based tests in the family-based association tests (FBAT) framework--FBAT-v, FBAT-lmm, FBAT-m, and FBAT-l--were used to analyze 20 pedigrees, and 2 variance component tests, sequence kernel association test (SKAT) and genome-wide complex trait analysis (GCTA), were used with 142 unrelated individuals in the sample. Both set-based and variance-component-based tests had high power and an adequate type I error rate. Of the various FBATs, FBAT-l demonstrated superior performance, indicating the potential for it to be used in rare-variant analysis. The updated FBAT package is available at: http://www.hsph.harvard.edu/fbat/ webcite.

Introduction: Hearing impairment occurs when a child has hearing loss greater than 30dB in their better hearing ear and an adult cannot detect sound lower than 40dB in the better hearing ear. It is a common sensory disorder that affecting approximately 360 million worldwide, with an incidence of 6 in 1000 live births in developing countries such as those in Sub-Saharan Africa. 50 % of hearing impairment, in developed countries, is due to genetic factors, with 70% of genetic hearing impairment being classified as non-syndromic hearing impairment, which occurs when the hearing impairment presents with no other clinical manifestations. Hearing impairment is associated with over 150 genes, of which two connexin genes, GJB2 and GJB6, are the most prevalent genes associated with hearing impairment in European, Asian and North American of European ancestries populations. These genes have however been shown to be insignificant causes of Hearing Impairment in African populations. Aim: The aim of this study is to determine the rates for putative pathogenic variants in 172 hearing impairment associated genes, among Cameroonian patients affected by hearing impairment, and non-hearing-impaired controls. Methods: Patients and controls Patients were recruited from various schools of the Deaf and Ear, Nose and Throat (ENT) clinics in Cameroon. The patients were examined by qualified medical geneticists and ophthalmologist and detailed family history and medical history was obtained from the patients and their parents. 19 patients, who were negative for GJB2 and GJB6 mutations and presented with putative non-syndromic hearing impairment, were selected from a cohort of 582 patients for the present study. The control population consisted of 130 ethnically matched groups without any personal or familial history of hearing impairment. The controls were recruited from Yaoundé Central Hospital and Laquintinie Hospital in Cameroon. Whole exome sequencing DNA was extracted from whole blood using the salting out procedure and the Puregene Blood kit®. The DNA was subjected to spectrometry and gel electrophoresis to determine the quantity and quality of the DNA samples. The samples were then subjected to whole exome sequencing on the Illumina platform using the Nextera Rapid Capture Exome Kit at an average read depth of 30X, whereby only 18 patients were successfully sequenced. The exomes were then subjected to FastQC and SolexaQC++ for quality control measures and aligned to the hg19 reference genome using GATK and VariantMetaCaller. Bioinformatics analysis Variant annotation was performed using Annovar and the annotated variants were filtered based in rarity and pathogenicity. Tests for genetic differentiation and principle component analysis was performed on the combined patient exomes and combine control exomes. The first principle component analysis included data from African populations from the 1000 Genomes Phase 3 as well as six control samples from the Democratic Republic of Congo; and the second principle component analysis analysed on the Cameroonian patients and control population. Population structure analysis was followed by protein-protein interaction analysis using custom python and R script and pathway enrichment analysis using Enrichr combined with a second custom R script. The proportion of derived and ancestral alleles was computed by downloading the SNP ancestral alleles from Ensembl and verifying the presence of the SNPs in dbSNP database. The combined patient and control exomes were annotated using the VCFtools “fillOaa” script. The ancestral alleles were computed by dividing the number of times the alternative allele matched the ancestral allele with the number of copies of all the alternative alleles across all samples at the particular position. The ancestral alleles were categorised into six bins, based on their minor allele frequency, in the patient and control populations and this was used to contrast their proportions of derived and ancestral alleles. Furthermore, the proportion of ancestral and derived alleles in hearing impairment associated genes was computed at SNP based level for the Cameroonian population and contrasted with population from the Democratic Republic of Congo. Variants validation by Sanger sequencing Primers were designed to amplify the fragment surrounding the purported SNPs in MYO15A, MYO3A, and COL9A3 as well as for the fragments surrounding the population specific SNPs in VTN, RPL3L and DHRS4L2. Polymerase chain reaction was performed for the MYO15A, and MYO3A fragments. This was followed by purification of the PCR products and direct cycle Sanger sequencing of the PCR products. The sequencing products were then purified through ethanol precipitation and the fragments were suspended in HiDi Formamide and run on the capillary electrophoresis. The variants in MYO3A, MYO15A and COL9A3 were viewed in Integrated Genomics Viewer using the Bam files as well. Results Putative deleterious variants Single nucleotide polymorphism (SNPs) in MYO3A, MYO15A and COL9A3, were filtered out as putative causative mutations for three, four and two patients respectively. Direct Sanger Sequencing and viewing the patients BAM files did not confirm the presence of any of these putative pathogenic in the patients. Variations in USH2A, HSD17B4 and MYO1A were also filtered out but these variants were not considered disease causing, after a careful genotype to phenotypes correlations. Population genetics variants differentiations At a population level, specific variations were identified in FOXD4L2, DHRS2L6, RPL3L and VTN. Significant genetic differentiation was shown to exist between the control population and the patients’ population with regard to specific variants in VTN and RPL3L; furthermore, it was shown that these variants in VTN and RPL3L interact with other hearing impairment associated proteins with evidences that that VTN is hub protein for a hearing impairment associated pathway along with nine other genes. Conversely, this was not the case for variants described in FOXD4L2 and DHRS2L6. In known hearing Impairment genes, the proportion of ancestral alleles was lowest for the patients’ population for variations with minor allele frequencies between 0.0 and 0.1. The proportion of derived and ancestral alleles was also shown to differ between the Cameroonian and the population from the Democratic Republic of Congo, indication possible regional differences in aetiology of Hearing impairment amongst multiple African populations. Discussion Low putative pathogenic variants in known hearing impairment genes among Africans The low pick up rate for putative pathogenic variants in our patients follows a similar trend observed in the African American populations, with hearing impairment, as well as data from targeted exome sequencing from South African and Nigerian populations. This result is also in agreeance with other studies that interrogated hearing impairment in African populations utilising other means besides next generation sequencing. This result also highlights the importance of validating any results obtained from next generation sequencing through traditional approaches such as Sanger Sequencing or viewing the BAM files on IGV, specifically in African population, poorly represented in Exome databases. Bioinformatics Analysis Exhibited some Specific Variants among Cameroonian Protein-protein interactions and enrichment analysis indicated that VTN and RPL3L, and their interacting proteins, are significantly associated with osteoclast differentiation, which is associated with hearing impairment in osteogenesis imperfecta. VTN was further shown as a hub protein of a protein subnetwork, along ATPB2. The presence of a second protein acting as a hub protein may account for why aberrations in VTN have not been associated with a disease; whereby ATPB2 may ameliorate the pathogenic phenotype that ought to be observed in the presence of null mutations in VTN. Evolutionary adaptation of human hearing Data indicates the patient population carried a higher proportion of derived alleles in known hearing impairment genes, at low minor allele frequencies; possibly indicating, the interactive modifiers capacities of multiple hearing impairment genes, or alternatively, the polygenetic nature of hearing impairment in some patients. The proportion of ancestral and derived alleles was contrasted in the Cameroonian and the population from the Democratic Republic of Congo and it indicated that the variations that may result in hearing impairment in the one population may not be the same variations that result in hearing impairment in the other population Due to this, it is necessary to determine the causative variants resulting in disease in each of these populations independently. Conclusion and perspectives The results support a low pick up rate of putative variants in 172 known genes in groups of Cameroonian patients with HI, underscoring the current Targeted panel sequencing for HI may not be relevant for some African populations. The result also support the need of confirmation of variants found in WES, as well careful genotype to phenotypes correlations, particularly among African, whose sequences exome is relatively low in Exomes databases, and as a result could lead to more false positive results. Population genetic analysis has provided novel insight in the genetic architecture of HI among this group of Africans; particularly, the differential frequencies of ancestral alleles vs derived alleles in HI genes among patients vs controls underline the possibility of multigenic influence on the phenotype of Hearing Impairment that have not been well investigated, and may also signal evolutionary enrichment of some variants of HI genes in the populations as the result of natural selections, that deserve further investigation. The result supports the need of intensive familial studies in multiple African populations in order to unravel the novel genes and those variants that are relevant in clinical practice for people of African ancestry.

In this dissertation I addressed the problem of SNP array bias when finding runs of ho- mozygosity. I demonstrated the pitfalls of using uninformed methods for finding runs of homozygosity and provide better alternatives, including a more reliable algorithm for identi- fying runs of homozygosity than the most commonly used program. I then provide a review of Ashkenazi population genetics. Next, I developed software to efficiently run millions of whole chromosome simulations, which is publicly available through GitHub, DockerHub, and on the CyVerse Discovery Environment. I applied my computational method to use Approximate Bayesian Computation to test models of Ashkenazi Jewish demographic his- tory. I found that the Ashkenazi Jews are comprised of genetically distinct subgroups from Eastern and Western Europe, as a result of massive population growth in the Eastern Ashkenazi Jews, but not in the Western Ashkenazi Jews. I further confirmed that the Ashkenazi Jews do not primarily originate from Khazaria. Finally, I created a correction for SNP array ascertainment bias in the median and total length of runs of homozygosity, and applied this correction to world-wide human populations. However, I found that ascertainment bias plays a minor role compared to SNP array bias in human populations.

Reconstructing the origins and evolutionary journey of humans is a central piece of biology. Complementary to archeology, population genetics studying genetic variation among individuals in extant populations has made considerable progress in understanding the evolution of our species. Particularly, studies in indigenous humans provide valuable insights on the prehistory of humans because their life history closely resembles that of our ancestors. Despite these efforts, it can be difficult to disentangle population genetic inferences because of the interplay among evolutionary forces, including mutation, recombination, selection, and demographic processes. To date, few studies have adopted a comprehensive framework to jointly account for these confounding effects. The shortage of such an approach inspired this dissertation work, which centered on the development of model-based analysis and demonstrated its importance in population genetic inferences. Indigenous African Pygmy hunter-gatherers have been long studied because of interest in their short stature, foraging subsistence strategy in rainforests, and long-term socio-economic relationship with nearby farmers. I proposed detailed demographic models using genomes from seven Western African Pygmies and nine Western African farmers (Appendix A). Statistical evidence was shown for a much deeper divergence than previously thought and for asymmetric migrations with a larger contribution from the farmers to Pygmies. The model-based analyses revealed significant adaption signals in the Pygmies for genes involved in muscle development, bone synthesis, immunity, reproduction, etc. I also showed that the proposed model-based approach is robust to the confounding effects of evolutionary forces (Appendix A). Contrary to the low-latitude African homeland of humans, the indigenous Siberians are long-term survivors inhabiting one of the coldest places on Earth. Leveraging whole exome sequencing data from two Siberian populations, I presented demographic models for these North Asian dwellers that include divergence, isolation, and gene flow (Appendix B). The best-fit models suggested a closer genetic affinity of these Siberians to East Asians than to Europeans. Using the model-based framework, seven NCBI BioSystems gene sets showed significance for polygenic selection in these Siberians. Interestingly, many of these candidate gene sets are heavily related to diet, indicating possible adaptations to special dietary requirements in these populations in cold, resource-limited environments. Finally, I moved beyond studying the history of extant humans to explore the origins of our species in Africa (Appendix C). Specifically, with statistical analyses using genomes only from extant Africans, I rejected the null model of no archaic admixture in Africa and in turn gave the first whole-genome evidence for interbreeding among human species in Africa. Using extensive simulation analyses under various archaic admixture models, the results suggest recurrent admixture between the ancestors of archaic and modern Africans, with evidence that at least one such event occurred in the last 30,000 years in Africa.

Previously considered a disease of importance strictly to veterinary medicine Cryptosporidium has emerged as a highly successful opportunistic parasitic protozoan posing a significant threat to public health. Intricate transmission dynamics, a complex epidemiology, and parasite robustness and persistence have all hampered efforts for the prevention and control of Cryptosporidium. Genetic diversity is a prerequisite to better understand the role of parasite variation in disease etiology and pathobiology. The extent of genetic structure among C. hominis and C. parvum, the two most prevalent species of Ciyptosporidium, is insufficiently understood with the population structure still largely suspect. We report on the distribution of genetic diversity and possible existence of geographic partitions among C. hominis subpopulations from Australia, Kenya, Peru and Scotland. We studied C. hominis population genetic structure using a multi-locus SNP-type (M1St) established from 45 single nucleotide polymorphic loci covering 13 bio-functionally relevant proteins. A total of 77 isolates from 4 intercontinental subpopulations were genetically typed. Twenty-four unique M1St’s were identified, 25% of which were found to be located within one or more subpopulations. Diversity statistical tests to discern the degree of ultrapopulation and inter-population diversity, genetic distance, and genetic identity variation were used to examine the population genetic structure. Within-population differences among subpopulations account for 69.6% of genetic variation; differentiation among subpopulations constitute 30.4%. Genetic distances among subpopulations averaged 0.048 and varied from 0.03 4 between the Australian and Scotland subpopulations to 0.061 between Scotland and Kenya. More broadly, our results argue that too wide of a geographic boundary can impede rather than advance genetic population studies and that the practice of sampling more regional subpopulations be adopted. A fifth subpopulation, a combination of C. hominis and C. parvum isolates, was drawn upon to determine whether or not a pre-defined allelic profile of single nucleotide polymorphisms (SNPs) was an efficient and reliable means for species specific identification. Results showed the SNP-typing approach’s ability to distinguish between different species as well as being capable of uncovering potential novel SNPs within an individual isolate. We propose that the patterns of genetic variation are influenced by geography and that the identification of host adapted geographically conserved sub-genotypes within a defined geographic cohort versus widespread dissemination of genetically stable isolates could ultimately provide a valuable basis for the predictive epidemiology of Cryptosporidiwn infection. Our fmdings provide an alternative method for species detection, a crucial element to epidemiological investigations.

In this work we present a new whole genome sequencing dataset with samples gathered from the Spanish Eastern Pyrenees (SEP) with more than 40x coverage. We apply both classical and new methods to unveil their particular demographic histories and we present the use of a newly in-house developed algorithm to detect genetic barriers taking into account the use of geo-statistics. With these analyses we detect fine population substructure for the first time in this region. We also report the presence of an important batch effect in one of the most important datasets used in genomics: the 1,000 Genomes Project. We find this batch effect when considering very low frequency variants, such as loss of function mutations and the amount of singletons (both ancestral and derived) detected in each sample.
En aquest treball presentem un nou dataset de whole genome sequencing amb mostres recollides del Pirineu Oriental espanyol (SEP) amb un coverage superior a 40x. Apliquem mètodes clàssics i nous per descobrir les seves particulars històries demogràfiques i presentem l’ús d’un algorisme desenvolupat recentment en el nostre laboratori per detectar barreres genètiques tenint en compte l’ús de geoestadística. Amb aquestes anàlisis detectem, per primera vegada, una delicada subestructura de poblacions en aquesta regió. També informem de la presència d’un important batch effect en un dels datasets més importants utilitzats en genòmica: the 1.000 Genomes Project. Trobem aquest batch effect quan considerem variants rares, com per exemple mutacions que comporten pèrdua de funció i la quantitat de singletons (tant ancestrals com derivats) detectats en cada mostra.

The concept of species in bacteria is a matter of contention. The current definition is based on DNA-DNA hybridisation and does not account for evolutionary forces that are important in demarcating species. In this thesis we investigate two evolutionary forces that are important in speciation in bacteria, propose novel statistical models for them and infer parameters of interest. We present the first attempt at inferring the bias in the recombination process from whole bacterial genomes. Despite empirical evidence that recombination is biased and theoretical results that this bias is important in speciation, it is usually ignored. We propose a coalescent based model that accounts for the bias in the recombination process. We use approximate Bayesian computation for inference and describe an efficient method for simulating from the model. We show that our method performs well on simulated datasets and is robust to slight misspecification of the history of the samples. Application of our method to a Bacillus cereus dataset shows that it contain evidence that the recombination process depends on the evolutionary distance between donors and recipients. We demonstrate that the rate of bias in the recombination process for this dataset is far lower than what theoretical studies require for the spontaneous generation of populations that can be called species under neutral model. Next we propose a model for occurrence of adaptive events on a phylogenetic tree. We use the model to infer the boundaries of clusters on a phylogenetic tree that correspond to ecologically distinct lineages. we characterise our method using simulated datasets and show that it is conservative in estimating the number of adaptive events. Finally we apply our method to two bacterial datasets of Salmonella enterica and Vibrionaceae. We show that there is decisive evidence that isolates in these datasets partition into numerous ecologically distinct lineages and use our method to delineate the boundaries of these lineages.

The basking shark, Cetorhinus maximus, has historically been a target of international fisheries, leading to well-documented declines in parts of its global distribution. Currently, the basking shark is listed as globally ‘Vulnerable’ and regionally ‘Endangered’ (North Pacific and Northeast Atlantic) on the IUCN Red List of Threatened Species, rendering the species an international conservation priority. Here, we assessed the global matrilineal genetic population structure and evolutionary history of the basking shark by completing the first whole mitochondrial genome sequence level survey of animals sampled from three globally widespread geographic regions: the western North Atlantic (n = 11), the eastern North Atlantic (n = 11), and within New Zealand territorial waters (n = 12). Despite the relatively large amount of sequence data assessed (~16,669 bp per individual), whole mitogenome analyses showed no evidence of population differentiation (ΦST = -0.047, P > 0.05) and very low nucleotide diversity (π = 0.0014 ± 0.000) across a global seascape. The absence of population structure across large distances and even between ocean basins is indicative of long-dispersal by this species, including an ability to cross known biogeographic barriers known to differentiate populations of other highly vagile pelagic fishes. Notably, evolutionary analyses of the mitogenome sequences revealed two globally sympatric but evolutionary divergent lineages, with a Bayesian framework estimated coalescence time of ~2.46 million years ago. Coalescent-based Bayesian skyline analysis uncovered subtle evidence of Pleistocene demographic flux for this species, including a potential decline in female effective population size. Thus, historical population changes may be responsible for the occurrence of the two highly divergent, yet sympatric lineages, as population declines may have resulted in the loss of intermediate haplotypes and resulted in an overall loss of genetic diversity. This work supports the recognition of basking sharks as a single matrilineal global population, and as such requires the application of a cooperative multiagency and international approach to fisheries management to conserve this highly vulnerable and ecologically unique species.

From an ecological perspective, knowledge of demographic history is highly valuable because population size fluctuations can be matched to known climatic events, thereby revealing great insight into a species’ reaction to past climate change. This in turn enables us to predict how they might respond to future climate scenarios. Prominently, with the advent of high-throughput sequencing it is now becoming possible to assemble genomes of non-model organisms thereby providing unprecedented resolution to the study of demographic history and speciation. This thesis utilises four species of grouse (Aves, subfamily Tetraoninae) in order to explore the demographic history and speciation within this lineage; the willow grouse, red grouse, rock ptarmigan and the black grouse. I, and my co-authors, begin by reviewing the plethora of methods used to estimate contemporary effective population size (Ne) and demographic history that are available to animal conservation practitioners. We find that their underlying assumptions and necessary input data can bias in their application, and thus we provide a summary of their applicability. I then use the whole genomes of the black grouse, willow grouse and rock ptarmigan to infer their population dynamics within the last million years. I find three dominant periods that shape their demographic history: early Pleistocene cooling (3-0.9 Mya), the mid-Brunhes event (430 kya) and the last glacial period (110-10 kya). I also find strong signals of local population history – recolonization and subdivision events – affecting their demography. In the subsequent study, I explore the grouse dynamics within the last glacial period in more detail by including more distant samples and using ecological modelling to track habitat distribution changes. I further uncover strong signals of local population history, with multiple fringe populations undergoing severe bottlenecks. I also determine that future climate change is expected to drastically constrict the distribution of the studied grouse. Lastly, I use whole genome sequencing to uncover 6 highly differentiated regions, containing 7 genes, hinting at their role in adaptation and speciation in three grouse taxa. I also locate a region of low differentiation, containing the Agouti pigmentation gene, indicating its role in the grouse plumage coloration.

This investigative study identified a missense moesin protein variant R171WMSN as the disease-causing mutation in an unknown primary immunodeficiency disorder (PID) through an exome sequencing (WES) approach. As PIDs can confer incidence of lymphoproliferative disorders, candidate genes and variants identified by WES were also investigated in another lymphoid abnormality, i.e. non-Hodgkin lymphoma (NHL), to determine association with NHL subtypes. In addition, variants located within microRNAs and their targets were investigated in association with NHL susceptibility in an Australian cohort of matched NHL cases and healthy controls where SNPs in MIR143 were shown to be significantly associated with NHL risk.

Africa is the origin source of modern humans. Despite that African populations harbor the highest levels of genetic diversity worldwide, they remain underrepresented in genetic studies. Therefore, in order to fully understand modern human evolutionary history it is fundamental to include more African populations in genetic studies. The work in this thesis is a small contribution to the study of African evolutionary history. In particular we have focused on two different locations of Africa, eastern and southern Africa. We have tried to unravel candidates of positive (or adaptive) selection through the analysis of whole-genome sequences of five Ethiopian populations and one KhoeSan population. Moreover, we have tried to fill the gap between genotype and phenotype of a candidate of adaptive selection in an Ethiopian population.
Àfrica és la font d'origen dels humans moderns. Malgrat que les poblacions Africanes són les que contenen la major diversitat genètica al món, estan molt poc representades en estudis genètics. Així doncs, per poder plenament entendre la història evolutiva humana és fonamental incloure més poblacions Africanes en estudis genètics. Aquesta tesi és una petita contribució en l'estudi de la història evolutiva humana a l'Àfrica. Ens hem centrat en dos localitzacions diferents, a l'est i al sud de l'Àfrica. Hem intentat dilucidar les possibles senyals de selecció positiva (o adaptativa) a través de l'anàlisi de seqüències completes de genomes de cinc poblacions d'Etiòpia i una KhoeSan. A més a més, en l'última part de la tesi s'ha intentat entendre a nivell funcional la relació entre el genotip i el fenotip d'un candidat de selecció adaptativa descobert en una població d'Etiòpia.

Erreger des Leishmania donovani Komplexes (LDC) verursachen viszerale Leishmaniose (VL), eine der häufigsten durch Sandmücken übertragenen Infektionskrankheiten beim Menschen. Die vorliegende von der EU geförderte Dissertation untersucht die weltweite Populationsstruktur des LDC mit besonderem Schwerpunkt auf dem Indischen Subkontinent (ISC), wo das gehäufte Auftreten von Therapieversagen ein Problem für die geplante Eliminierung von VL darstellt. Zwei hoch diskriminierende molekulare Typisierungsverfahren wurden angewendet. 845 LDC-Isolate wurden mittels Multi-Lokus-Mikrosatelliten-Typisierung (MLMT) charakterisiert. Die Parasiten wurden in Gebieten mit endemischer VL aus unterschiedlichen Wirten isoliert und repräsentieren verschiedene klinische Formen der Leishmaniose. Eine 125 Parasiten umfassende Teilprobe wurde vollständig sequenziert und in einem next-generation Multi-Lokus-Sequenz-Ansatz (ng-MLSA) typisiert, welcher auf der Analyse von genomweiten Single-Nukleotid-Polymorphismen (SNP) beruht. Sowohl die MLMT- als auch die SNP-Daten wurden mit den gleichen populationsgenetischen Methoden ausgewertet. Der ng-MLSA Ansatz bestätigte weitgehend die Populationsstrukturen des mit dem MLMT analysierten größeren Datensatzes, die genetische Struktur korrelierte mit der geographischen Herkunft der Isolate. Die Unempfänglichkeit der Parasiten gegenüber Antimon- oder Miltefosin sowie die in vitro gemessene Resistenz der Isolate vom ISC konnten nicht auf einen spezifischen Genotyp zurückgeführt oder mit einem spezifischen genetischen Merkmal verknüpft werden. Die Gesamtgenomsequenzierung konnte bisher keine Mutationen im Parasitengenom nachweisen, die in Zusammenhang mit der Antimon- und Miltefosin-Unempfindlichkeit bzw. dem Therapieversagen gebracht werden könnten. Analysen basierend auf ausgewählten Sequenzen deuten auf eine variable chromosomale Ploidie und eine erhöhte Kopienzahl einiger Gene hin, die zur Entstehung von Arzneimittelresistenzen beitragen könnten.
Parasites of the Leishmania donovani species complex (LDC) cause most cases of visceral leishmaniasis (VL), one of the most fatal vector-borne parasitic human diseases. As part of an EU funded project, this dissertation has investigated the worldwide genetic population structure of parasites of the LDC, with special focus on the Indian subcontinent (ISC) where unresponsiveness to anti-leishmanial drugs has recently become an urgent problem for the containment of VL. Two types of highly discriminatory approaches have been used. Multi-locus microsatellite typing (MLMT) has been applied to 845 LDC isolates from numerous Old and New World foci of VL, from different clinical forms of the disease and from various hosts. A subset of 125 fully sequenced isolates, reflecting the worldwide distribution of the LDC, was analysed using a next-generation multi-locus sequence approach (ng-MLSA) including single nucleotide polymorphisms (SNP). Both microsatellite and SNP data sets were analysed using, in general, the same population genetic tools. The ng-MLSA approach has, in general, corroborated the population structures obtained with MLMT for the larger data set. With the exception of non MON-1 parasites, the genetic structure revealed was largely associated with the geographic origin of the isolates, but not with the clinical presentation, host specificity and the immune status of the host or year of parasite isolation. Unresponsiveness to antimony or miltefosine treatment as well as the respective resistances measured in vitro could not be linked to a specific genotype or genetic trait. Wg sequencing also failed, so far, to identify mutations, which could be related to the unresponsiveness of LDC isolates from the ISC to antimony and miltefosine therapy. Analyses of selected targets have revealed extensive variation in chromosomal ploidy in all wg sequenced isolates under study and copy number variations for some genes possibly involved in drug resistance.

Understanding the transmission dynamics of infectious diseases is important to well-informed public health policy, responsive infection control and individual patient management. The on-going revolution in whole-genome sequencing provides unprecedented resolution for detecting evidence of recent transmission and characterising population-level transmission dynamics. In this thesis, I develop and apply evolutionary approaches to investigating transmission, focusing on three globally important pathogens. Hepatitis C virus (HCV) is a major cause of liver disease affecting 150 million people and killing 350,000 annually. I conducted a meta-analysis of twentieth-century HCV epidemics, finding that the age of the epidemic can be predicted by genetic diversity. Using the coalescent, I fitted classic susceptible-infected (SI), susceptible-infected-susceptible (SIS) and susceptible-infected-recovered (SIR) epidemiological models. Most epidemics showed signatures of SI dynamics, but three, from Argentina, Hong Kong and Thailand, revealed complex SIR dynamics. Norovirus is the leading viral cause of diarrhoea, estimated to cost the NHS around £115 million annually. I analysed whole norovirus genomes via a stochastic transmission model, finding that up to 86% of hospital infection was attributable to transmission from another patient in the hospital. In contrast, the rate of new introductions to hospital by infected patients was extremely low (<0.0001%), underlining the importance of ward management during outbreaks. Campylobacter is the most commonly identified cause of bacterial gastroenteritis worldwide. I developed a zoonotic transmission model based on phylogeography approaches to test whether three strains previously associated with multiple host species were in fact aggregates of strongly host-restricted sub-strains, or genuine generalists. Members of the same strain isolated from different host species were often more closely related than those isolated from the same host species. I estimated 419, 389 and 31 zoonotic transmissions in ST-21, ST-45 and ST-828 respectively, strongly supporting the hypothesis that these strains are adapted to a generalist lifestyle.

Human genome project published their first human whole genome sequence on 2001 at the cost of billions of dollars. Since, the cost of sequencing is decreasing faster than Moore’s law. Now, we not only have sequenced thousands of modern humans’ whole genome, we also obtained whole genome sequences of extinct hominin and other ancient modern humans with relatively good quality. These sequences granted us some unexpected results: like how recently modern humans left Africa and populated around all over the world (which is called recent African origin model) while doing so how they have admixed with multiple hominin populations. Until now modern biology (unlike physics) always dominated by empirical results compared to theoretical concepts, which forces people to perceive biology as a descriptive science. As we are obtaining more and more data every day, it is now time to push our theoretical concepts before empirical results in biology. Here in this thesis, we provided deeper knowledge about ancestry of Indian, Asian and Pacific populations. We were also able to reveal an unknown hominin population existed even before it is sequenced. In addition to these, we demonstrated strong natural selection could change human morphology drastically in a short period.
El projecte del genoma humà va publicar la primera seqüència completa del genoma humà el 2001 amb un cost de milers de millions de dòlars. Després d'això, el cost de la seqüenciació està disminuint més ràpid que la llei de Moore. Actualment no només tenim la seqüència de del genoma humà, sinó que tenim la de molts humans i d’homínids extingits amb una qualitat relativement bona. L’estudi de les seqüències de molts genomes humans varen proporcionar la base per postular que els humans moderns es varen originar a Àfrica, i en la sortida d’Àfrica (Out Of Africa) varen poblar la resta del món, amb una certa barreja amb diferents poblacions d'homínids. La base del treball en biologia i en genòmica evolutiva ha estat fonamentalment empírica (a diferència de la física), però actualment la disponibilitat de moltes dades permet empenyer la recerca cap a aspectes molt més analítics: aquest és l’enfocament del nostre treball en seqüències de DNA. Aquí, en aquesta tesi, hem proporcionat un coneixement més profund sobre l’origen i l'ascendència de poblacions indígenes, d’Àsia i del Pacífic, centrant-nos en la India continental i especialment en les Illes Andaman. També hem estat capaços de revelar l’existència d’una població d'homínids desconeguts que es va barrejar amb els ancestres d’aquestes poblacions. A més, hem demostrat que una forta selecció natural pot canviar dràsticament la morfologia humana en un curt període de temps i que explicaria la morfologia pigmea del pobladors de les illes Andaman.

The aim of this doctoral thesis was to study the incidence, risk factors and outcomes of type 1 diabetes for children in South Australia, born from 1999-2013. The incidence of type 1 diabetes has doubled in the last four decades in many countries including Australia, and has substantial individual and economic consequences. Evidence from studies on type 1 diabetes aetiology and its implications is mixed. In this thesis, the linkage of multiple population-wide administrative data over 15 years, and use of rigorous epidemiological approaches has resulted in a better understanding of the risk factors and implications of type 1 diabetes. There are four studies in this doctoral thesis. In the first descriptive study, the incidence of type 1 diabetes was estimated by individual and area-level socioeconomic characteristics among children (aged ≤11 years) in South Australia, born from 2002-2013. Findings of the study showed that type 1 diabetes incidence rates differed depending on the measures of socioeconomic characteristics. Individual-level indicators showed higher type 1 diabetes incidence among more advantaged children, however, there was no clear area-level socioeconomic patterning of type 1 diabetes. Area-level measures of socioeconomic position are likely to have a greater risk of misclassification from true socioeconomic position, which suggests that the use of area-level measures may be misleading. Socioeconomic position is a major determinant of health and can modify the risk factors of type 1 diabetes. For example, as per hygiene hypothesis, the socioeconomically dis-advantaged children are less likely to have type 1 diabetes, which is supported by the findings of individual-level socioeconomic patterning of type1 diabetes in the first study. In addition, socioeconomically disadvantaged women are less likely to have a caesarean birth and more likely to smoke in pregnancy. I chose to study these two risk factors of type 1 diabetes because the evidence was inconsistent, and some studies had methodical limitations. Evidence about the effect of caesarean section on childhood type 1 diabetes is mixed; ranging from very small or no risk to 20-30% increased risk. A prevailing theory is that exposure to the gut and vaginal microbiota during a vaginal birth protects against type 1 diabetes. Therefore, in the second study, the impact of caesarean birth on childhood type 1 diabetes (aged ≤15 years) was estimated. This involved linking multiple administrative datasets of children in South Australia, born from 1999-2013. The question was extended to whether type 1 diabetes risk differed for children born by prelabour or intrapartum caesarean to further test the idea of microbiota exposure on type 1 diabetes. That is because children born by prelabour caesarean do not get exposure to maternal vaginal microbiota, and intrapartum caesarean births may have some exposure. Findings of the study obtained from Cox proportional hazard regression analysis showed a negligible 5% higher incidence (HR = 1.05, 95% CI 0.86-1.28) for caesarean births compared with normal vaginal delivery, with wide confidence intervals including the null. Contrary to the hypothesis of a higher type 1 diabetes risk for prelabor caesarean (because of non-exposure to maternal vaginal microbiota) type 1 diabetes risk for intrapartum caesarean was slightly higher (HR = 1.08, 95% CI 0.82-1.41) than prelabor caesarean (HR = 1.02, 95% CI 0.79-1.32). This negligible risk of type 1 diabetes for children who had caesarean birth, either prelabor or intrapartum, and the potential for unmeasured confounding suggested that birth method induced variation in neonatal microbiota might not be involved in modifying type 1 diabetes risk. Like caesarean section, maternal smoking in pregnancy is also a debated risk factor for childhood type 1 diabetes. Evidence about maternal smoking on childhood type 1 diabetes is inconsistent; studies have been small, and many did not adjust for important confounders or address missing data. In the third study of this doctoral thesis, the effect of maternal smoking in pregnancy on childhood type 1 diabetes was estimated using Cox proportional hazard regression analysis, once again by linking multiple administrative datasets of children in South Australia, born from 1999-2013. The analytical approach for this study ranged; from Cox proportional hazard analysis with adjustment for wide range of confounders using the SA ECDP linked data, involving multiple imputation for missing data; to conducting meta-analysis in order to get more precise estimate. But smoking is notoriously residually confounded, therefore, I made special efforts to investigate the possibility of residual confounding by using a negative control and E-value. The findings demonstrated that maternal smoking in pregnancy was associated with a 16% (HR 0.84, 95% CI 0.67, 1.08) lower childhood type 1 diabetes incidence, compared with unexposed children, which was also supported by the meta-analytic estimates of population-based cohort studies (HR 0.72, 95% CI 0.62, 0.82) and case-control studies (OR 0.71, 95% CI 0.55, 0.86). The negative control outcome and E-value analyses indicated the potential for residual confounding in the effect of maternal smoking on childhood type 1 diabetes. Triangulation of evidence from this study along with the results of similar population-based studies, suggested a small reduced risk of childhood type 1 diabetes for children exposed to maternal smoking in pregnancy. However, the mechanisms linking maternal smoking in pregnancy with childhood type 1 diabetes require further investigation. In the fourth study of this thesis, the impact of childhood type 1 diabetes on children’s educational outcomes in year/grade 5 at age ~10 were estimated, linking population-wide data of children in South Australia, born from 1999-2005. In this study, a doubly-robust analytical method called augmented inverse probability weighting (AIPW) was used to compute the average treatment effect of type 1 diabetes on children’s educational outcomes. AIPW gives an unbiased estimate if either the outcome model or the treatment model is correctly specified. The findings of this study demonstrated that children with type 1 diabetes are not disadvantaged in terms of educational outcomes in year 5, potentially reflecting improvement in type 1 diabetes management in Australia. In summary, the work in this doctoral thesis has demonstrated that type 1 diabetes incidence differed depending on the measure of socioeconomic position. The hygiene hypothesis was only supported by the individual-level socioeconomic pattering of type 1 diabetes incidence in South Australia. The involvement of birth method induced variation in neonatal microbiota in type 1 diabetes was not supported by the caesarean and childhood type 1 diabetes study. Despite the evidence of residual confounding in the estimate of maternal smoking in pregnancy on childhood type 1 diabetes, triangulation of the evidence suggested small reduced risk for children exposed to maternal smoking in pregnancy, but further research will be needed to understand the mechanism. The findings of similar educational outcomes for children with and without type 1 diabetes, highlighted the importance of improvements in diabetes management.
Thesis (Ph.D.) -- University of Adelaide, School of Public Health, 2020

Cultural conflict is endemic in diverse societies and schools. It manifests in both subtle and overt ways, permeating the whole school environment and posing tremendous challenges for society. The purpose of this study is to devise an education strategy to reduce cultural conflict in schools administered by mines in Zimbabwe, with a particular reference to language and teacher capacity to cope with diversity in mining-town schools. This study was guided by three theoretical frameworks: Bourdieu’s capital theory, Nussbaum’s cosmopolitan education theory and unhu/ubuntu moral theory. Nine models for the reduction of cultural conflict in diversity were reviewed in order to gain insight relating to cultural conflict in mining-town schools. The qualitative research design of the study was approached from a phenomenological perspective with regard to document analysis, face-to-face and focus group interviews as well as classroom observation. Three school administrators, three SDC members, two company managers, three Grade 2 teachers and 30 Grade 6 learners were purposively selected to participate in the study. It emerged from the study that conflict was attributable to teachers with no command of language(s) spoken by the school-going population and lacked training and apititude for the task of dealing with language and cultural diversity in the classroom. It was also found that cultural conflict as described above could be reduced by establishing well-resourced language learning centres that foster essentially civilised values like respect, tolerance and dialogue. Participants also saw an ethnic match between staff and learners as significant in averting cultural conflict. The study recommended that the government should provide services that address diverse learners’ unique needs.
Early Childhood Education
D. Ed. (Socio-Education)

Humans have altered natural landscape since the agricultural revolution, but it has been most destructive since human globalization and rampant industrialization in the last two centuries. These activities deteriorate and fragments natural habitat of many wild species that creates small isolated populations that lose genetic diversity over time. Loss of genetic diversity reduces the adaptive capacity of a population to respond to future environmental change and increases their extinction risks. Implementing strategies for wildlife conservation is a challenge primarily because of our lack of understanding of the biology of many wild species, the risks they are currently facing, and their evolutionary histories. With the advent of genomic and computational techniques, it is now possible to address these concerns. In my research, I used genomics to study the evolutionary history of the Montezuma Quail (Cyrtonyx montezumae) and created monitoring tools that can be readily applied by wildlife managers for its conservation. Montezuma Quail is a small gamebird found mostly in Mexico with peripheral populations existing in Arizona, New Mexico, and Texas. Montezuma Quail are going through species wide decline in the United States and are listed as vulnerable in the state of Texas due to their small population sizes and geographic isolation from rest of the range. My results show that Texas quail are genetically distinct and significantly less diverse than Arizona quail. Analysis of whole genome sequences from multiple individuals show that due to small population sizes and isolation, Texas quail are significantly more inbred and genetic drift is the major contributor for loss of genetic diversity we see today. Inbreeding is negatively impacting Texas quail as they carry more deleterious alleles within their genome that reduce fitness of the individuals. Demographic models predict that both Arizona and Texas populations were formed via founding bottlenecks around 20,000 years ago. Texas populations have maintained small population sizes since its split from the ancestral populations and are less efficient in purging new deleterious mutations that arise post-bottleneck. The inferences from my research not only carries direct implications for Montezuma Quail conservationists, but also illustrate the power of evolutionary genomics in implementing targeted management strategies for any species that face existential threats in today’s waning world.

Les Inuits du Nunavik regroupent des peuples autochtones de l'Arctique qui au fil de l’histoire ont formé une petite population isolée dans la région du Nunavik (nord de la province de Québec, Canada). Le profil génétique unique des Inuits du Nunavik est le résultat d’une adaptation à leur milieu de vie et il est considéré comme lié à certaines de leurs susceptibilités pathologiques. Une évolution neutre, ainsi qu’une suite d’événements adaptatifs, ont façonné le génome de ces Inuits et indirectement engendré leur prédisposition accrue à certains troubles cardio-vasculaires et cérébro-vasculaires (ex : hypertension et anévrismes intracrâniens (AI)). Les AI sont des faiblesses cérébro-vasculaires localisées pouvant mener à des dilatations et renflements localisés de la paroi vasculaire. De telles distorsions sont susceptibles de perturber les vaisseaux et entrainer des hémorragies sous-arachnoïdiennes. Les AI sont un désordre complexe dont la prévalence est élevée (4-8%) et différentes populations (non reliées aux Inuits) ont aussi un risque accru de développer des AI. Le développement des AI est associé à la fois à des facteurs environnementaux et génétiques; plusieurs études génomiques ont identifié des régions associées aux AI. Une grande part de l'héritabilité génétique des AI demeure encore inexpliquée, en particulier dans des populations autres que les finnois et les japonais. Toutefois il est à noter que peu d’études génétiques des AI ont tenu compte de la contribution de variations génétiques spécifiques à la population étudiée. Pour améliorer nos connaissances sur la part encore inexpliquée de l'héritabilité des AI (qui implique une grande hétérogénéité génétique et des variations peu pénétrantes), nous avons combiné le séquençage à haut débit au génotypage des polymorphismes sur puces afin d’établir la signature génétique des deux populations fondatrices du Québec prédisposées aux AI (Inuits du Nunavik et Canadiens français). Comme ces populations ont des caractéristiques distinctes, nous avons utilisé des approches différentes pour tenter d’identifier des facteurs de risque génétiques. Les Inuits du Nunavik représentent une population autochtone et de nombreux aspects de leur signature génétique diffèrent de celles des principales populations, nous avons choisi d’approfondir leur histoire et profil génomique avant de vérifier si des associations génomiques pouvaient être établies avec les IA. Nous avons tout d'abord examiné les régions codantes du génome et observé de nombreuses composantes génétiques spécifiques aux Inuits du Nunavik qui reflètent que la population s’est adaptée à son environnement (ex: ascendance Inuit homogène, augmentation du déséquilibre de liaison et signature génétique). Des signes de sélection naturelle, jusqu’alors non-identifiés, ont révélé une accumulation de variations génétiques dans des gènes impliqués dans le processus d'adhésion cellulaire et de la réponse immunitaire (ex. CPNE7 et ICAM5). D'autres analyses ont révélé un variant dans le gène CCM2 qui présente une sélection positive et est significativement associé aux AI chez les Inuits du Nunavik. En ce qui concerne l'étiologie génétique des AI dans la population des Canadiens français, nous avons adopté une approche différente et utilisé des variations spécifiques aux Canadiens français, qui ont été identifiées par le séquençage complet de l'exome. Ces variations ont permis de générer une liste de gènes à risque potentiel, qui ont ensuite été priorisés en utilisant un test d'association par gène de type « burden ». RNF213 est apparu comme le meilleur gène candidat; il est vraisemblablement la conséquence d’une dérive génétique. Les mesures génétiques et fonctionnelles subséquentes ont validé la contribution possible de RNF213 au développement des AI chez les Canadiens français. Les résultats présentés dans cette thèse soulignent l'importance de prendre en compte le contexte génétique spécifique apporté par l'évolution lorsqu'une maladie complexe est étudiée. Il a également été montré que les variations d’un gène spécifique (ex. CCM2 et RNF213) peuvent contribuer au développement de différentes pathologies lorsqu'ils sont observés dans des populations distinctes. D'une manière générale, nos découvertes génétiques ont permis d’identifier de nouvelles « pièces » génétiques et pour avancer le « casse-tête » incomplet de l'héritabilité génétique des AI ; la génétique des populations a été un élément clé pour cette avancée.
Nunavik Inuit is a group of Arctic indigenous people, who have historically presented as a small and isolated population across the Nunavik region of northern Quebec (Canada). The unique genetic profile of Nunavik Inuit is the result of years of adaptation to their living condition, and it is likely responsible for their increased susceptibility to certain pathological conditions. Prior studies have shown that as a consequence of neutral evolution or past adaptive events, today’s Inuit are predisposed to cardio-cerebrovascular disorders, e.g. hypertension and intracranial aneurysm (IA). IA is defined as localized cerebrovascular weakness which leads to vascular dilation or ballooning, and such distortions are susceptible to disrupt the affected vessels and lead to subarachnoid hemorrhage. It is a complex disorder with a high prevalence (4-8%) and certain populations have been observed to present an increased risk of developing IA. Both environmental and genetic factors are deemed to contribute to the development of IA and in regards to the latter, independent genome-wide association studies (GWAS) have identified multiple loci associated with IA. Nonetheless, there is still a large portion of the genetic heritability of IA, especially in different populations other than Finnish and Japanese that remains unexplained. However, fewer IA genetic studies have taken in consideration the contribution of population specific genetic variants. To address some of the IA missing heritability that is deemed to be accountable to its genetic heterogeneity and low penetrance, we have combined high throughput sequencing (HTS) with SNP-chip genotyping to examine the genetic signatures of two founder populations from Quebec that are predisposed to IA, including Nunavik Inuit and French-Canadians (FC). Because these populations have distinct genetic characteristics, we used different approaches for the identification of genetic risk factors. Nunavik Inuit is an indigenous population and many aspects of its genetic signatures differ from those of separate world-wide major populations; therefore we chose to conduct extensive population genetic studies in regards to their genetic history and genomic profile before we undertook to test if any association could be established between genomic loci and disease susceptibility. We observed many genetic components that are specific to the Nunavik Inuit population, including its homogeneous Inuit ancestry, increased linkage disequilibrium (LD) and genetic signatures which reflect the population had a long history of adaptations to their environment. Previously unidentified signals of natural selection, which focused on coding regions of the genome revealed an accumulation of genetic variants in genes involved in the processes of cell adhesion and immune responses (e.g. CPNE7 and ICAM5). Further analyses revealed a variant in CCM2 to be under positive selection and significantly associated with IA in Nunavik Inuit. In regard to the genetic etiology of IA in the French-Canadian population, we took a different approach and used French-Canadian specific variants that were identified by whole exome sequencing to generate a list of potential risk genes; which were further prioritized using a gene based burden association test. RNF213 emerged as a prime candidate gene that had undergone possible genetic drift and the follow-up genetic and functional examinations further supported its potential contribution to the development of IA among French-Canadians. The results presented in this thesis highlighted the importance of taking into consideration the specific genetic background brought by natural selection or genetic drift, both are driving forces of evolution, when a complex disease is being studied. It also further confirmed that variants in a specific gene (e.g. RNF213 or CCM2) may contribute to the development of different pathogenesis when examined in distinct populations. Overall as our genetic findings identified new genetic “pieces” that further completed the missing heritability “puzzle” of IA genetics; evidence for these “pieces” were interestingly highlighted through population genetics.

This thesis investigates the molecular evolutionary and macroevolutionary consequences of flight loss in insects. Chapter 2 tests the hypothesis that flightless groups have smaller effective population sizes than related flighted groups, expected to result in a consistent pattern of increased non-synonymous to synonymous ratios in flightless lineages due to the greater effect of genetic drift in smaller populations. Chapter 3 tests the hypothesis that reduced dispersal and species-level traits such as range size associated with flightlessness increase extinction rates, which over the long term will counteract increased speciation rates in flightless lineages, leading to lower net diversification. The wide-spread loss of flight in insects has led to increased molecular evolutionary rates and is associated with decreased long-term net diversification. I demonstrate that the fundamental trait of dispersal ability has shaped two forms of diversity—molecular and species—in the largest group of animals, and that microevolutionary and macroevolutionary patterns do not necessarily mirror each other.
Generously funded by NSERC with a Canada Graduate Scholarship and the Government of Ontario with an Ontario Graduate Scholarship to T. Fatima Mitterboeck; NSERC with a Discovery Grant to Dr. Sarah J. Adamowicz

Les facteurs génétiques peuvent apporter des réponses à plusieurs questions que nous nous posons sur les traits humains, les maladies et la réaction aux médicaments, entre autres. Avec le temps, le développement continu d'outils d'analyse génétique nous a permis d'examiner ces facteurs et de trouver des explications pertinentes. Cette thèse explore plusieurs méthodes et outils génétiques, tels que le séquençage pan-exomique et le génotypage sur puce, dans un contexte d'analyse familial et populationnel pour étudier ces facteurs génétiques qui jouent un rôle dans une maladie rare, la cardiomyopathie dilatée (DCM), et dans deux traits complexes soient les globules rouges et les plaquettes. DCM est une maladie rare qui est définie par un ventricule gauche dilaté et une dysfonction systolique. Environ 30% des cas de DCM sont héréditaires, et plus de 50 gènes ont été associés à un rôle dans la pathogénicité de DCM. Le dépistage génétique est un outil de référence dans la gestion clinique de DCM familiale. Par contre, pour la majorité des patients, les tests génétiques ne parviennent pas à identifier une mutation causale dans un gène candidat. Les cellules sanguines remplissent une variété de fonctions biologiques, incluant le transport de l'oxygène, les fonctions immunologiques, ainsi que la guérison de plaies. Les niveaux de ces cellules et leurs paramètres auxiliaires sont mesurés par un test sanguin, et une différence avec les valeurs optimales peut signifier certains troubles. De plus, ces traits sont étudiés méticuleusement dans le contexte des maladies cardiovasculaires (CVD) où différents niveaux sont associés avec un risque variable de CVD ou sont des prédicteurs de complications de CVD. iii J'ai examiné la DCM et les traits sanguins avec comme objectif de découvrir des nouvelles associations de mutations génétiques. Pour la DCM, j'ai évalué la pertinence d'un séquençage pan-exomique dans un environnement clinique. Je rapporte plusieurs nouvelles mutations dans des gènes candidats (DSP, LMNA, MYH7, MYPN, RBM20, TNNT2) et des mutations nonsenses dans deux gènes nouvellement associés (TTN et BAG3), et je démontre que les mutations nonsenses influencent la maladie d'une manière différente des autres mutations causales. Je rapporte aussi une mutation dans un nouveau gène, FLNC, qui cause une forme rare et distincte de cardiomyopathie. Pour l'étude des traits complexes, dans le grand consortium Blood Cell Consortium (BCX), j'ai utilisé l’exomechip pour disséquer le rôle des variantes rares et communes dans les globules rouges et les plaquettes. J'ai identifié 16 nouvelles régions génomiques associées avec les globules rouges et 15 avec les plaquettes, parmi lesquelles se retrouvent plusieurs variantes de basses fréquences (MAP1A, HNF4A, ITGA2B, APOH), et j'ai démontré un chevauchement significatif de régions associées avec d'autres traits, incluant les lipides. Mes résultats sur la DCM ont mis en évidence le rôle de plusieurs gènes candidats, et suggèrent un traitement différent au niveau de la gestion clinique des patients qui portent des mutations dans BAG3 et FLNC. En ce qui concerne les traits sanguins, mes résultats contribuent à enrichir le répertoire de régions associées avec ces traits, soulignant l'importance de l'utilisation de grands ensembles de données pour détecter les variantes rares ou de basses fréquences. La découverte de gènes dans les maladies rares et les traits complexes contribue à la compréhension des mécanismes sous-jacents qui ultimement favorisera de meilleurs diagnostics, gestions et traitements de maladies.
Genetic factors hold within them the answers to many questions we have on human traits, disease, and drug response among others. With time, the continuously advancing genetic tools have enabled us to examine those factors and provided and continue to provide astonishing answers. This thesis utilizes various methods of genetic tools such as exome sequencing and chip-based genotyping data in the context of both family and population-based analyses to interrogate the genetic factors that play a role in a rare disease, dilated cardiomyopathy (DCM), and in two complex traits, red blood cells and platelets. DCM is a rare disease that is defined by a dilated left ventricle and systolic dysfunction. It is estimated that 30% of DCM cases are hereditary and more than 50 genes have been linked to play a role in the pathogenesis of DCM. Genetic screening of known genes is a gold standard tool in the clinical management of familial DCM. However, in the majority of probands, genetic testing fails to identify the causal mutation. Blood cells play a variety of biological functions including oxygen transport, immunological functions, and wound healing. Levels of these cells and their associated indices are measured by a blood test, and deviation from optimal values may indicate certain disorders. Additionally, these traits are heavily studied in the context of cardiovascular disease (CVD) where different levels associate with a variable risk of CVD or are predictors of CVD complications or outcomes (for example, a higher level of white blood cells or lower level of hemoglobin). I examined both DCM and blood cell traits and aimed to discover new mutations and variants that are associated with each. For DCM, I evaluated the value of whole exome vi sequencing in a clinical setting, and I report a number of novel mutations in candidate genes (DSP, LMNA, MYH7, MYPN, RBM20, TNNT2) and truncating mutations in two newly established genes, TTN and BAG3, and I demonstrate that truncating mutations in the latter influence disease differently than other causal mutations. I also report a mutation in a novel gene, FLNC that causes a rare and distinct form of cardiomyopathy. In examining complex traits, I dissected the role of common and rare variants in red blood cells and platelets within a large consortium, the Blood Cell Consortium (BCX) using the ExomeChip, and identified 16 novel loci associated with red blood cell traits and 15 with platelet traits, some of which harbored low-frequency variants (MAP1A, HNF4A, ITGA2B, APOH), and demonstrated a substantial overlap with other phenotypes predominantly lipids. My results on DCM establish the role of a number of candidate genes in this disorder and suggest a different course of clinical management for patients that carry mutations in BAG3 and FLNC. As for blood cell traits, my results contributed to expanding the repertoire of loci associated with red blood cell and platelet traits and illustrate the importance of using large datasets to discover low-frequency or rare variants. Gene discovery in rare disease and complex traits gives insight into the underlying mechanisms which ultimately contributes to a better diagnosis, management, and treatment of disease.