Les variants du nombre de copies (CNV) offre un cadre riche pour étudier les mécanismes neurobiologiques qui sous tendent la vulnérabilité aux troubles neuropsychiatriques. Notamment, les délétions du 16p11.2 et 22q11.2 sont parmi les facteurs génétiques les plus fréquents associés au trouble du spectre de l’autisme (TSA) et à la schizophrénie (SCZ). À l’heure actuelle, les perturbations fonctionnelles cérébrales qui sous-tendent cette vulnérabilité cognitive restent mécomprises. Récemment, l’analyse par gradient du connectome humain a révélé une réorganisation le long de l’axe dominant sensorimoteur à transmodal dans le TSA et la SCZ. Dans cette étude, nous avons cherché à étendre cette approche analytique aux porteurs d’une délétion du 16p11.2 et du 22q11.2 conférant un risque élevé pour de mêmes conditions. À cette fin, nous avons utilisé les données d’imagerie par résonance magnétique au repos combinant les données de deux cohortes génétiques, pour un total de 180 sujets incluant 61 porteurs. Par le biais d’un paradigme cas-contrôle, nous rapportons la première évidence d’une compression du gradient fonctionnel sensorimoteur à transmodal chez les porteurs de telles délétions. En dernier lieu, nous présentons une étude exploratoire d’association endophénotype-phénome dans la population générale du UK Biobank. Nous démontrons que la ressemblance aux profils de compression corticale des délétions est reliée à plusieurs traits humains complexes, en concordance avec les dimensions cliniques impactées par ces mêmes CNV. / Copy number variants (CNVs) present a unique opportunity to study the neural mechanisms underlying vulnerability to neuropsychiatric disorders. Notably, deletions of the 16p11.2 and 22q11.2 region are among the most common genetic variations associated with autism spectrum disorder (ASD) and schizophrenia (SCZ). However, brain functional disruptions underlying this cognitive vulnerability remains unclear. Recent gradient analysis framework developed to study parsimonious connectome dimensions at the system-level have reported disruptions along the overarching sensorimotor-to-transmodal gradient in ASD and SCZ. In this study, we sought to extend this gradient approach to carriers of a deletion at the 16p11.2 and 22q11.2 region. To achieve this, we pooled resting-state functional magnetic resonance imaging data from a total of 180 subjects, including 61 carriers, distributed among two genetic cohorts. By the means of a case-control study design, we provide the first evidence of a compressed cortical functional gradient in CNV carriers compared to healthy controls. Finally, we provide an exploratory endophenotype-phenome association study in the general UK Biobank population. We demonstrate that resemblance to 16p11.2 and 22q11.2 deletion profiles of cortical compression is related to several complex human traits, in concordance with clinical dimensions known to be impacted by the same CNV.

Optical Coherence Tomography (OCT) has been around for more than 30 years and is still being continuously improved. The department of ophthalmology is a part of Sahlgrenska Hospital that heavily uses OCT for helping people with the treatment of eye diseases. They are currently facing a problem where the time to go from an OCT scan to treatment is being increased due to having an overload of patient visits every day. Since it requires a trained expert to analyze each OCT scan, the increase of patients is too overwhelming for the few experts that the department has. It is believed that the next phase of this medical field will be through the adoption of machine learning technology. This thesis has been issued by Sahlgrenska University Hospital (SUH), and they want to address the problem that ophthalmology has by introducing the use of machine learning into their workflow. This thesis aims to determine the best suited CNN through training and testing of pre-trained models and to build a tool that a model can be integrated into for use in ophthalmology. Transfer learning was used to compare three different types of pre-trained models offered by Keras, namely VGG16, InceptionResNet50V2 and ResNet50V2. They were all trained on an open dataset containing 84495 OCT images categorized into four different classes. These include the three diseases Choroidal Neovascularization (CNV), Diabetic Macular Edema (DME), drusen and normal eyes. To further improve the accuracy of the models, oversampling, undersampling, and data augmentation were applied to the training set and then tested in different variations. A web application was built using Tensorflow.js and Node.js that the best-performed model later was integrated into. The VGG16 model performed the best with only oversampling applied out of the three. It yielded an average of 95% precision, 95% recall and got a 95% F1-score. The second was the Inception model with only oversampling applied that got an average of 93% precision, 93% recall and a 93% F1-score. Last came the ResNet model with an average of 93% precision, 92% recall and a 92% F1-score. The results suggest that oversampling is the overall best technique for this given dataset. The chosen data augmentation techniques only lead to models performing marginally worse in all cases. It also suggests that pre-trained models with more parameters, such as the VGG16 model, have more feature mappings and, therefore, achieve higher accuracy. On this basis, parameters and better mappings of features should be taken into account when using pre-trained models.

Les duplicacions segmentàries (DSs), o també anomenades duplicons o Low copy Repeats (LCRs), són regions de coma mínim 1 kb amb un alt nivell d'identitat (>90%), que estan presents almenys dues vegades en el genoma. La regió 8p23.1 consta de 6.5 Mb a la part distal del braç curt del cromosoma 8 i està flanquejada per duplicacions segmentàries. Degut a la seva arquitectura genòmica aquesta regió és susceptible a patir reordenaments mediats per recombinació homòloga no al·lèlica entre les DSs, com per exemple la inversió polimòrfica de 8p23.1 [inv(8)(p23)], present en un de cada quatre individus de la població general europea i japonesa, així com d'altres reorganitzacions menys corrents.El treball realitzat en aquesta tesi doctoral pretén aprofundir en la caracterització de la complexa arquitectura genòmica d'aquesta regió. En la nostra primera aproximació a l'estudi de les DSs que flanquegen la regió cromosòmica 8p23.1, es va identificar una nova família gènica específica de primats, la família gènica FAM90A.Així, bona part d'aquesta tesi doctoral està centrada en l'anàlisi de l'origen, formació, evolució i expansió de FAM90A en els homínids. Per altra banda també s'ha analitzant en detall la variabilitat de FAM90A com a variant en número de còpia (CNV) en diferents poblacions humanes.Finalment, s'ha establert la freqüència de la inversió que afecta a 8p23.1 en població espanyola. També s'ha procedit a genotipar diversos individus homozigots per la inversió i s'ha predit l' estatus de la inversió en 150 individus del projecte HapMap i s'ha analitzat l'efecte que té aquesta reorganització sobre els nivells d'expressió dels gens de la regió. / Segmental duplications (SDs), also known as duplicons or Low Copy Repeats (LCRs), are regions of a minimum of 1 kb with a high sequence identity level (>90%), which are present at least two times in the genome. The 8p23.1 region extends 6.5 Mb at the distal part of the short arm of chromosome 8 and it is flanked by segmental duplications. Due to its genomic architecture the region is prone to suffer rearrangements mediated by non-allelic homologous recombination between these SDs, such as the polymorphic inversion of 8p23.1 [inv(8)(p23)], which is present in one out of every four of European and Japanese general population individuals, as well as other less frequent rearrangements.The aim of the work presented in this doctoral thesis is to get insights in the characterization of the genomic architecture of this complex region. Our first approach to study the SDs flanking 8p23.1 region resulted in the identification of a novel gene family which is primate specific, the FAM90A gene family. Thus, this doctoral thesis is mainly focused on the analysis of the origins, formation, evolution and expansion of FAM90A in hominoids. It has also been analyzed in detail the variability of FAM90A as a copy number variant (CNV) in different human populations.Finally, it has been established the frequency of the inversion affecting 8p23.1 region in the Spanish population. Several homozygous inverted individuals have been genotyped and the status for the inversion has been predicted for 150 HapMap individuals, as well as the effect of this rearrangement on the gene expression levels of the genes contained in the region.

[pt] A dissertação Comissão Nacional da Verdade, Arte e Intervenção Pública pretende estabelecer um diálogo entre design / comunicação visual, arte política e história do período ditatorial no Brasil, tendo como base empírica o Relatório da CNV (especificamente o Volume III: Mortos e Desaparecidos Políticos). A partir da análise do Relatório da Comissão Nacional da Verdade, criamos oficinas de estratégias de comunicação visual no âmbito da intervenção no espaço público, com a participação de jovens na faixa etária de 18 a 22 anos. Nessa pesquisa de campo, a metodologia desenvolvida propõe-se a provocar um debate ético e estético com o público alvo. O processo criativo desenvolvido com os alunos de graduação em design da disciplina de Linguagem e Comunicação Visual II, ministrada pela professora Simone Formiga - 2017.1 - PUC-Rio, proporcionou a construção de narrativas imagéticas sobre questões morais relativas às gravíssimas violações de direitos humanos deflagradas pelo regime ditatorial e expostas no Relatório. Ou seja, a partir dos conteúdos discursivos gerados nesta disciplina, desenvolvemos narrativas visuais ocupando o espaço público, com a finalidade de provocar questionamentos e reflexões na população acerca das vítimas do período do regime militar brasileiro. / [en] The dissertation National Commission of Truth, Art and Public Intervention intends to establish a dialogue between design - visual language -, political art and history of the dictatorial period in Brazil, with empirical basis on the CNV Report (specifically Volume III: Political Dead and Disappeared). Analyzing the work of the National Commission of Truth, we created workshops on visual communication strategies in the framework of artistic intervention in public space, with the participation of a group aged from 18 to 22 years. In the field research, the methodology developed aims to provoke an ethical and aesthetic debate with the target audience. The creative process developed with the undergraduate design students at Language and Visual Communication II discipline, given by Professor Simone Formiga - 2017.1 - PUC-Rio, provided the construction of imaginative narratives on moral issues about the severe violations of human rights triggered by the dictatorial period and exposed in the documents of the National Commission of Truth. So, from the discursive contents generated in this discipline, we developed visual narratives occupying the public space, with the purpose of provoking questions and reflections about the victims of the Brazilian military coup.

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New approaches are needed to manage and analyze the enormous quantity of biological data generated by modern technologies. Existing solutions are often fragmented and uncoordinated and, thus, they require considerable bioinformatics skills from users. Three applications have been developed illustrating different strategies to help users without extensive IT knowledge to take maximum profit from their data. SNPator is an easy-to-use suite that integrates all the usual tools for genetic association studies: from initial quality control procedures to final statistical analysis. CHAVA is an interactive visual application for CNV calling from aCGH data. It presents data in a visual way that helps assessing the quality of the calling and assists in the process of optimization. Haplotype Association Pattern Analysis visually presents data from exhaustive genomic haplotype associations, so that users can recognize patterns of possible associations that cannot be detected by single-SNP tests. / Calen noves aproximacions per la gestió i anàlisi de les enormes quantitats de dades biològiques generades per les tecnologies modernes. Les solucions existents, sovint fragmentaries i descoordinades, requereixen elevats nivells de formació bioinformàtica. Hem desenvolupat tres aplicacions que il•lustren diferents estratègies per ajudar als usuaris no experts en informàtica a aprofitar al màxim les seves dades. SNPator és un paquet de fàcil us que integra les eines usades habitualment en estudis de associació genètica: des del control de qualitat fins les anàlisi estadístiques. CHAVA és una aplicació visual interactiva per a la determinació de CNVs a partir de dades aCGH. Presenta les dades visualment per ajudar a valorar la qualitat de les CNV predites i ajudar a optimitzar-la. Haplotype Pattern Analysis presenta dades d’anàlisi d’associació haplotípica de forma visual per tal que els usuaris puguin reconèixer patrons de associacions que no es possible detectar amb tests de SNPs individuals.

Only 40 years ago, just three individuals made the journey from Finland/Russia to found the current wolf population in the southwest of Sweden. This population, that to this date descends from less than 10 founders, has a substantial increased extinction risk due to inbreeding. Several previous studies have used SNPs to monitor the level of inbreeding and homozygosity in the population, as well as measure immigration and the inflow of new genetic material. This study uses both short- and long-read data to discover structural variants (SVs) and small indels in the population, so that they may be used to extend the analyses and provide more insight into the current state of the Scandinavian wolf population. After the calling of the SVs, strict filtering and manual curation were applied to the data, thereby removing many false positive calls and increasing confidence in the remaining SVs. Short-read and long-read SV-callers found 31,800 and 57,821 SVs respectively, with relatively little overlap between the two sets. By far, the most common SV-types were deletions and insertions, at about 30,000 each with varying length ranging from a 50 base pairs to several tens of Mbp. Analyses on the data, such as PCAs and parent-offspring trio analyses, reveal high-confidence calls and consistent results between SV-types and SV-callers, as well as a low estimated genotyping error rate. PCAs performed on the SVs resembled those performed on SNPs, which strengthens the credibility of the identified variants. Finally, this study suggests several alternative steps for possible improvement to the dataset, along with some proposals for subsequent research topics that may use the variants discovered in this study.

L’obésité est en croissance rapide à l’échelle mondiale et représente un facteur de risque important pour plusieurs pathologies, dont la dégénérescence maculaire liée à l’âge (DMLA). Dans l’obésité, le tissu adipeux blanc (WAT) subi un remodelage pathologique caractérisé par le recrutement de macrophages pro-inflammatoires facilitant l’établissement de l’inflammation stérile systémique. Contrairement au WAT, les tissus adipeux brun (BAT) et beige (BgAT) participent à la thermogénèse, un processus qui libère de la chaleur en métabolisant les lipides. En raison de leurs potentiels effets physiologiques bénéfiques, le recrutement d’adipocytes et l’activation de ces types spécifiques de tissu adipeux (AT) ont fait l’objet de multiples recherches et débats. Malgré les avancées considérables dans le domaine, les mécanismes impliqués dans l’activation du BAT et du BgAT ainsi que les mécanismes impliqués dans le développement de l’obésité et leur contribution à des maladies comme la DMLA, restent mal définis. Dans un premier temps, nous avons développé le protocole RELi pour permettre une extraction et une quantification fiable des protéines du AT murin saturé en lipides. Notre protocole élimine les lipides contaminants en excès, réduit la variabilité du chargement de protéines pour le western blot et l’usage de gènes de ménage standards (Article #1). Ensuite, nous avons étudié l’inflammation au niveau du BAT dans un modèle d’obésité induite par l’alimentation. La délétion de la Neuropiline 1 (NRP1) chez les macrophages résidents du tissu adipeux (ATMs) a provoqué une diminution des densités de la vasculature et de l’innervation. De plus ces souris sont devenues plus sensibles à l’exposition au froid suggérant un rôle des ATMs-Nrp1+ dans la régulation de l’homéostasie du BAT et de la température corporelle (Article #2). Finalement, nous avons exploré l’axe BgAT-DMLA; plus spécifiquement son impact potentiel sur la néovascularization choroïdienne (CNV) en utilisant des approches in vivo et in vitro. Nous avons démontré que la délétion génétique de PRD1-BF1-RIZ1 homologous domain containing 16 (PRDM16), un gène impliqué dans la thermogénèse, conduit à une réduction de la CNV, et que la réintroduction d’AT-PRDM16+ exacerbe la formation de CNV pathologique. Le traitement d’explants de choroïde avec du milieu conditionné par des adipocytes-PRDM16+ augmente la croissance des vaisseaux sanguins. Ensemble, les données suggèrent un rôle sécrétoire potentiel pour le BgAT-PRDM16+ capable d’influencer la formation distale de CNV qui pourrait être pertinente pour la DMLA (Article #3). Les travaux présentés dans cette thèse établissent les bases d’un protocole permettant l’obtention de résultats reproductibles dans l’étude du AT, soulignent l’importance des ATMs- Nrp1+ dans la régulation de l’homéostasie du BAT et explorent pour la première fois l’implication du BgAT-PRDM16+ chez la DMLA neovasculaire. Ce travail établit les bases de la compréhension des mécanismes moléculaires reliant la régulation du AT thermogénique et les pathologies caractérisées par un excès de gras. Ce travail souligne également l’importance d’évaluer l’activation du BgAT chez les patients atteints de la DMLA. / Obesity is rapidly growing worldwide and represents a significant risk factor to several pathologies, including age-related macular degeneration (AMD). In obesity, the white adipose tissue (WAT) undergoes a strong remodeling characterized by the recruitment of pro- inflammatory macrophages, facilitating low-grade chronic inflammation. Unlike WAT, brown (BAT) and beige (BgAT) adipose tissues participate in thermogenesis, a process that releases heat by metabolizing lipids. Due to the likely beneficial physiological effects of BAT and BgAT, the recruitment of adipocytes and activation of these specific types of adipose tissue (AT) has been the subject of much research and debate. Despite considerable advances in the field, the mechanisms involved in BAT- and BgAT-activation as well as mechanisms involved in the development of obesity and their contribution to diseases such as AMD, remain ill-defined. First, we developed the RELi protocol to allow a reliable extraction and quantification of proteins from murine AT saturated with lipids. Our protocol eliminates excess contaminating lipids, reduces the variability of protein loading in Western blot and stabilizes expression of housekeeping genes (Article #1). Next, we investigated the inflammatory component of BAT in a diet-induced obesity model. The deletion of NRP1 in resident adipose tissue macrophages (ATMs) led to the expansion of the BAT and affected the densities of the vasculature and the innervation. Moreover, these mice became more sensitive to cold exposure, suggesting a role of ATMs-Nrp1+ in the regulation of BAT homeostasis and body temperature (Article #2). Lastly, we explored the axis of BgAT and AMD; more specifically, its potential impact on choroidal neovascularization (CNV) using in vivo and in vitro approaches. We demonstrated that the genetic deletion in BgAT of PRD1-BF1-RIZ1 homologous domain containing 16 (PRDM16), a gene involved in thermogenesis, leads to a reduction of CNV, and that the reintroduction of BgAT-PRDM16+ via AT transplantation exacerbates the formation of pathological CNV. Treatment of choroid explants with PRDM16+-adipocyte-conditioned medium augmented blood vessel growth. Altogether, the data suggest a potential secretory role for BgAT-PRDM16+ to influence distal CNV formation that could be relevant to AMD (Article #3). The work presented in this thesis establishes the basis of a protocol allowing reproducible results in the study of AT, underlines the importance of ATMs-Nrp1+ in the regulation of BAT homeostasis and explores, for the first time, the involvement of BgAT-PRDM16+ in neovascular AMD. This work sets the basis for the understanding of the molecular mechanisms linking the regulation of thermogenic AT and pathologies characterized by an excess of fat. This work also highlights the importance of assessing the activation of BgAT in patients with AMD.

Recent research demonstrated that besides a role in sex determination and male fertility, the Y chromosome is involved in additional functions including prostate cancer, sex-specific effects on the brain and behaviour, graft-versus-host disease, nociception, aggression and autoimmune diseases. The results presented in this thesis include an analysis of sex-biased genes encoded on the X and Y chromosomes of rodents. Expression data from six different somatic tissues was analyzed and we found that the X chromosome is enriched in female biased genes and depleted of male biased ones. The second study described copy number variation (CNV) patterns in a world-wide collection of human Y chromosome samples. Contrary to expectations, duplications and not deletions were the most frequent variations. We also discovered novel CNV patterns of which some were significantly overrepresented in specific haplogroups. A substantial part of the thesis focuses on analysis of spatial expression of two Y-encoded brain-specific genes, namely PCDH11Y and NLGN4Y. The perhaps most surprising discovery was the observation that X and Y transcripts of both gene pairs are mostly expressed in different cells in human spinal cord and medulla oblongata. Also, we detected spatial expression differences for the PCDH11X gene in spinal cord. The main focus of the spatial investigations was to uncover genetically coded sexual differences in expression during early development of human central nervous system (CNS). Also, investigations of the expression profiles for 13 X and Y homolog gene pairs in human CNS, adult brain, testes and still-born chimpanzee brain samples were included. Contrary to previous studies, we found only three X-encoded genes from the 13 X/Y homologous gene pairs studied that exhibit female-bias. We also describe six novel non-coding RNAs encoded in the human MSY, some of which are polyadenylated and with conserved expression in chimpanzee brain. The description of dimorphic cellular expression patterns of X- and Y-linked genes should boost the interest in the human specific gene PCDH11Y, and draw attention to other Y-encoded genes expressed in the brain during development. This may help to elucidate the role of the Y chromosome in sex differences during early CNS development in humans. / <p>chinese, finnish, norwegian, schizophrenia, bipolar, bipolar disorder, msy, male specific region Y, PAR1, PAR2, pseudoautosomal, male-biased, female-biased, male biased, female biased, ashkenazi population, structure, variants, YHRD, Elena Jazin, Björn Reinius, Per Ahlberg, brain, hjärna, CNS, central nervous system, IR2, inverted repeat 2, isodicentric, genetics, genetik, padlock, rolling circle, amplification, PCR, sY1191, sY1291, STS, DDX3Y, DAZ, AZFa, AZFb, AZFc, AZF, Repping, haplogroup J, rearrangements, DE-M145, I-M170, E-M96, Q-M242, R-M207, O-M175, G-M201, D-M174, C-M130, NO-M214, N-M231, poland</p>

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