To see the other types of publications on this topic, follow the link: Variant rara.
Dissertations / Theses on the topic 'Variant rara'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'Variant rara.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
1
Muiños, Gimeno Margarita. "Analysis of genetic variation in microrna-mediated regulation and the susceptibility to anxiety disorders." Doctoral thesis, Universitat Pompeu Fabra, 2009. http://hdl.handle.net/10803/7192.
Full textAbstract:
We have investigated genetic variation in microRNA-mediated regulation as a susceptibility factor for anxiety disorders following two different approaches. We first studied two isoforms of the candidate gene NTRK3 by re-sequencing its different 3'UTRs in patients with Panic (PD) and Obsessive Compulsive disorders (OCD) as well as controls. Two rare variants that altered microRNA-mediated regulation were identified in PD. Conversely, association of a common SNP with OCD hoarding subtype was found. Moreover, we have also studied a possible involvement of microRNAs in anxiety disorders. Consequently, we have analysed the genomic organisation and genetic variation of miRNA-containing regions to construct a panel of SNPs for association analysis. Case-control studies revealed several associations. However, it is worth remarking the associations of miR-22 and miR-488 with PD; two microRNAs for which functional assays and transcriptome analysis after microRNA overexpression showed significant repression of a subset of genes involved in physiological pathways linked to PD development.Hem investigat la variació genètica a la regulació mediada per microRNAs com a factors de susceptibilitat pels trastorns d'ansietat seguint dues aproximacions diferents. Primer vam estudiar dues isoformes del gen candidat NTRK3 mitjançant la reseqüenciació dels seus diferents 3'UTRs a pacients de pànic (TP), a pacients amb trastorn obsessiu compulsiu (TOC) i a controls. Dues variants rares que alteren la regulació mediada per microRNAs foren identificades per TP. D'altra banda, es trobà associació d'un SNP comú amb el subtipus acumulador de TOC. A més, també hem estudiat la possible implicació dels microRNAs als trastorns d'ansietat. Conseqüentment, hem analitzat l'organització genòmica i la variació genètica a regions que contenen microRNAs per construir un panell d'SNPs per fer anàlisis d'associació. Els estudis cas-control van revelar algunes associacions. Tanmateix, val la pena destacar les associacions del miR-22 i el miR-488 amb TP; dos microRNAs pels quals assajos funcionals i anàlisis de transcriptoma després de la seva sobreexpressió han mostrat una repressió significativa d'un grup de gens implicats en vies fisiològiques lligades al desenvolupament del TP.
2
Bhatia, Gaurav. "Rare variant analysis for common diseases." Diss., [La Jolla] : University of California, San Diego, 2009. http://wwwlib.umi.com/cr/ucsd/fullcit?p1467448.
Full textAbstract:
Thesis (M.S.)--University of California, San Diego, 2009.Title from first page of PDF file (viewed August 25, 2009). Available via ProQuest Digital Dissertations. Includes bibliographical references (p. 20-23).
3
Alshahrani, Mohammed Nasser D. "Statistical methods for rare variant association." Thesis, University of Leeds, 2018. http://etheses.whiterose.ac.uk/22436/.
Full textAbstract:
Deoxyribonucleic acid (DNA) sequencing allows researchers to conduct more complete assessments of low-frequency and rare genetic variants. In anticipation of the availability of next-generation sequencing data, there is increasing interest in investigating associations between complex traits and rare variants (RVs). In contrast to association studies of common variants (CVs), due to the low frequencies of RVs, common wisdom suggests that existing statistical tests for CVs might not work, motivating the recent development of several new tests that analyze RVs, most of which are based on the idea of pooling/collapsing RVs. Genome-wide association studies (GWAS) based on common SNPs gained more attention in the last few years and have been regularly used to examine complex genetic compositions of diseases and quantitative traits. GWASs have not discovered everything associated with diseases and genetic variations. However, recent empirical evidence has demonstrated that low-frequency and rare variants are, in fact, connected to complex diseases. This thesis will focus on the study of rare variant association. Aggregation tests, where multiple rare variants are analyzed jointly, have incorporated weighting schemes on variants. However, their power is very much dependent on the weighting scheme. I will address three topics in this thesis: the definition of rare variants and their call file (VCF) and a description of the methods that have been used in rare variant analysis. Finally, I will illustrate challenges involved in the analysis of rare variants and propose different weighting schemes for them. Therefore, since the efficiency of rare variant studies might be considerably improved by the application of an appropriate weighting scheme, choosing the proper weighting scheme is the topic of the thesis. In the following chapters, I will propose different weighting schemes, where weights are applied at the level of the variant, the individual or the cell (i.e. the individual genotype call), as well as a weighting scheme that can incorporate quality measures for variants (i.e., a quality score for variant calls) and cells (i.e., genotype quality).
4
Li, Samuel. "Rare Germline Variant Contributions to Myeloid Malignancy Susceptibility." Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case158654099909817.
Full text
5
Wang, Sophie. "Optimizing rare variant association studies in theory and practice." Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11430.
Full textAbstract:
Genome-wide association studies (GWAS) have greatly improved our understanding of the genetic basis of complex traits. However, there are two major limitations with GWAS. First, most common variants identified by GWAS individually or in combination explain only a small proportion of heritability. This raises the possibility that additional forms of genetic variation, such as rare variants, could contribute to the missing heritability. The second limitation is that GWAS typically cannot identify which genes are being affected by the associated variants. Examination of rare variants, especially those in coding regions of the genome, can help address these issues. Moreover, several studies have recently identified low-frequency variants at both known and novel loci associated with complex traits, suggesting that functionally significant rare variants exist in the human population.
6
Indap, Amit R. "Discovering rare variants from populations to families." Thesis, Boston College, 2013. http://hdl.handle.net/2345/3927.
Full textAbstract:
Thesis advisor: Gabor T. MarthPartitioning an individual's phenotype into genetic and environmental components has been a major goal of genetics since the early 20th century. Formally, the proportion of phenotypic variance attributable to genetic variation in the population is known as heritability. Genome wide association studies have explained a modest percentage of variability of complex traits by genotyping common variants. Currently, there is great interest in what role rare variants play in explaining the missing heritability of complex traits. Advances of next generation sequencing and genomic enrichment technologies over the past several years have made it feasible to re-sequence large numbers of individuals, enabling the discovery of the full spectrum of genetic variation segregating in the human population, including rare variants. The four projects that comprise my dissertation all revolve around the discovery of rare variants from next generation sequencing datasets. In my first project, I analyzed data from the exon sequencing pilot of the 1000 Genomes Project, where I discovered variants from exome capture sequencing experiments in a worldwide sample of nearly 700 individuals. My results show that the allele frequency spectrum of the dataset has an excess of rare variants. My next project demonstrated the applicability of using whole-genome amplified DNA (WGA) in capture sequencing. WGA is a method that amplifies DNA from nanogram starting amounts of template. In two separate capture experiments I compared the concordance of call sets, both at the site and genotype level, of variant calls derived from WGA and genomic DNA. WGA derived calls have excellent concordance metrics, both at the site and genotypic level, suggesting that WGA DNA can be used in lieu of genomic DNA. The results of this study have ramifications for medical sequencing experiments, where DNA stocks are a finite quantity and re-collecting samples maybe too expensive or not possible. My third project kept its focus on capture sequencing, but in a different context. Here, I analyzed sequencing data from Mendelian exome study of non-sensorineural hearing loss (NSHL). A subset of 6 individuals (5 affected, 1 unaffected) from a family of European descent were whole exome sequenced in an attempt to uncover the causative mutation responsible for the loss of hearing phenotype in the family. Previous linkage analysis uncovered a linkage region on chr12, but no mutations in previous candidate genes were found, suggesting a novel mutation segregates in the family. Using a discrete filtering approach with a minor allele frequency cutoff, I uncovered a putative causative non-synonymous mutation in a gene that encodes a transmembrane protein. The variant perfectly segregates with the phenotype in the family and is enriched in frequency in an unrelated cohort of individuals. Finally, for my last project I implemented a variant calling method for family sequencing datasets, named Pgmsnp, which incorporates Mendelian relationships of family members using a Bayesian network inference algorithm. My method has similar detection sensitivities compared to other pedigree aware callers, and increases power of detection for non-founder individuals
Thesis (PhD) — Boston College, 2013
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
7
Seabra, Catarina Morais. "Rare structural variants in severe spermatogenic impairment." Master's thesis, Universidade de Aveiro, 2012. http://hdl.handle.net/10773/9537.
Full textAbstract:
Mestrado em Biomedicina MolecularA azoospermia afeta aproximadamente 15% de todos os homens inférteis e é frequentemente causada por anomalias cromossómicas e microdeleções do cromossoma Y. No entanto, em aproximadamente 70% dos casos de azoospermia não-obstrutiva (NOA) as causas permanecem por identificar. Nos últimos anos, a descoberta de variantes genómicas de número de cópia (CNVs), como as causadas por deleções, revelou uma fonte de variação genómica que afecta a dosagem génica e que poderá resultar em haploinsuficiência. De facto, observa-se uma sobre-representação de CNVs raros (<1% na população), sobretudo de grandes deleções de novo, em pacientes com diferentes distúrbios do desenvolvimento, comparados com controlos saudáveis. Porém, uma possível contribuição, para a infertilidade masculina, de variantes estruturais ligados ao cromossoma X e aos autossomas foi ainda pouco explorada. Este estudo foca-se na validação de deleções encontradas apenas em pacientes inférteis, no cromossoma X e em 11p13, que contêm genes candidatos a participar na espermatogénese. Estas deleções, previamente identificadas por arrays de oligonucleótidos, de elevada densidade (Affymetrix 6.0 SNP Array), numa coorte de 171 pacientes Portugueses com disfunção severa da espermatogénese (NOA e oligozoospermia severa), foram agora confirmadas por técnicas convencionais de genética molecular. Adicionalmente, a caraterização dos locais de quebra nestas deleções foi realizada por aCGH. Ainda que não se tenham validado as deleções menos extensas (em Xq21.1, Xq25, Xp11.4, Xq22.1 e Xq26.3), confirmou-se a nulizigotia em Xq28 nestes indivíduos, que abrange genes candidatos com uma função sugestiva na espermatogénese: MAGE-A8, expresso em testículo e em alguns cancros e o microRNA hsa-miR-4330, envolvido na regulação pós-transcricional de vários genes com expressão na linha germinal. Foi ainda validada, por MLPA, uma deleção extensa num paciente infértil não-sindrómico da nossa coorte. Estes resultados apontam a haploinsuficiência de WT1 como a causa mais provável de azoospermia neste paciente, já que não foram detetadas mutações germinais no alelo restante. Mutações no gene WT1, que codifica um factor de transcrição muito conservado, crucial para o desenvolvimento e manutenção gonadal em mamíferos, geralmente interferem com a ligação desta proteína ao DNA e estão principalmente associadas a síndromes que envolvem anomalias reprodutivas. Motivados pela nossa descoberta de uma deleção de WT1 num homem infértil embora saudável, decidimos abordar a contribuição de mutações exónicas no gene WT1 para a azoospermia isolada. Testámos a hipótese de que mutações localizadas em domínios que não aqueles essenciais à ligação ao DNA pudessem resultar na disfunção não-sindrómica da espermatogénese. Assim, analisámos a sequência codificante de WT1 num subgrupo de 40 pacientes azoospérmicos. Como resultado, descrevemos uma nova variação missense c.185C>T (P130L; ENST00000332351) no primeiro exão de WT1, inserida no domínio proteico de auto-associação. A nova variante descrita deverá ter um impacto menos drástico na função da proteína WT1, comparativamente com as mutações descritas no mesmo exão até à data, as quais resultam em proteínas truncadas e fenótipos severos de disfunção gonadal, incluindo a formação de tumores renais. Estes resultados revelam novos genes candidatos a um papel na espermatogénese e sugerem que a haploinsuficiência de proteínas importantes para o desenvolvimento do sistema reprodutor masculino podem resultar em azoospermia. Estudos futuros poderão clarificar a utilidade dos nossos genes candidatos como biomarcadores da infertilidade masculina. A implementação de novos biomarcadores beneficiaria os doentes azoospérmicos através da melhoria do diagnóstico, aconselhamento genético e acompanhamento destes pacientes, podendo vir a limitar a necessidade de procedimentos invasivos.
Azoospermia affects approximately 15% of all infertile males and it is frequently caused by chromosomal abnormalities and Yq microdeletions. However, despite considerable research efforts in the last decades, in approximately 70% of the cases of non-obstructive azoospermia (NOA) the causes are yet to be identified. In the last years, the discovery of genomic copy number variants, such as those caused by deletions, revealed a source of genomic variation which impacts gene dosage and may result in haploinsufficiency. In fact, rare CNVs (<1% population), mainly large de novo deletions, are over-represented in patients with different developmental disorders, compared to healthy controls. However, a possible contribution of X-linked and autosomal structural variants to male infertility is still largely unexplored. This study focused on the validation of rare patient-specific deletions found on the X chromosome and at 11p13 of infertile patients, which harbor candidate spermatogenesis genes. These deletions had been previously identified by high density oligonucleotide arrays (Affymetrix 6.0 SNP Array), in a cohort of 171 Portuguese patients with severe spermatogenic impairment (non-obstructive azoospermia and severe oligozoospermia) and were now confirmed by conventional molecular genetics techniques. Additionally, breakpoint characterization was carried out by aCGH. In fact, even though the smaller deletions (at Xq21.1, Xq25, Xp11.4, Xq22.1 and Xq26.3) were not validated, we confirmed nullizygosity at Xq28 in two patients, spanning either MAGE-A8, a known cancer-testis antigen, or hsa-miR-4330, a microRNA involved in post-transcription regulation, both with a suggestive role in spermatogenesis pathways. We have also validated by MLPA a large deletion at 11p13, in a non-syndromic infertile patient from our cohort. These results support WT1 haploinsufficiency as the likely cause of azoospermia in this patient, as no other germline mutations were detected in the remaining WT1 copy. Mutations in WT1, an evolutionarily conserved transcription factor crucial for gonadal development and maintenance in mammals, typically interfere with the DNA-binding properties of the protein and are mainly associated with syndromes involving reproductive abnormalities. Motivated by our finding of a WT1 deletion in an infertile but otherwise healthy man we addressed the contribution of WT1 exonic mutations to isolated azoospermia. We reasoned that mutations located in domains not essential for DNA binding could result in non-syndromic spermatogenic impairment. Thus, we analyzed the WT1 coding sequence in a subgroup of 40 azoospermic patients. As a result of the exon screening, we report a novel c.185C>T (P130L; ENST00000332351) WT1 missense variant on exon 1, within the protein self-association domain. While all exon 1 mutations as yet reported result in truncated proteins and severe phenotypes, including the formation of renal tumors, this novel variant is expected to have a milder impact on WT1 function. These results reveal new candidate genes for a role in spermatogenesis and suggest that haploinsufficiency of proteins important for the development of the male reproductive system can lead to azoospermia. Further studies will clarify the utility of our candidate genes as biomarkers of male infertility. The implementation of new biomarkers would benefit azoospermic men by improving diagnosis, genetic counseling and patient care, eventually limiting the need for invasive procedures.
8
Weir, Gregory A. "Investigating rare genetic variants in common migraine." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:2aad341d-91fb-4ee8-8c55-ddd81b33247e.
Full textAbstract:
Migraine is a highly prevalent headache disorder imposing a significant burden of disability on human health worldwide. The headache is believed to arise from activation of trigeminal pain pathways, with CNS regions also playing an integral role in attack initiation and progression. Recent genetic associations have been made, but there is a need to convert these into relevant experimental models to study underlying disease mechanisms. Herein, I detail functional analysis of two deleterious variants in the genes KCNK18 and SLC12A3, that segregate with migraine with aura in one large pedigree. Gene function has been studied in a range of cell models, from heterologous expression systems and primary neuronal cultures, to Induced Pluripotent Stem (iPS) cell-derived nociceptors. In this context, the protein products of KCNK18 and SLC12A3 have been shown to modulate parameters of neuronal excitability, including baseline membrane properties and firing patterns. Migraine attacks are not wholly attributable to perturbations in peripheral pathways. I have shown that these genes are also expressed within the CNS in a small number of discreet regions, suggesting a possible role in central processing. Utilizing recently defined genetic variants and physiological cell- based models, will provide a platform for mechanistic insights into migraine pathogenesis and allow for the development of drug screening assays for new migraine therapies.
9
Zhao, Jing. "Rare and common genetic variant associations with quantitative human phenotypes." Diss., Georgia Institute of Technology, 2015. http://hdl.handle.net/1853/53923.
Full textAbstract:
This dissertation aims at investigating the association between genotypes and phenotypes in human. Both common and rare regulatory variants have been studied. The phenotypes include disease risk, clinical traits and gene expression levels. This dissertation describes three different types of association study. The first study investigated the relationship between common variants and three sub-clinical traits as well as three complex diseases in the Center for Health Discovery and Well Being study (CHDWB). The second study is GWAS analysis of TNF-α and BMI/CRP conducted as a contribution to meta-GWAS analyses of these traits with investigators at the University of Groningen in the Netherlands, and the 1000 Genomes Consortium. The third study was the most original contribution of my thesis as it assessed the association between rare regulatory variants in promoter regions and gene expression levels. The results clearly show an enrichment of rare variants at both extremes of gene expression. This dissertation provides insight into how common and rare variants associate with broadly-defined quantitative phenotypes. The demonstration that rare regulatory variants make a substantial contribution to gene expression variation has important implications for personalized medicine as it implies that de novo and other rare alleles need to be considered as candidate effectors of rare disease risk.
10
Kleinecke, Mariana [Verfasser], Jeanette [Akademischer Betreuer] Erdmann, and Hauke [Gutachter] Busch. "Rare variants and coronary artery disease : Seltene Varianten und koronare Herzerkrankung / Mariana Kleinecke ; Gutachter: Hauke Busch ; Akademischer Betreuer: Jeanette Erdmann." Lübeck : Zentrale Hochschulbibliothek Lübeck, 2020. http://d-nb.info/1207954705/34.
Full text
11
Barnes, Mariana [Verfasser], Jeanette [Akademischer Betreuer] Erdmann, and Hauke [Gutachter] Busch. "Rare variants and coronary artery disease : Seltene Varianten und koronare Herzerkrankung / Mariana Kleinecke ; Gutachter: Hauke Busch ; Akademischer Betreuer: Jeanette Erdmann." Lübeck : Zentrale Hochschulbibliothek Lübeck, 2020. http://d-nb.info/1207954705/34.
Full text
12
Mistry, Vanisha. "Uncovering rare genetic variants predisposing to coeliac disease." Thesis, Queen Mary, University of London, 2013. http://qmro.qmul.ac.uk/xmlui/handle/123456789/8649.
Full textAbstract:
Coeliac disease is a common (1% prevalence) inflammatory disease of the small intestine, involving the role of tissue transglutaminase and HLA-‐DQ binding immuno-‐dominant wheat peptides. The disease is highly heritable, however, at most only 40% of this heritability is explained by HLA-‐DQ and risk variants from genome wide association and fine mapping studies. The hypothesis of the research in this thesis is that rare (minor allele frequency <0.5%) mutations of large effect size (odds ratios ~2 – 5) exist, especially in multiply affected pedigrees, which account for the missing heritability of disease. NimbleGen exome capture and Illumina GAIIx high throughput sequencing was performed in 75 coeliac disease individuals from 55 multiply affected families. Candidate genes were chosen from various analytical strategies: linkage, shared variants between multiple related subjects and gene burden tests for multiple potentially causal variants. Highly multiplexed amplicon sequencing, using Fluidigm technology, of all RefSeq exons from 24 candidate genes in 2,304 coeliac cases and 2,304 controls was performed to locate further rare variation. Gene burden tests on a highly stringent post quality control dataset identified no significant associations (P<1x10-‐3) at the resequenced candidate genes. The strategy of sequencing multiply affected families, and deep follow up of candidate genes, has not identified new disease risk mutations. Common variants (and other factors, e.g. environmental) may instead account for familial clustering in this common autoimmune disease.
13
Niu, Yue, Ning Hao, and Lingling An. "Detection of rare functional variants using group ISIS." BioMed Central, 2011. http://hdl.handle.net/10150/610089.
Full textAbstract:
Genome-wide association studies have been firmly established in investigations of the associations between common genetic variants and complex traits or diseases. However, a large portion of complex traits and diseases cannot be explained well by common variants. Detecting rare functional variants becomes a trend and a necessity. Because rare variants have such a small minor allele frequency (e.g., <0.05), detecting functional rare variants is challenging. Group iterative sure independence screening (ISIS), a fast group selection tool, was developed to select important genes and the single-nucleotide polymorphisms within. The performance of the group ISIS and group penalization methods is compared for detecting important genes in the Genetic Analysis Workshop 17 data. The results suggest that the group ISIS is an efficient tool to discover genes and single-nucleotide polymorphisms associated to phenotypes.
14
Sosa, Daniel N. "Principled "convergence" non-coding rare variant association testing in complex disease." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/113171.
Full textAbstract:
Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2017Cataloged from PDF version of thesis.
Includes bibliographical references (pages 29-31).
Although many genetic loci pertinent to complex diseases have been identified and despite the fact that complex diseases remain an immense burden to healthcare globally, many details about the mechanism of these diseases are still unknown. Thus far, genome-wide association studies (GWAS) have only explained a small proportion of disease heritability, indicating that there is a large number of additional loci that contribute to complex diseases like type 2 diabetes (T2D), which is the primary case study in this work. We overcome some of the limitations of rare variant studies by conducting weighted aggregate association tests in a framework we call "Convergence". We compare potential cell type specific regulatory loci assigned to genes, which serve as the basis for grouping variants and integrated predictors of functional consequence of variants, which serve as variant weights. We demonstrate that this methodology is able to detect significant association to T2D for genes relevant for body weight homeostasis, adipocyte proliferation, and inflammation. As a result, this work provides a principled framework for improving the efficacy of RVAS by successfully converging the abundant epigenetic information available to understand complex disease.
by Daniel N. Sosa.
M. Eng.
M.Eng. Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science
15
Ndungu, Anne. "Rare genetic variants and susceptibility to severe bacterial diseases." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:9c5745f9-50f9-469a-8771-2e49e75db7ac.
Full textAbstract:
Infectious diseases are a major cause of morbidity and mortality worldwide. Streptococcus pneumoniae and Neisseria meningitidis are major causes of severe bacterial disease which can manifest as invasive disease such as bacteraemia and meningitis. Exposure to these pathogens is relatively widespread, yet only a minority of individuals develop invasive disease. A host genetic component to infectious disease susceptibility has been implied from twin and adoptee studies. A role for rare large effect genetic variants in predisposition to infection has been demonstrated through the study of individuals with primary immunodeficiencies. However, a majority of these studies have been undertaken in individuals with a history of recurrent disease or in multi-case families. The relative role of rare genetic variants of moderate to large effect at the population level has not been widely explored. This thesis presents effort made using next generation sequencing methods to identify rare genetic variants that lead to increased susceptibility to bacterial disease focussing on meningococcal disease, pleural infection(empyema), pneumococcal disease and sepsis phenotypes. Using an exome sequencing approach in 13 cases with invasive meningococcal disease, a novel mutation leading to a complement deficiency and increased risk of meningococcal infection was identified and functionally validated in one individual. This mutation in the CFP gene was demonstrated as leading to impaired properdin secretion. Further analysis implicated loss of function mutations in CD4 and ZAP70 as novel loci for meningococcal disease susceptibility. A case control association analysis for sepsis susceptibility highlighted the possible role for small Rho GTPases in sepsis pathology. By aggregating all rare predicted deleterious mutations in a gene, four genes in this pathway, (ROCK2, ARHGAP18, FYN and CDC42BPG) were implicated as having an excess of rare deleterious variants in sepsis samples compared to population controls. A similar approach identified low frequency genetic variants in the CD109 gene as predisposing to empyema susceptibility in children. Finally, preliminary evidence from adult individuals with invasive pneumococcal disease points to a potential role of the RNASE7 gene in invasive pneumococcal disease susceptibility. This association was primarily due to a predicted deleterious missense mutation present in cases and absent in controls. Taken together, these results have identified a number of potential loci with rare variants associated with susceptibility to severe phenotypes of bacterial diseases.
16
Onoufriadis, Alexandros. "Characterisation of rare genetic variants conferring susceptibility to psoriasis." Thesis, King's College London (University of London), 2013. https://kclpure.kcl.ac.uk/portal/en/theses/characterisation-of-rare-genetic-variants-conferring-susceptibility-to-psoriasis(78905027-5f07-4927-a535-0ca34f99977d).html.
Full textAbstract:
Psoriasis is an immune-mediated skin disorder that is inherited as a complex trait. Although genome-wide association studies (GWAS) have identified a number of common disease susceptibility alleles, a substantial fraction of psoriasis heritability remains unexplained, suggesting the possibility that rare variants may also be pathogenic. The aim of this project was to further investigate this hypothesis and explore different approaches to the identification of rare susceptibility alleles. A candidate gene approach was initially undertaken, through the re-sequencing of RNF114, a gene that had been associated with psoriasis in various GWAS. This led to the identification of four novel promoter variants (c.-66C>A, C.-64C>A, C.-41C>T and c.-9A>C) which collectively demonstrate significant association with the disease (P < 0.01). The functional characterisation of two representative substitutions showed that they both affected Spl binding as well as RNF114 promoter activity. In the second part of the study, a positional cloning approach was applied to the analysis of a multigenerational psoriasis pedigree, where the disease appeared to segregate as an autosomal dominant trait. Tentative evidence for linkage (LOD > -2) was obtained for two regions on chromosomes 2p21 and 15q25. However, next-generation sequencing of an affected family member failed to identify any pathogenic mutation within the above intervals. In the final part of the study, five unrelated patients affected by a rare and severe variant of psoriasis (generalised pustular psoriasis) were analysed by whole-exome sequencing. This led to the identification of two recessive mutations (p.Ser113Leu and p.Arg48Trp) of the IL36RN gene, which encodes a protein antagonizing the activity of IL-36 cytokines. An ex-vivo analysis of patient cells demonstrated a marked increase in cytokine reduction upon IL-36A stimulation, suggesting that GPP mutations may affect the anti-iflammatory function of IL36RN. While this work suggests that rare variants are likely to contribute to the pathogenesis of psoriasis, it also highlights a number of methodological issues that will need to be considered in the design of future studies.
17
張艷馨 and Yim-hing Cheung. "Rare types and polymorphic variants of HPV in Hong Kong." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2002. http://hub.hku.hk/bib/B31970448.
Full text
18
Cheung, Yim-hing. "Rare types and polymorphic variants of HPV in Hong Kong." Hong Kong : University of Hong Kong, 2002. http://sunzi.lib.hku.hk/hkuto/record.jsp?B25176559.
Full text
19
Calafato, Maria Stella Francesca. "Uncovering the role of common and rare variants in migraine." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610802.
Full text
20
Albers, Patrick K. "Rare and low-frequency variants and predisposition to complex disease." Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:2d569297-5d2a-49c8-a1ca-32a978aec49d.
Full textAbstract:
Advances in high-throughput genomic technologies have facilitated the collection of DNA information for thousands of individuals, providing unprecedented opportunities to explore the genetic architecture of complex disease. One important finding has been that the majority of variants in the human genome are low in frequency or rare. It has been hypothesised that recent explosive growth of the human population afforded unexpectedly large amounts of rare variants with potentially deleterious effects, suggesting that rare variants may play a role in disease predisposition. But, importantly, rare variants embody a source of information through which we may learn more about our recent evolutionary history. In this thesis, I developed several statistical and computational methods to address problems associated with the analysis of rare variants and, foremost, to leverage the genealogical information they encode. First, one constraint in genome-wide association studies is that lower-frequency variants are not well captured by genotyping methods, but instead are predicted through imputation from a reference dataset. I developed the meta-imputation method to improve imputation accuracy by integrating genotype data from multiple, independent reference panels, which outperformed imputations from separate references in almost all comparisons (mean correlation with masked genotypes r2>0.9). I further demonstrated in simulated case-control studies that meta-imputation increased the statistical power to identify low-frequency variants of intermediate or high penetrance by 2.2-3.6%. Second, rare variants are likely to have originated recently through mutation and thereby sit on relatively long haplotype regions identical by descent (IBD). I developed a method that exploits rare variants as identifiers for shared haplotype segments around which the breakpoints of recombination are detected using non-probabilistic approaches. In coalescent simulations, I show that such breakpoints can be inferred with high accuracy (r2>0.99) around rare variants at frequencies <0.05%, using either haplotype or genotype data. Third, I show that technical error poses a major problem for the analysis of whole-genome sequencing or genotyping data, particularly for alleles below 0.05% frequency (false positive rate, FPR=0.1). I therefore propose a novel approach to infer IBD segments using a Hidden Markov Model (HMM) which operates on genotype data alone. I incorporated an empirical error model constructed from error rates I estimated in publicly available sequencing and genotyping datasets. The HMM was robust in presence of error in simulated data (r2>0.98) while nonprobabilistic methods failed (r2<0.02). Lastly, the age of an allele (the time since its creation through mutation) may provide clues about demographic processes that resulted in its observed frequency. I present a novel method to estimate (rare) allele age based on the inferred shared haplotype structure of the sample. The method operates in a Bayesian framework to infer pairwise coalescent times from which the age is estimated using a composite posterior approach. I show in simulated data that coalescent time can be inferred with high accuracy (rank correlation >0.91) which resulted in a likewise high accuracy for estimated age (>0.94). When applied to data from the 1000 Genomes Project, I show that estimated age distributions were overall conform with frequency-dependent expectations under neutrality, but where patterns of low frequency and old age may hint at signatures of selection at certain sites. Thus, this method may prove useful in the analysis of large cohorts when linked to biomedical phenotype data.
21
Li, Yali. "DETECTING ASSOCIATION OF COMMON AND RARE VARIANTS WITH COMPLEX DISEASES." Case Western Reserve University School of Graduate Studies / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1270176845.
Full text
22
He, Karen Yingyi. "DETECTING LOW FREQUENCY AND RARE VARIANTS ASSOCIATED WITH BLOOD PRESSURE." Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case157435735160471.
Full text
23
Luedders, Jonathan. "A Review of Common and Rare Genetic Variants in Schizophrenia." VCU Scholars Compass, 2011. http://scholarscompass.vcu.edu/etd/2540.
Full textAbstract:
Genetic epidemiology has shown a large role for genetic influences on schizophrenia. However, the nature of the variants involved is debated. The common disease-common variant (CDCV) hypothesis suggests that schizophrenia is caused by common alleles with small effect sizes. According to the common disease-rare variant (CDRV) hypothesis, schizophrenia is caused by rare variants with large effect sizes. In recent years, evidence has been found for both common and rare variants in schizophrenia. Several SNPs have been associated with schizophrenia through genome-wide association studies (GWAS), supporting the CDCV hypothesis. In support of the CDRV hypothesis, individuals with schizophrenia have been found to have a higher burden of rare copy-number variants (CNVs). Also, several specific rare CNVs have been associated with schizophrenia. The exact mechanisms of these variants are unknown, but common and rare variants appear to affect many of the same pathways in the etiology of schizophrenia.
24
Liang, Jingjing. "Searching for rare variants associated with OSAHS-related phenotypes through pedigrees." Case Western Reserve University School of Graduate Studies / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=case1554477894167055.
Full text
25
Zhou, Xiaofei. "Bayesian Lasso for Detecting Rare Genetic Variants Associated with Common Diseases." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1563455460578675.
Full text
26
Zak, Jaroslav. "Functional genetics of cancer and congenital disorders." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:58844495-fca0-4090-8462-22e6f919f127.
Full textAbstract:
The genetic architectures of cancer and congenital disorders are heterogeneous and incompletely mapped. Rare and low-frequency variants of incomplete penetrance are emerging as an important class of germline and somatic variation, but their contribution to disease remains poorly characterised. This thesis aims to identify and assess pathogenic mutations in the 1q41q42 microdeletion syndrome, neural tube defects, neuropsychiatric disorders and cancer. Rare microdeletions at the 1q41q42 locus cause a clinically heterogeneous syndrome characterized by developmental delay, characteristic dysmorphic features and brain morphological abnormalities. Examining new and published patients with 1q41q42 microdeletions, we found that TP53BP2, encoding ASPP2, is a strong candidate for being the gene responsible for brain morphological abnormalities of the syndrome. Mice deficient for Trp53bp2 show multiple abnormalities overlapping the features of the 1q41q42 microdeletion syndrome such as dysmorphic lateral ventricles, heart and urogenital abnormalities. ASPP2 deficiency also causes neural tube defects, hopping gait, and male-specific motion hyperactivity in mice. We further identify candidate pathogenic TP53BP2 duplications, implicating TP53BP2 dosage sensitivity in the ganglionic eminences of the developing brain, manifested by structural abnormalities in the striatum and lateral ventricles of both deletion and duplication patients. ASPP2 controls neuroepithelial cell polarity via Par3 and genetic disruption of aPKC-Par3 interaction by rare missense variants was implicated in human neural tube defects. An integrative analysis of cancer genomic data revealed that PPP1R13B, encoding ASPP1, bears many hallmarks of a tumour suppressor gene, despite being mutated at a low absolute frequency. A subset of missense somatic mutations in ASPP genes genetically interact with TP53 mutations, disrupting an autoinhibitory mechanism to modulate p53-dependent transcription. In summary, this work identified novel candidate pathogenic variants in developmental disorders and cancer, and explored the mechanisms underlying their respective genotype-phenotype links.
27
Pepler, A. "Identification of novel disease-causing variants in rare diseases using trio exome sequencing." Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/1565182/.
Full textAbstract:
The use of trio exome next-generation sequencing (NGS), an analysis of the entire complement of coding exons within an affected index patient and unaffected parents, is increasingly being utilised in the analysis of patients with congenital diseases. This thesis describes the use of trio exome sequencing in the analysis of three distinct circumstances. First, the analysis of a cohort of eight trios in which the index patients suffer from startle disease, characterized by dysfunction of inhibitory glycinergic synapses. This revealed a single case of allelic drop-out of a known GLRA1 p.Y307C variant in a novel de novo pattern of inheritance, three cases where known or expected pathogenic variants had been identified in genes known to cause a seizure phenotype (DOLK and DMD), and an association with variants in ATRN, a null mutant of which is associated with a seizure phenotype in Mus musculus. Second, whole exome analysis of three individual cases with rare diseases was performed; a case of hypomyelinating leukodystrophy with a homozygous NKX6-2 p.L54Qfs variant, a case of microcephaly and pontocerebellar hypoplasia with a MED14 de novo p.R1162C variant, and a case of syndromic intellectual disability with hypotonia and a homozygous DRG1 p.Y295* variant. None of these genes had yet been implicated in disease, but all show some functional implication in each of the respective disorders. Third, novel de novo GRIN1 p.M818R and GRIN2B p.M824V variants were identified in further cases with developmental delay and hypotonia, adding to recent publications expanding the phenotype of variants within the NMDA receptor subunits. In each of these cases, trio exome sequencing was requested due to unclear disease aetiology and the resulting data indicates, in the majority of these cases, novel or putative genotype-phenotype correlations.
28
Lin, Y. C. "Identification and characterisation of rare CACNG5 genetic variants in bipolar disorder and schizophrenia." Thesis, University College London (University of London), 2015. http://discovery.ucl.ac.uk/1469324/.
Full textAbstract:
Schizophrenia (SCZ) and bipolar disorder (BPD) are common, highly heritability psychiatric disorders. Genome-wide association studies have found evidence of shared genetic susceptibility to both diseases. The most notable example is CACNA1C which encodes the 1 subunit of L-type calcium channels. Several other calcium channel genes have also been implicated in BPD and/or SCZ and together there is support for a role for these genes in both diseases. The primary function of several subunit calcium channel genes appears to be the regulation of AMPA receptor localisation and function. Collectively these are known as Transmembrane AMPA receptor Regulatory Proteins (TARPs). This thesis aimed to identify disease relevant genetic variation in one such TARP, CACNG5, and to study the effect of these variants. CACNG5 variants in the exons and promoter region were identified in 1098 BPD, 618 SCZ, and 1087 control individuals. Four novel non-synonymous SNPs (nsSNPs) and four nsSNPs were identified. Burden analysis of nsSNPs in BPD and SCZ found evidence for association (p=0.0022). This association was strengthened by inclusion of data from European samples in the 1000 Genomes project (p=0.00057). However, combined data with the UK10K and Swedish exome sequence studies founds a weakened association signal (p=0.0082). Functional analyses using co-expression of AMPAR2 and CACNG5 constructs containing the eight nsSNPs were used to analyse changes in the expression and/or trafficking of 5 and AMPA receptors. Four of the variants were associated with decreased AMPAR2 expression as a consequence of altered trafficking to the cell surface. V146M (identified in 2 SCZ patients) overexpression increased AMPAR2 trafficking to the cell surface (p<0.005); conversely, T164L (identified in one SCZ patient) overexpression decreased the expression of AMPAR2 and its cell surface trafficking (p<0.05). Our results suggest a role for CACNG5 variants in SCZ and/or BPD and that this may be mediated via dysregulation of AMPARs.
29
Lim, Teng Ting. "Exploring the genetic landscape of complex diseases using the recessive model." Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11490.
Full textAbstract:
High-throughput sequencing technologies have changed the way we identify, study and understand the role of rare variation in Mendelian diseases. Sequencing in complex diseases have proven to be more challenging to interpret, but methods and approaches are being developed to aid in our understanding of variation in these diseases.
30
Girard-Bock, Camille. "Un nouveau variant rare entrainant la modification post-traductionnelle de l'enzyme UGT2B7 et affectant son activité." Master's thesis, Université Laval, 2016. http://hdl.handle.net/20.500.11794/27398.
Full textAbstract:
La superfamille des UDP-glucuronosyltransférases (UGT) est constituée de glycoprotéines résidant au réticulum endoplasmique et sujettes aux modifications post-traductionnelles (PTM, post-translational modifications). L’enzyme UGT2B7 est d’un intérêt particulier vu son action sur une grande variété de médicaments. La plupart des études actuelles n’ont pour sujet que les variants communs de cette enzyme et n’examinent donc qu’une fraction de la diversité génétique de celle-ci. En effet, les variants rares (fréquence allélique en deçà de 1%) peuvent potentiellement avoir un effet considérable puisqu’ils sont prédits comme étant bien plus nombreux que les variants communs au sein du génome humain. La présente étude fait état de la découverte d’un variant rare d’UGT2B7 possédant un intérêt pharmacogénétique potentiel et encodant une substitution d’acide aminé au codon 121. Cette variation peu fréquente, retrouvée chez deux individus au sein d’une population de 305 sujets sains, mène à la traduction d’une asparagine (Asn) plutôt qu’un acide aspartique (Asp) au codon 121 (UGT2B7 p.D121N). Cette substitution est prédite comme créant un motif de N-glycosylation NX(S/T) subséquemment validé par traitement à l’endoglycosidase de fractions microsomales issues de surexpressions dans des cellules HEK293 et par inhibition à la tunicamycine de la N-glycosylation d’UGT2B7 produites de façon endogène dans des HEK293. De plus, la présence d’un oligosaccharide additionnel sur l’enzyme UGT2B7, affectant potentiellement son repliement, résulte en la diminution, respectivement par 49 et 40%, de la formation de glucuronides à partir de la zidovudine et de l’acide mycophénolique. Une analyse de la base de données dbSNP a permis la découverte de 32 variants rares pouvant potentiellement créer ou abolir des motifs de N-glycosylation au sein d’enzymes UGT2B. Ensemble, ces variants ont le potentiel d’augmenter la proportion de la variance de la voie des UGT qui est expliquée par des modifications post-traductionnelles telles la N-glycosylation, affectant ainsi le métabolisme des médicaments.The UDP-glucuronosyltransferase (UGT) superfamily consists of glycoproteins resident of the endoplasmic reticulum membranes that undergo post-translational modifications (PTM). UGT2B7 is of particular interest because of its action on a wide variety of drugs. Most studies currently survey common variants and are only examining a small fraction of the genetic diversity. However, rare variants (frequency < 1%) might have significant effect as they are predicted to greatly outnumber common variants in the human genome. Here, we discovered a rare single nucleotide UGT2B7 variant of potential pharmacogenetic relevance that encodes a nonconservative amino acid substitution at codon 121. This low-frequency variation, found in two individuals of a population of 305 healthy volunteers, leads to the translation of an asparagine (Asn) instead of an aspartic acid (Asp) (UGT2B7 p.D121N). This amino acid change was predicted to create a putative N-glycosylation motif NX(S/T) subsequently validated upon endoglycosidase H treatment of microsomal fractions and inhibition of N-glycosylation of endogenously produced UGT2B7 with tunicamycin from HEK293 cells. The presence of an additional N-linked glycan on the UGT2B7 enzyme, likely affecting proper protein folding, resulted in a significant decrease, respectively by 49 and 40%, in the formation of zidovudine and mycophenolic acid glucuronides. A systematic survey of the dbSNP database uncovered 32 rare and naturally occurring missense variations predicted to create or disrupt N-glycosylation sequence motifs in the other UGT2B enzymes. Collectively, these variants have the potential to increase the proportion of variance explained in the UGT pathway due to changes in PTM such as N-linked glycosylation with consequences on drug metabolism.
31
Zanoni, P., S. A. Khetarpal, D. B. Larach, W. F. Hancock-Cerutti, J. S. Millar, M. Cuchel, S. DerOhannessian, et al. "Rare variant in scavenger receptor BI raises HDL cholesterol and increases risk of coronary heart disease." American Association for the Advancement of Science, 2016. http://hdl.handle.net/10150/623258.
Full textAbstract:
Scavenger receptor BI (SR-BI) is the major receptor for high-density lipoprotein (HDL) cholesterol (HDL-C). In humans, high amounts of HDL-C in plasma are associated with a lower risk of coronary heart disease (CHD). Mice that have depleted Scarb1 (SR-BI knockout mice) have markedly elevated HDL-C levels but, paradoxically, increased atherosclerosis. The impact of SR-BI on HDL metabolism and CHD risk in humans remains unclear. Through targeted sequencing of coding regions of lipid-modifying genes in 328 individuals with extremely high plasma HDL-C levels, we identified a homozygote for a loss-of-function variant, in which leucine replaces proline 376 (P376L), in SCARB1, the gene encoding SR-BI. The P376L variant impairs posttranslational processing of SR-BI and abrogates selective HDL cholesterol uptake in transfected cells, in hepatocyte-like cells derived from induced pluripotent stem cells from the homozygous subject, and in mice. Large population-based studies revealed that subjects who are heterozygous carriers of the P376L variant have significantly increased levels of plasma HDL-C. P376L carriers have a profound HDL-related phenotype and an increased risk of CHD (odds ratio = 1.79, which is statistically significant).
32
Adhikari, Kaustubh. "Statistical Methodology for Sequence Analysis." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10178.
Full textAbstract:
Rare disease variants are receiving increasing importance in the past few years as the potential cause for many complex diseases, after the common disease variants failed to explain a large part of the missing heritability. With the advancement in sequencing techniques as well as computational capabilities, statistical methodology for analyzing rare variants is now a hot topic, especially in case-control association studies. In this thesis, we initially present two related statistical methodologies designed for case-control studies to predict the number of common and rare variants in a particular genomic region underlying the complex disease. Genome-wide association studies are nowadays routinely performed to identify a few putative marker loci or a candidate region for further analysis. These methods are designed to work with SNP data on such a genomic region highlighted by GWAS studies for potential disease variants. The fundamental idea is to use Bayesian methodology to obtain bivariate posterior distributions on counts of common and rare variants. While the first method uses randomly generated (minimal) ancestral recombination graphs, the second method uses ensemble clustering method to explore the space of genealogical trees that represent the inherent structure in the test subjects. In contrast to the aforesaid methods which work with SNP data, the third chapter deals with next-generation sequencing data to detect the presence of rare variants in a genomic region. We present a non-parametric statistical methodology for rare variant association testing, using the well-known Kolmogorov-Smirnov framework adapted for genetic data. it is a fast, model-free robust statistic, designed for situations where both deleterious and protective variants are present. It is also unique in utilizing the variant locations in the test statistic.
33
Tang, Wai-kiu, and 鄧慧翹. "Re-sequencing of neuregulin 1 to search for rare variants in Chinese hirschsprung patients." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46599897.
Full text
34
Jeng, Xinge Jessie, Zhongyin John Daye, Wenbin Lu, and Jung-Ying Tzeng. "Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level." Public Library of Science, 2016. http://hdl.handle.net/10150/618985.
Full textAbstract:
Genetic association analyses of rare variants in next-generation sequencing (NGS) studies are fundamentally challenging due to the presence of a very large number of candidate variants at extremely low minor allele frequencies. Recent developments often focus on pooling multiple variants to provide association analysis at the gene instead of the locus level. Nonetheless, pinpointing individual variants is a critical goal for genomic researches as such information can facilitate the precise delineation of molecular mechanisms and functions of genetic factors on diseases. Due to the extreme rarity of mutations and high-dimensionality, significances of causal variants cannot easily stand out from those of noncausal ones. Consequently, standard false-positive control procedures, such as the Bonferroni and false discovery rate (FDR), are often impractical to apply, as a majority of the causal variants can only be identified along with a few but unknown number of noncausal variants. To provide informative analysis of individual variants in large-scale sequencing studies, we propose the Adaptive False-Negative Control (AFNC) procedure that can include a large proportion of causal variants with high confidence by introducing a novel statistical inquiry to determine those variants that can be confidently dispatched as noncausal. The AFNC provides a general framework that can accommodate for a variety of models and significance tests. The procedure is computationally efficient and can adapt to the underlying proportion of causal variants and quality of significance rankings. Extensive simulation studies across a plethora of scenarios demonstrate that the AFNC is advantageous for identifying individual rare variants, whereas the Bonferroni and FDR are exceedingly over-conservative for rare variants association studies. In the analyses of the CoLaus dataset, AFNC has identified individual variants most responsible for gene-level significances. Moreover, single-variant results using the AFNC have been successfully applied to infer related genes with annotation information.
35
Riveros, Mckay Aguilera Fernando. "Genetic studies of cardiometabolic traits." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/289420.
Full textAbstract:
Diet and lifestyle have changed dramatically in the last few decades, leading to an increase in prevalence of obesity, defined as a body mass index >30Kg/m2, dyslipidaemias (defined as abnormal lipid profiles) and type 2 diabetes (T2D). Together, these cardiometabolic traits and diseases, have contributed to the increased burden of cardiovascular disease, the leading cause of death in Western societies. Complex traits and diseases, such as cardiometabolic traits, arise as a result of the interaction between an individual's predisposing genetic makeup and a permissive environment. Since 2007, genome-wide association studies (GWAS) have been successfully applied to complex traits leading to the discovery of thousands of trait-associated variants. Nonetheless, much is still to be understood regarding the genetic architecture of these traits, as well as their underlying biology. This thesis aims to further explore the genetic architecture of cardiometabolic traits by using complementary approaches with greater genetic and phenotype resolution, ranging from studying clinically ascertained extreme phenotypes, deep molecular profiling, or sequence level data. In chapter 2, I investigated the genetic architecture of healthy human thinness (N=1,471) and contrasted it to that of severe early onset childhood obesity (N=1,456). I demonstrated that healthy human thinness, like severe obesity, is a heritable trait, with a polygenic component. I identified a novel BMI-associated locus at PKHD1, and found evidence of association at several loci that had only been discovered using large cohorts with >40,000 individuals demonstrating the power gains in studying clinical extreme phenotypes. In chapter 3, I coupled high-resolution nuclear magnetic resonance (NMR) measurements in healthy blood donors, with next-generation sequencing to establish the role of rare coding variation in circulating metabolic biomarker biology. In gene-based analysis, I identified ACSL1, MYCN, FBXO36 and B4GALNT3 as novel gene-trait associations (P < 2.5x10-6). I also found a novel link between loss-of-function mutations in the "regulation of the pyruvate dehydrogenase (PDH) complex" pathway and intermediate-density lipoprotein (IDL), low-density lipoprotein (LDL) and circulating cholesterol measurements. In addition, I demonstrated that rare "protective" variation in lipoprotein metabolism genes was present in the lower tails of four measurements which are CVD risk factors in this healthy population, demonstrating a role for rare coding variation and the extremes of healthy phenotypes. In chapter 4, I performed a genome-wide association study of fructosamine, a measurement of total serum protein glycation which is useful to monitor rapid changes in glycaemic levels after treatment, as it reflects average glycaemia over 2-3 weeks. In contrast to HbA1c, which reflects average glucose concentration over the life-span of the erythrocyte (~3 months), fructosamine levels are not predicted to be influenced by factors affecting the erythrocyte. Surprisingly, I found that in this dataset fructosamine had low heritability (2% vs 20% for HbA1c), and was poorly correlated with HbA1c and other glycaemic traits. Despite this, I found two loci previously associated with glycaemic or albumin traits, G6PC2 and FCGRT respectively (P < 5x10-8), associated with fructosamine suggesting shared genetic influence. Altogether my results demonstrate the utility of higher resolution genotype and phenotype data in further elucidating the genetic architecture of a range of cardiometabolic traits, and the power advantages of study designs that focus on individuals at the extremes of phenotype distribution. As large cohorts and national biobanks with sequencing and deep multi-dimensional phenotyping become more prevalent, we will be moving closer to understanding the multiple aetiological mechanisms leading to CVD, and subsequently improve diagnosis and treatment of these conditions.
36
Tervasmäki, A. (Anna). "Hereditary predisposition to breast cancer:evaluating the role of rare copy number variant, protein-truncating and missense candidate alleles." Doctoral thesis, Oulun yliopisto, 2018. http://urn.fi/urn:isbn:9789526220826.
Full textAbstract:
Abstract Breast cancer is the most common cancer among women, and inherited predisposition is one of the major recognized causes of increased breast cancer risk. Only about half of the hereditary cases are explained by mutations in the known susceptibility genes, including the DNA damage response genes BRCA1, BRCA2 and PALB2, leaving the majority still uncovered. Identification of the missing genetic predisposing factors is important for more effective diagnostics and counseling of the risk families, and also for better understanding of the etiology and cellular characteristics of breast cancer. The first aim of this study was to investigate the cancer associations of six rare germline copy number variant (CNV) deletions, which were previously identified in breast cancer patients by a genome-wide microarray approach. The second aim was to identify novel susceptibility alleles, both protein-truncating variants and missense mutations, by next-generation sequencing (NGS) of nearly 800 DNA damage response genes in 189 hereditary breast cancer patients. The cancer-associations of all selected candidate alleles (6 CNVs, 39 protein-truncating variants and 35 missense mutations) were studied by case-control approach using DNA samples from several hundred breast cancer patients and healthy controls. The prevalence of the studied CNVs did not significantly differ between the cases and controls, but when studying the associations with specific clinical parameters, deletion in the CYP2C19 gene showed enrichment in the breast cancer patients with hormonally triple-negative tumors (p=0.021). As CYP2C19 functions in estrogen metabolism, the results indicate that disturbance of hormonal balance due to enzyme defects may predispose specifically to the estrogen receptor-negative subtype of breast cancer. Two protein truncating-variants, TEX15 c.7253dupT and FANCD2 c.2715+1G>A showed significant breast cancer association in the Northern Finnish cohort (p=0.018 and p=0.036, respectively). Similarly, two of the studied missense variants, RECQL p.Ile156Met (p=0.043) and POLG p.Leu392Val (p=0.010), were enriched in the breast cancer cases. Thus, this study provided novel connections between increased breast cancer risk and inherited mutations in TEX15, FANCD2 and POLG genes, and further supported the recently established role of RECQL as a breast cancer susceptibility geneTiivistelmä Rintasyöpä on naisten yleisin syöpä, ja perinnöllinen alttius on yksi merkittävimmistä sairastumisriskiin vaikuttavista tekijöistä. Tunnetuimpia alttiustekijöitä ovat mutaatiot BRCA1-, BRCA2- ja PALB2-DNA-vauriovastegeeneissä, mutta ne yhdessä muiden altistavien geenimutaatioiden kanssa selittävät kuitenkin vain noin puolet perinnöllisistä rintasyöpätapauksista. Uusien alttiusgeenien löytäminen mahdollistaa tehokkaamman diagnostiikan ja korkeassa syöpäriskissä olevien sukujen perinnöllisyysneuvonnan, sekä auttaa ymmärtämään syvemmin rintasyövän etiologiaa ja syntymekanismeja solutasolla. Tämän väitöskirjan ensimmäisenä päämääränä oli tutkia tarkemmin aiemmin genominlaajuisella mikrosirumenetelmällä rintasyöpäpotilailta tunnistettujen harvinaisten perinnöllisten DNA-kopiolukuvariaatioiden (CNV) yhteyttä rintasyöpäriskiin. Toisena tavoitteena oli tunnistaa uusia rintasyöpäalttiusalleeleja, sekä proteiinitrunkaatioita että missense-mutaatioita, hyödyntämällä uuden sukupolven sekvensointitekniikkaa, jonka avulla tutkittiin mutaatioita lähes 800 DNA-vauriovastegeenistä 189 pohjoissuomalaiselta rintasyöpäpotilaalta. Valittujen kandidaattialleelien (6 deleetion aiheuttavaa CNV:tä, 39 proteiinitrunkaatiota ja 35 missense-mutaatiota) yhteyttä rintasyöpään tutkittiin tapaus-verrokkimenetelmällä käyttäen DNA-näytteitä usealta sadalta rintasyöpäpotilaalta ja terveeltä kontrollihenkilöltä. Tutkittujen CNV:iden esiintyvyydessä ei ollut merkitseviä eroja potilaiden ja kontrollien välillä, mutta tarkasteltaessa yhteyttä potilaiden kasvaimista saatuihin kliinisiin parametreihin, deleetio CYP2C19-geenissä oli yleisempi hormonaalisesti kolmoisnegatiivisissa rintatuumoreissa kuin muissa tuumorityypeissä (p=0.021). Koska CYP2C19 on estrogeenimetaboliaan osallistuva entsyymi, sen viallinen toiminta voi mahdollisesti altistaa erityisesti estrogeenireseptorinegatiiviselle rintasyövälle. Kaksi tutkituista proteiinitrunkaatioista, TEX15 c.7253dupT ja FANCD2 c.2715+1G>A, olivat rikastuneet perinnöllisessä rintasyöpäpotilasaineistossa verrattuna kontrolleihin (p=0.018 ja p=0.036). Myös kaksi missense-alleelia, RECQL p.Ile156Met (p=0.043) ja POLG p.Leu392Val (p=0.010), olivat yleisempiä rintasyöpäpotilailla. Tulokset osoittivat uuden yhteyden kohonneen rintasyöpäriskin ja perinnöllisten muutosten TEX15-, FANCD2- ja POLG-geenien välillä, sekä tukivat aiempia tutkimustuloksia, joiden mukaan RECQL on kohtalaisen riskin rintasyöpäalttiusgeeni
37
Jacobi, Simon Friedrich [Verfasser]. "Evaluation of a Rare Glucose-Dependent Insulinotropic Polypeptide Receptor Variant in a Patient with Diabetes / Simon Friedrich Jacobi." Berlin : Medizinische Fakultät Charité - Universitätsmedizin Berlin, 2021. http://d-nb.info/1234984768/34.
Full text
38
Mentoor, J. L. D. (Juliet Lewie Dionee). "Identification of rare gene variants in South African breast cancer families through next generation sequencing." Thesis, University of Pretoria, 2017. http://hdl.handle.net/2263/63043.
Full textAbstract:
Breast cancer (BC) has become the leading cancer amongst women in South Africa. The
overall life time risk for developing this disease is one in 12 (National Cancer registry, 2000-
2011). A strong family history (≥3 affected) is an important factor for inherited predisposition to
BC that accounts for approximately 10% of cases worldwide. Mutations in several high- and
moderate risk breast cancer genes have been associated with familial BC and includes
BRCA1, BRCA2, TP53, PALB2, and CHEK2. Individuals that carry germline mutations in
BRCA1 and BRCA2 possess an 80% lifetime risk for BC. Mutations in BRCA1 and BRCA2 are
responsible for 29% and 25% of familial BC worldwide. In South Africa BRCA1 mutations
account for 19% and BRCA2 for 47% of familial breast cancer. Mutations associated with a
moderate risk for BC account for ~1% of cases. This data suggests that ~30% of South African
BC families are not characterised by pathogenic mutations in known breast/ovarian (BC/OVC)
genes. The purpose of the present study was to identify gene variants that may predispose to breast
cancer. Next generation sequencing was performed to investigate the germline DNA of highrisk
BC/OVC families that have previously tested negative for premature truncating mutations
in BRCA1/2, PALB2 and RAD51C. Paired-end whole exome sequencing was performed with
nine index cases, selected from six families with a strong background for BC/OVC. This
resulted in the discovery of an average of 26 000 coding variants in index cases. Gene
prioritisation strategies were incorporated to filter all exome variants and identify high-priority
genes for further analysis. After sequence verification, three high-priority genes were selected
for further analysis. The three genes coded for; a novel putative tumour suppressor (TCHP) that is pro-apoptotic;
the XPF-endonuclease homolog, EME2; and a POLQ like helicase enzyme (HELQ). Prioritised
genes were screened in a total of 61 high-risk families and cohorts of patients with BC or OVC
without a family history for their disease. Two potentially damaging variants (stop-gain & inframe
amino acid deletion) were identified in TCHP, four (frameshift, nonsense & two in-frame
deletions) in EME2 and one frameshift mutation in HELQ in high-risk families and cases that
were without a family history for BC/OVC.
The analyses performed in the last section of this project was aimed at identifying other
potential genes of interest by making use of a list of 516 well recognised and putative DNA repair genes. Through this approach, one additional truncating mutation in POLN
(p.Q837SfsX7) was highlighted as a potential gene of interest for future investigation.
Despite the key roles that the high-priority genes play in their respective processes, the
present study could not verify that the potential loss of function variants discovered make an
appreciable contribution towards BC/OVC susceptibility in our setting. Further investigation is
necessary to validate their involvement in breast/ovarian cancer predisposition.Thesis (PhD)--University of Pretoria, 2017.
Genetics
PhD
Unrestricted
39
Miossec, Matthieu Josepth. "Whole-exome capture and next-generation sequencing to discover rare variants predisposing to congenital heart disease." Thesis, University of Newcastle upon Tyne, 2016. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.701158.
Full textAbstract:
Congenital heart disease (CHD) is the most common congenital malformation, affecting 8 out of 1000 lives births, yet its aetiology remains largely unresolved. The rapidly growing number of point mutations implicated in isolated CHD suggests that single mutations may contribute significantly to CHD risk. This thesis presents an investigation of the genetic underpinnings of various types of CHD following different study designs. First, I designed a new approach to variant calling which I implemented as the variant caller BAMily. My aim was to develop a method of uncovering putative variants in next-generation sequencing data, shared by a subset of individuals and absent in another subset. I tested the variant caller’s performance against other known variant callers and demonstrated that it provides comparable; and often better, results. This novel variant caller was applied to a study of 8 families in which a disease trait was segregating; along with the variant caller SAMtools, leading to the discovery of likely disease-causing variants in 5 families. Second, I studied de novo mutation in 32 sporadic cases of transposition of the great arteries (TGA) in an attempt to identify genes that, when mutated, lead to TGA. The 32 patients with TGA were sequenced with their parents; as well as one unaffected sibling. To achieve this aim, three variant callers were used: SAMtools, GATK Unified Genotyper and BAMily, the latter acting as a filter. Potential de novo variants were found in GREB1, RBP5, SNX13. Results suggested a complex genetic etiology underlying TGA. Finally, I studied a large series of cases of tetralogy of Fallot (ToF). The study involved 824 patients which ToF and a comparator set of 490 patients with neurodevelopmental disorders lifted from the UK10K project. The aim of the study was to identify genes that, when mutated, play a role in the manifestation of ToF might cluster. For this, I first categorised variants according to their potential to disrupt protein function. I then compared genes in which potentially disease-causing rare variants occurred to lists of genes previously implicated in CHD in the literature. Following this, I identified the clustering of potentially deleterious rare variants across the coding region of genes and exons in ToF patients, hypothesising that variants influencing ToF would cluster in ToF patients. This study led to the discovery of candidate variants in FLT4 and NOTCH1 for non-syndromic ToF. As with TGA, the results I have obtained suggested a complex etiology for ToF.
40
Winchester, Laura. "Identification of candidate disease genes in common and rare disorders using copy number variant detection from single nucleotide polymorphism arrays." Thesis, University of Oxford, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.542993.
Full text
41
Xia, Shuang. "Detecting Rare Haplotype-Environment Interaction and Dynamic Effects of Rare Haplotypes using Logistic Bayesian LASSO." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1406246686.
Full text
42
Zhang, Han. "Detecting Rare Haplotype-Environmental Interaction and Nonlinear Effects of Rare Haplotypes using Bayesian LASSO on Quantitative Traits." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu149969433115895.
Full text
43
Schubert, Jeffrey A. B. S. "The Use of Genetic Analyses and Functional Assays for the Interpretation of Rare Variants in Pediatric Heart Disease." University of Cincinnati / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1535724045195581.
Full text
44
Lau, Winnie. "Studies of human EKLF mutations associated with the In(Lu) blood group phenotype and a rare variant of congenital dyserlthropoietic anaemia." Thesis, University of Bristol, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.529878.
Full text
45
Veyssiere, Maëva. "Etude de la composante génétique de la Polyarthrite Rhumatoïde par séquençage d'exomes : contribution des variants rares." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLE023/document.
Full textAbstract:
La Polyarthrite Rhumatoïde (PR) est une maladie auto-immune inflammatoire complexe qui touche près de 0,3% de la population française. A ce jour, malgré l'identification d'un facteur génétique majeur (HLA-DRB1), et d'une centaine de facteurs de susceptibilité d'effet faible à modéré (majoritairement identifiés par des études d'associations pangénomiques - GWAS), on ne peut expliquer au plus que 50% de la composante génétique de la maladie. Les GWAS se focalisant sur les variants fréquents (fréquence de l'allèle mineure (MAF) ≥ 1%) et considérant l'effet de ces variants comme indépendants, nous avons cherché dans ces travaux à identifier de nouveaux facteurs génétiques de la PR via l'analyse de variants rares (variants d'un seul nucléotide (SNVs) ou petites insertions et délétions (InDels)) pour lesquels peu d'études sont référencées dans la littérature. Nous avons ensuite étudié les interactions gène/gène (GxG) dans des voies biologiques enrichies par les variants rares identifiés.Pour cela, nous avons travaillé sur deux jeux de données obtenus par séquençage d'exomes. Dans le premier échantillon (data1), nous avons cherché à évaluer la contribution des variants rares dans 1080 gènes candidats séquencés chez 240 cas et 240 témoins français. Dans le second échantillon (data2), notre objectif était d'identifier de nouveaux facteurs génétiques par l'analyse de variants rares chez 30 individus (dont 19 atteints) appartenant à 9 familles françaises à cas multiples de PR. Nous avons mis en place un workflow afin de réaliser toutes les étapes de traitement des séquences obtenues jusqu'à l'identification des variants (alignement des lectures sur la séquence de référence du génome humain GRCh37, nettoyage de l'alignement, identification des variants (SNV et Indels) et filtre qualité des variants identifiés).Avec data1, nous avons répliqué l'association entre la PR et le gène BTNL2 (p-value = 3,0E-6) et identifié trois nouveaux gènes à risque (p-value ≤ 4,0E-3), impliqués dans la différentiation et l'activation des cellules du système immunitaire, en combinant les multiples variants de fréquences faibles à modérées identifiés dans ces gènes (analyses d'association de type burden). Dans data2, nous avons effectué une étude d'association-liaison, par laquelle nous avons identifié 3 gènes - SUSD5, MNS1 et SMYD5 - présentant une agrégation de variants (rares et fréquents) associée à la PR (p-value < 0,04 après 10E6 permutations), et un gène nommé SUPT20H dont le signal d'association était porté par un seul variant rare à pénétrance complète dans une famille et sans phénocopie. Nous avons aussi mis en évidence, via une étude d'enrichissement, une agrégation de variants rares dans plusieurs voies biologiques dont l'adhésion focale. Dans cette voie, nous avons identifié 9 interactions candidates pour lesquelles plusieurs combinaisons génotypiques semblent conférer un risque supplémentaire de développer la PR (p-value ≤ 5,0E-5)Rheumatoid arthritis (RA) is a complex inflammatory autoimmune disease affecting about 0.3% of French population. Today, despite the identification of a major genetic factor (HLA-DRB1), and more than one hundred susceptibility factors with low to moderate effect (mainly identified by Genome-Wide association studies - GWAS), we cannot explain more than 50% of RA genetic component. Knowing that GWAS only study frequent variants (minor allele frequency (MAF) ≥ 1%) and consider that all of them are independent, we tried to identify new RA genetic factors by focusing on rare variants (single nucleotide variants (SNVs) or small insertions and deletions (InDels)) for which, to date, only few studies has been conducted. In addition, we studied gene/gene interactions (GxG) in biological pathways enriched for rare susceptible variants.To this end, we worked on two datasets obtained by exome sequencing. With the first dataset (data1), we wanted to evaluate the contribution of rare variants to RA risk into 1080 candidate genes sequenced in 240 cases et 240 controls from French population. With the second dataset (data2), our aim was to identify new genetic factors by focusing on rare variants selected from 30 individuals (including 19 affected) belonging to 9 French multiplex families. We set up in the laboratory a workflow to process the produced sequences up to the identification of variants (read alignment on human reference genome GRCh37, alignment refinement, variant identification (SNV et Indels) and quality filters).In data1, we replicated the association between RA and BTNL2 gene (p-value = 3,0E-6) and identified 3 new RA risk genes (p-value ≤ 4,0E-3), involved in the differentiation and activation of immune system cells, by combining rare to low frequency variants (burden association analysis). In data2, with a linkage – association study, we identified 3 genes - SUSD5, MNS1 and SMYD5 – presenting an aggregation of rare and frequent variants associated with RA (p-value < 0.04 with 10E6 permutations), and another gene SUPT20H in which we identified one rare variant with complete penetrance in one of the family and without phenocopy. Finally, we identified, by enrichment analysis, several biological pathways presenting an aggregation of rare variants. In one of them (focal adhesion), we extracted 9 candidate GxG interactions for which multiple genotype combinations seem to increase RA risk (p-value ≤ 5,0E-5)
46
Medway, Christopher William. "Exploring the association of common and rare variants in CNTN2, FGA and SPARCL1 with late-onset Alzheimer’s disease." Thesis, University of Nottingham, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.588064.
Full textAbstract:
Alzheimer's disease (AD) is an incurable neurodegenerative disorder, and the most common form of dementia, characterised neuropathologically by Aβ plaques and tau tangles. Although the late-onset form of AD (LOAD) is highly heritable (-80%), genetic studies to date have only accounted for approximately half of this. Identification of the remaining risk may require new approaches. In this thesis three candidate genes/loci (CNTN2, FGA and SPARCL 1), encoding putative LOAD cerebro-spinal fluid biomarkers (Contactin-2, Fibrinogen alpha-chain and Sparc-like-1), have been subjected to complementary genetic approaches to unearth novel LOAD risk alleles. An 'LD-aware' meta-analysis of three LOAD genome-wide datasets was conducted to investigate disease association with common (MAF>5%) variation in each candidate gene. Secondly, SOliD next-generation resequencing of 150 samples (75 LOAD, 75 controls), PCR enriched for candidate loci, was conducted to identify novel rare variation. Selected variants were subsequently validated and replicated in larger series (n=1453) using TaqMan genotyping. Meta-analysis revealed linked SNPs (rs7523477, rs4951168) downstream of CNTN2 associated with LOAD (p=3x10-5, OR=1.23(1.01-1.49) n=4898). However, this has not been replicated by subsequent GWAS. Resequencing identified 28 novel rare variations over all candidate loci. A SPARCL 1 variant (located at 88451921 (hg19)) showed association with LOAD in a UK population (p=0.023, OR=1.95(1.1 0-3.46)). Replication of this association will be required in independent series. In the post-GWAS era, new approaches to identify the remaining heritability of LOAD must be embraced. Not only will the identification of new mutations conferring risk for Alzheimer's disease benefit diagnosis, it will also foster a greater understanding of disease pathways - to which treatments can be targeted.
47
Wathen, Michael J. "Population Affiliation Prediction Based on Rare Variants and Using Lancaster Importance Estimator, Principal Component Analysis, and Random Forest." University of Cincinnati / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1460730716.
Full text
48
Reis, Viviane Neri de Souza. "Variações de novo e raras no genoma de pacientes com transtornos do espectro do autismo verbais e não verbais." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/5/5142/tde-08122014-121628/.
Full textAbstract:
Estudos de gêmeos e famílias demonstram que os transtornos do espectro do autismo (TEA) apresentam um grande componente genético (~50%), porém sua etiologia ainda é desconhecida, possivelmente devido aos TEA serem caracterizados como doenças complexas, poligênicas e multifatoriais. Recentemente, variações no número de cópias (CNVs, do inglês Copy Number Variations) e mutações pontuais (SNV, do inglês Single Nucleotide Variant) raras, de novo e herdadas foram associadas com TEA, sugerindo novos loci e genes candidatos. No entanto, a grande maioria das alterações descritas são individuais, de forma que analises por agrupamento das mesmas em genes, e busca de funções biológicas ou vias hiper-representadas tem sido uma abordagem para a compreensão dos possíveis mecanismos etiopatológicos dos TEA. Como os TEA são muito heterogêneos clinicamente o uso de endofenótipos específicos para agrupamento das alterações gênicas pode auxiliar a discriminação de vias e processos biológicos relacionados a dimensões fenotípicas. Considerando os estudos realizados em autismo, e a natureza das variações comuns e raras, nesse trabalho foi realizado o sequenciamento do exoma de 1 família de dois irmãos com TEA sindrômico (sequenciamento piloto) e 18 trios de casos esporádicos de TEA, em busca alterações muito raras e/ou de novo com provável impacto funcional nos pacientes; Além disso, foi analisado se existe diferença entre as vias biológicas hiper-representadas de redes gênicas crescidas a partir dos genes que apresentavam variações raras e de novo, comparando pacientes de TEA com: (1) pouca ou nenhuma comunicação, chamados de não verbais e (2) média a boa comunicação, chamados de verbais. No sequenciamento piloto da família dos irmãos com TEA sindrômico, encontramos 1 duplicação em 4p16.3 e 1 deleção em 8p23.3, em ambos os irmãos; alterações estas encontradas em estudos previos em pacientes com características sindrômicas e TEA; na análise de SNVs e Indels foi encontrada 1 variação de novo e 117 variações não-sinônimas raras herdadas de um dos pais na irmã e 150 variações não-sinônimas raras herdadas de um dos pais no irmão; a análise de vias revelou que os genes com as mutações pontuais raras estavam hiper-representados em regiões cromossômicas diferentes em cada irmão (no cromossomo 1 na paciente do sexo feminino e no cromossomo 16 no paciente do sexo masculino), o que pode estar relacionado às diferenças fenotípicas por eles apresentadas. No sequenciamento do exoma dos trios foram encontradas alterações de novo em 9 dos pacientes: 1 CNV de novo (deleção) de 1,5Mb na região 3q29, região previamente associada com síndrome e transtornos do desenvolvimento; e 8 genes alterados por mutações pontuais de novo, dos quais um dele é o GABBR2, que apresenta evidência de associação com TEA. A análise de vias e redes das variantes herdadas raras, mostrou que muitos dos genes relacionados aos dois grupos verbais e não verbais são genes já associados com TEA ou que apresentam interação com aqueles genes associados ao TEA. As analises de vias e redes precisam ser replicadas em amostras maiores, mas com nossos resultados preliminares podemos perceber que nosso estudo contribui com alterações em genes de vias relacionadas a neurogênese e sinaptogênese, independentemente do fenótipo, que possam refletir um conjunto de genes específicos e ou numero de alterações relacionadas a gravidade do TEAStudies of twins and families have shown that autism spectrum disorders (ASD) are highly heritable (~50%), but its etiology is still unknown, possibly because it is a very heterogeneous phenotype and have multiple genes involved in its development, what characterizes a complex disease such as ASD. Recently, copy number variations (CNVs) and point mutations (SNVs) rare, inherited e de novo, were associated with ASD, suggesting new candidate genes and loci. Because they are very rare, the vast majority of the changes described are individual, so the analysis of different variations grouped by genes and searching for biological functions or hyper represented pathways has been an approach for understanding possible pathogenic mechanisms of ASD. As ASD is clinically very heterogeneous, the use of endophenotypes, specific grouping of genomic changes can help discriminating pathways and biological processes related to phenotypic dimensions. Considering the studies in autism, and the nature of common and rare variants, we sequenced all exons (exome) of 1 family with syndromic ASD (pilot sequencing) and 18 trios of sporadic ASD cases to search for de novo and rare variations with probable functional impact on Brazilian patients; Also, we analyzed whether there is a difference in the enrichment of biological pathways of gene networks from the list of genes affected with de novo and rare deleterious variants in two groups of ASD patients: (1) cases with little or no communication, called nonverbal and (2) cases with average to good communication, called verbal. In the pilot exome sequencing (ASD syndromic family), we found a duplication in 4p16.3 and a deletion in 8p23.3 in both siblings, alterations that were found in patients with syndromes and ASD in previously studies; the analysis of SNVs showed 1 variation de novo and 117 nonsynonymous rare variations inherited from only 1 of the parents in the female sibling, and 150 nonsynonymous rare variations inherited from only 1 of the parents in the male sibling; Pathway analysis revealed enrichment differences of chromosomal regions for each sibling (chromosome 1 for the female patient and chromosome 16 for the male patient), what may be related to their phenotypic differences. In the exome sequencing of trios, as expected, it was found de novo variation in 9 of the patients: 1 de novo CNV (deletion) of 1.5 Mb in the region 29 of the long arm of chromosome 3, a region previously associated with syndrome and developmental disorders; and 8 genes altered by de novo variations, one of those is in the GABBR2, gene with previous evidence of association with ASD. The pathways and networks analysis of rare inherited variants showed that many of the genes related to the two groups verbal and nonverbal are already associated with ASD or interacts with those genes associated with ASD. This pathway and gene network analyses need to be replicated in larger samples, but our preliminary results shows that our study contributes with variations in genes related to neurogenesis and synaptogenesis pathways, regardless of phenotype, with probable impact to specific genes that may be related to severity of clinical presentation
49
Zhang, Fan. "Statistical Methods for Characterizing Genomic Heterogeneity in Mixed Samples." Digital WPI, 2016. https://digitalcommons.wpi.edu/etd-dissertations/419.
Full textAbstract:
"Recently, sequencing technologies have generated massive and heterogeneous data sets. However, interpretation of these data sets is a major barrier to understand genomic heterogeneity in complex diseases. In this dissertation, we develop a Bayesian statistical method for single nucleotide level analysis and a global optimization method for gene expression level analysis to characterize genomic heterogeneity in mixed samples. The detection of rare single nucleotide variants (SNVs) is important for understanding genetic heterogeneity using next-generation sequencing (NGS) data. Various computational algorithms have been proposed to detect variants at the single nucleotide level in mixed samples. Yet, the noise inherent in the biological processes involved in NGS technology necessitates the development of statistically accurate methods to identify true rare variants. At the single nucleotide level, we propose a Bayesian probabilistic model and a variational expectation maximization (EM) algorithm to estimate non-reference allele frequency (NRAF) and identify SNVs in heterogeneous cell populations. We demonstrate that our variational EM algorithm has comparable sensitivity and specificity compared with a Markov Chain Monte Carlo (MCMC) sampling inference algorithm, and is more computationally efficient on tests of relatively low coverage (27x and 298x) data. Furthermore, we show that our model with a variational EM inference algorithm has higher specificity than many state-of-the-art algorithms. In an analysis of a directed evolution longitudinal yeast data set, we are able to identify a time-series trend in non-reference allele frequency and detect novel variants that have not yet been reported. Our model also detects the emergence of a beneficial variant earlier than was previously shown, and a pair of concomitant variants. Characterization of heterogeneity in gene expression data is a critical challenge for personalized treatment and drug resistance due to intra-tumor heterogeneity. Mixed membership factorization has become popular for analyzing data sets that have within-sample heterogeneity. In recent years, several algorithms have been developed for mixed membership matrix factorization, but they only guarantee estimates from a local optimum. At the gene expression level, we derive a global optimization (GOP) algorithm that provides a guaranteed epsilon-global optimum for a sparse mixed membership matrix factorization problem for molecular subtype classification. We test the algorithm on simulated data and find the algorithm always bounds the global optimum across random initializations and explores multiple modes efficiently. The GOP algorithm is well-suited for parallel computations in the key optimization steps. "
50
Basmanav, Fitnat Buket [Verfasser]. "Genetics of schizophrenia: Contribution of rare and low-frequency sequence variants in selected genomic regions to disease susceptibility / Fitnat Buket Basmanav." Bonn : Universitäts- und Landesbibliothek Bonn, 2015. http://d-nb.info/1096330105/34.
Full text