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Sequenciamento e análise do genoma mitocondrial de Gracilaria tenuistipitata (Gracilariales, Rhodophyta); Sequencing and analyzes of the mitochondrial genome of Gracilaria tenuistipitata (Gracilariales, Rhodophyta)

Takahashi, Mônica Miyuki
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 21/05/2010 PT
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35.88%
Mitocôndrias são organelas semi-autônomas responsáveis pela respiração celular. Diversas fontes de evidências indicam a origem endossimbiótica dessas organelas, onde um organismo unicelular teria engolfado um organismo procariótico, possivelmente uma α-proteobactéria. Durante a coevolução do endossimbionte e sua célula hospedeira, ocorreu uma redução do genoma do endossimbionte, parte dos genes sendo perdida e parte transferida para o núcleo. A organização e o tamanho do genoma mitocondrial é bastante variável nas diferentes linhagens filogenéticas. O acúmulo de dados moleculares ajuda a esclarecer a origem e evolução das mitocôndrias. Até o momento, foram sequenciados os genomas mitocondriais de apenas três espécies de Rhodophyta, Chondrus crispus, Cyanidioschyzon merolae e Porphyra purpurea. As algas vermelhas são economicamente importantes por serem utilizadas principalmente como alimento e para as extrações de polissacarídeos e pigmentos acessórios. Gracilaria tenuistipitata var. liui Zhang et Xia é uma macroalga vermelha que apresenta grande tolerância a fatores ambientais e alta taxa de crescimento, sendo utilizada como organismo modelo em estudos fisiológicos, bioquímicos e moleculares...

Genômica comparativa de Xylella fastidiosa: diversidade do pangenoma e análise de genes de patogenicidade; Comparative genomics of Xylella fastidiosa: pan-genome diversity and analysis of patogenicity genes

Santana, Wesley Oliveira de
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 04/02/2013 PT
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45.8%
O gênero Xylella é composto de uma única espécie, Xylella fastidiosa, bactéria Gram-negativa, não flagelada, que coloniza o xilema de uma diversidade de plantas cultivadas e silvestres em várias partes do mundo. Em algumas dessas plantas, a bactéria é considerada agente causal de doenças, como a Clorose Variegada do Citros em laranjeiras, a Doença de Pierce das videiras e escaldadura da folha de cafeeiro. Onze diferentes cepas de X. fastidiosa, isoladas de distintos hospedeiros, já tiveram seus genomas sequenciados, entre essas, as cepas 9a5c, isolada de laranjeira, e Temecula 1, isolada de videira. Análises desses genomas indicam uma razoável variabilidade entre suas respectivas sequências e evidenciam vários genes associados a mecanismos de virulência e patogenicidade desta bactéria. No presente trabalho descrevemos o sequenciamento, a montagem e a anotação dos genomas das cepas U24d e Fb7, isoladas de laranjeiras, e da cepa 3124 isolada de cafeeiro, os quais apresentam, respectivamente 2.681.334 pb, 2.733.974 pb e 2.748.594 pb. Destas, apenas a cepa U24d apresenta um plasmídeo, o qual é idêntico ao pXF51 previamente identificado na cepa 9a5c. O genoma da cepa U24d é praticamente colinear ao genoma da cepa 9a5c enquanto que os genomas das cepas Fb7 e 3124 apresentaram maior colinearidade com a cepa Temecula1. Entre as diversas alterações encontradas nas análises comparativas destes genomas...

Prospects and pitfalls in whole genome association studies

Lawrence, Robert W; Evans, David M; Cardon, Lon R
Fonte: The Royal Society Publicador: The Royal Society
Tipo: Artigo de Revista Científica
EN
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Recent large-scale studies of common genetic variation throughout the human genome are making it feasible to conduct whole genome studies of genotype–phenotype associations. Such studies have the potential to uncover novel contributors to common complex traits and thus lead to insights into the aetiology of multifactorial phenotypes. Despite this promise, it is important to recognize that the availability of genetic markers and the ability to assay them at realistic cost does not guarantee success of this approach. There are a number of practical issues that require close attention, some forms of allelic architecture are not readily amenable to the association approach with even the most rigorous design, and doubtless new hurdles will emerge as the studies begin. Here we discuss the promise and current challenges of the whole genome approach, and raise some issues to consider in interpreting the results of the first whole genome studies.

Genome Paths: A Way to Personalized and Predictive Medicine

Baranov, V. S.
Fonte: A.I. Gordeyev Publicador: A.I. Gordeyev
Tipo: Artigo de Revista Científica
Publicado em /10/2009 EN
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35.89%
The review is devoted to the impact of human genome research on progress in modern medicine. Basic achievements in genome research have resulted in the deciphering of the human genome and creation of a molecular landmarks map of the human haploid genome (HapMap Project), which has made a tremendous contribution to our understanding of common genetic and multifactorial (complex) disorders. Current genome studies mainly focus on genetic testing and gene association studies of multifactorial (complex) diseases, with the purpose of their efficient diagnostics and prevention . Identification of candidate ("predisposition") genes participating in the functional genetic modules underlying each common disorder and the use of this genetic background to elaborate sophisticated measures to efficiently prevent them constitutes a major goal in personalized molecular medicine. The concept of a genetic pass as an individual DNA databank reflecting inherited human predisposition to different complex and monogenic disorders, with special emphasis on its present state, and the numerous difficulties related to the practical implementation of personalized medicine are outlined. The problems related to the uncertainness of the results of genetic testing could be overcome at least partly by means of new technological achievements in genome research methods...

Complete Genome Sequence of Cronobacter sakazakii Temperate Bacteriophage phiES15

Lee, Ju-Hoon; Choi, Younho; Shin, Hakdong; Lee, Junghyun; Ryu, Sangryeol
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /07/2012 EN
Relevância na Pesquisa
45.76%
While most phage genome studies have been focused on the virulent phages, the inducible temperate bacteriophage genome study provides more detailed information about the interaction between the host strain and the phage. To study this interaction in detail, UV-induced phiES15 bacteriophage was isolated from the host strain Cronobacter sakazakii ES15 and its genome was completely sequenced. Here we announce the genome sequence of phiES15 and report major findings from the annotation.

Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

Rieber, Nora; Zapatka, Marc; Lasitschka, Bärbel; Jones, David; Northcott, Paul; Hutter, Barbara; Jäger, Natalie; Kool, Marcel; Taylor, Michael; Lichter, Peter; Pfister, Stefan; Wolf, Stephan; Brors, Benedikt; Eils, Roland
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 11/06/2013 EN
Relevância na Pesquisa
35.9%
The emergence of high-throughput, next-generation sequencing technologies has dramatically altered the way we assess genomes in population genetics and in cancer genomics. Currently, there are four commonly used whole-genome sequencing platforms on the market: Illumina’s HiSeq2000, Life Technologies’ SOLiD 4 and its completely redesigned 5500xl SOLiD, and Complete Genomics’ technology. A number of earlier studies have compared a subset of those sequencing platforms or compared those platforms with Sanger sequencing, which is prohibitively expensive for whole genome studies. Here we present a detailed comparison of the performance of all currently available whole genome sequencing platforms, especially regarding their ability to call SNVs and to evenly cover the genome and specific genomic regions. Unlike earlier studies, we base our comparison on four different samples, allowing us to assess the between-sample variation of the platforms. We find a pronounced GC bias in GC-rich regions for Life Technologies’ platforms, with Complete Genomics performing best here, while we see the least bias in GC-poor regions for HiSeq2000 and 5500xl. HiSeq2000 gives the most uniform coverage and displays the least sample-to-sample variation. In contrast...

Epidemiological studies of esophageal cancer in the era of genome-wide association studies

Wang, An-Hui; Liu, Yuan; Wang, Bo; He, Yi-Xuan; Fang, Ye-Xian; Yan, Yong-Ping
Fonte: Baishideng Publishing Group Inc Publicador: Baishideng Publishing Group Inc
Tipo: Artigo de Revista Científica
EN
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35.88%
Esophageal cancer (EC) caused about 395000 deaths in 2010. China has the most cases of EC and EC is the fourth leading cause of cancer death in China. Esophageal squamous cell carcinoma (ESCC) is the predominant histologic type (90%-95%), while the incidence of esophageal adenocarcinoma (EAC) remains extremely low in China. Traditional epidemiological studies have revealed that environmental carcinogens are risk factors for EC. Molecular epidemiological studies revealed that susceptibility to EC is influenced by both environmental and genetic risk factors. Of all the risk factors for EC, some are associated with the risk of ESCC and others with the risk of EAC. However, the details and mechanisms of risk factors involved in the process for EC are unclear. The advanced methods and techniques used in human genome studies bring a great opportunity for researchers to explore and identify the details of those risk factors or susceptibility genes involved in the process of EC. Human genome epidemiology is a new branch of epidemiology, which leads the epidemiology study from the molecular epidemiology era to the era of genome wide association studies (GWAS). Here we review the epidemiological studies of EC (especially ESCC) in the era of GWAS...

The Impact of Transposable Elements in Genome Evolution and Genetic Instability and Their Implications in Various Diseases

Ayarpadikannan, Selvam; Kim, Heui-Soo
Fonte: Korea Genome Organization Publicador: Korea Genome Organization
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
35.88%
Approximately 45% of the human genome is comprised of transposable elements (TEs). Results from the Human Genome Project have emphasized the biological importance of TEs. Many studies have revealed that TEs are not simply "junk" DNA, but rather, they play various roles in processes, including genome evolution, gene expression regulation, genetic instability, and cancer disposition. The effects of TE insertion in the genome varies from negligible to disease conditions. For the past two decades, many studies have shown that TEs are the causative factors of various genetic disorders and cancer. TEs are a subject of interest worldwide, not only in terms of their clinical aspects but also in basic research, such as evolutionary tracking. Although active TEs contribute to genetic instability and disease states, non-long terminal repeat transposons are well studied, and their roles in these processes have been confirmed. In this review, we will give an overview of the importance of TEs in studying genome evolution and genetic instability, and we suggest that further in-depth studies on the mechanisms related to these phenomena will be useful for both evolutionary tracking and clinical diagnostics.

Whole-Genome Sequence Analysis of the Naturally Competent Acinetobacter baumannii Clinical Isolate A118

Traglia, German M.; Chua, Katherina; Centrón, Daniela; Tolmasky, Marcelo E.; Ramírez, María Soledad
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Publicado em 26/08/2014 EN
Relevância na Pesquisa
35.89%
Recent studies have demonstrated a high genomic plasticity in Acinetobacter baumannii, which may explain its high capacity to acquire multiple antibiotic resistance determinants and to survive in the hospital environment. Acinetobacter baumannii strain A118 (Ab A118) was isolated in the year 1995 from a blood culture of an intensive care unit patient. As this particular strain showed some peculiar characteristic such as being naturally competent and susceptible to numerous antibiotics, we performed whole-genome comparison (WGC) studies to gain insights into the nature and extent of the genomic differences. The Ab A118 genome is approximately 3,824 kb long with a 38.4% GC content and contains 3,520 coding sequences. WGC studies showed that the Ab A118 genome has 98% average nucleotide identity with that of A. baumannii ATCC 17978, and 96% average nucleotide identity with that of strains AYE and ACICU. At least 12 inversions, 275 insertions, and 626 deletions were identified when the Ab A118 genome was compared with those of strains ATCC 17978, AYE, and ACICU using MAUVE WGC. Multiple gene order arrangements were observed among the analyzed strains. MAUVE WGC analysis identified 19 conserved segments, known as locally colinear blocks. The number of single nucleotide polymorphisms found when comparing the Ab A118 genome with that of strains ATCC 17978...

Genome studies of cereals / by Song Weining.

Song, Weining, 1958-
Fonte: Universidade de Adelaide Publicador: Universidade de Adelaide
Tipo: Tese de Doutorado Formato: 426829 bytes; application/pdf
Publicado em //1992 EN
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45.68%
This thesis investigates genome analysis of wheat, rye and barley. The objective is to evaluate the feasibility of using polymerase chain reaction (PCR) as a tool for studying cereal genomes. Results are compared for PCR and RFLP (restriction fragment length polymorphism); Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Science, 1994; Bibliography: leaves 93-114.; 114, [43] leaves, [30] leaves of plates : ill. ; 30 cm.; Title page, contents and abstract only. The complete thesis in print form is available from the University Library.

Genome studies at the PAG 2011 conference

Appels, R.; Adelson, D.; Moolhiujzen, P.; Webster, H.; Barrero, R.; Bellgard, M.
Fonte: Springer-Verlag Publicador: Springer-Verlag
Tipo: Artigo de Revista Científica
Publicado em //2011 EN
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45.79%
The contents of the plenary lectures presented at the Plant and Animal Genome (PAG) meeting in January 2011 are summarized in order to provide some insights into the advances in plant, animal and microbe genome studies as they impact on our understanding of complex biological systems. The areas of biology covered include the dynamics of genome change, biological recognition processes and the new processes that underpin investment in science. This overview does not attempt to summarize the diversity of activities that are covered during the PAG through workshops, posters and the suppliers of cutting-edge technologies, but reviews major advances in specific research areas.; R. Appels, D. L. Adelson, P. Moolhuijzen, H. Webster, R. Barrero and M. Bellgard

Genome-wide association study of major recurrent depression in the U.K. population

Lewis, C.; Cohen-Woods, S.
Fonte: Amer Psychiatric Press Inc Publicador: Amer Psychiatric Press Inc
Tipo: Artigo de Revista Científica
Publicado em //2010 EN
Relevância na Pesquisa
35.89%
OBJECTIVE: Studies of major depression in twins and families have shown moderate to high heritability, but extensive molecular studies have failed to identify susceptibility genes convincingly. To detect genetic variants contributing to major depression, the authors performed a genome-wide association study using 1,636 cases of depression ascertained in the U.K. and 1,594 comparison subjects screened negative for psychiatric disorders. METHOD: Cases were collected from 1) a case-control study of recurrent depression (the Depression Case Control [DeCC] study; N=1346), 2) an affected sibling pair linkage study of recurrent depression (probands from the Depression Network [DeNT] study; N=332), and 3) a pharmacogenetic study (the Genome-Based Therapeutic Drugs for Depression [GENDEP] study; N=88). Depression cases and comparison subjects were genotyped at Centre National de Génotypage on the Illumina Human610-Quad BeadChip. After applying stringent quality control criteria for missing genotypes, departure from Hardy-Weinberg equilibrium, and low minor allele frequency, the authors tested for association to depression using logistic regression, correcting for population ancestry. RESULTS: Single nucleotide polymorphisms (SNPs) in BICC1 achieved suggestive evidence for association...

From age correction to genome-wide association

Cohen-Woods, S.; Schosser, A.; McGuffin, P.
Fonte: Blackwell Munksgaard Publicador: Blackwell Munksgaard
Tipo: Artigo de Revista Científica
Publicado em //2009 EN
Relevância na Pesquisa
35.89%
OBJECTIVE: Eric Strömgren was one of the pioneers of psychiatric genetics and family studies. There has now been an explosion of interest in this field and research progress, including linkage and association studies, whole genome genotyping, copy number variants and epigenetics is reviewed here. METHOD:  An overview of this area of psychiatric research is presented and discussed based on the relevant literature aiming at giving a recent status of the progress. RESULTS:  Broadly speaking linkage and association are complementary approaches used to locate genes contributing to the genetic aetiology of psychopathology. Linkage can be detected over comparatively large distances, however power is problematic when searching for quantitative trait loci with small effect sizes. In contrast, association studies can detect small effects but only over very small distances. Therefore, while several genome-wide linkage studies in psychiatric disorders have been performed, the majority of association studies have investigated specific functional candidate genes. CONCLUSION:  Due to very recent technological advancements, genome-wide association studies have now become possible and have identified some completely novel susceptibility loci. Other recent advances include the discovery of epigenetic phenomena and copy number variants.; S. Cohen-Woods...

Genome-wide association analysis accounting for environmental factors through propensity-score matching: Application to stressful live events in major depressive disorder

Power, R.; Cohen-Woods, S.; Ng, M.; Butler, A.; Craddock, N.; Korszun, A.; Jones, L.; Jones, I.; Gill, M.; Rice, J.; Maier, W.; Zobel, A.; Mors, O.; Placentino, A.; Rietschel, M.; Aitchison, K.; Tozzi, F.; Muglia, P.; Breen, G.; Farmer, A.; et al.
Fonte: Wiley-Liss Publicador: Wiley-Liss
Tipo: Artigo de Revista Científica
Publicado em //2013 EN
Relevância na Pesquisa
35.89%
Stressful life events are an established trigger for depression and may contribute to the heterogeneity within genome-wide association analyses. With depression cases showing an excess of exposure to stressful events compared to controls, there is difficulty in distinguishing between "true" cases and a "normal" response to a stressful environment. This potential contamination of cases, and that from genetically at risk controls that have not yet experienced environmental triggers for onset, may reduce the power of studies to detect causal variants. In the RADIANT sample of 3,690 European individuals, we used propensity score matching to pair cases and controls on exposure to stressful life events. In 805 case-control pairs matched on stressful life event, we tested the influence of 457,670 common genetic variants on the propensity to depression under comparable level of adversity with a sign test. While this analysis produced no significant findings after genome-wide correction for multiple testing, we outline a novel methodology and perspective for providing environmental context in genetic studies. We recommend contextualizing depression by incorporating environmental exposure into genome-wide analyses as a complementary approach to testing gene-environment interactions. Possible explanations for negative findings include a lack of statistical power due to small sample size and conditional effects...

Genome-wide association study of body mass index in 23 000 individuals with and without asthma

Melen, E.; Palmer, L.
Fonte: Blackwell Science Publicador: Blackwell Science
Tipo: Artigo de Revista Científica
Publicado em //2013 EN
Relevância na Pesquisa
35.99%
BACKGROUND: Both asthma and obesity are complex disorders that are influenced by environmental and genetic factors. Shared genetic factors between asthma and obesity have been proposed to partly explain epidemiological findings of co-morbidity between these conditions. OBJECTIVE: To identify genetic variants that are associated with body mass index (BMI) in asthmatic children and adults, and to evaluate if there are differences between the genetics of BMI in asthmatics and healthy individuals. METHODS: In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent...

Linear mixed models for genome-wide association studies; Lineare gemischte Modelle für genomweite Assoziationsstudien

Lippert, Christoph
Fonte: Universidade de Tubinga Publicador: Universidade de Tubinga
Tipo: Dissertação
EN
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35.93%
Genome-wide association studies aim at uncovering genetic loci that regulate a phenotype of interest by performing statistical tests for association between observed genetic variants and the phenotype. However, confounding factors like population structure, family relatedness, and cryptic relatedness often lead to false positive findings, if not accounted for in the analysis. Linear mixed models are among the richest class of models used today for genome-wide association studies, and in contrast to other methods have been shown to be capable of to capture all of these forms of relatedness simultaneously, without knowledge of which are present and without the need to tease them apart. Despite their benefits the use of linear mixed models so far has been limited to smaller studies, due to the large computational burden. In this thesis, we investigate linear mixed models for genome-wide association studies and present new algorithms to scale up linear mixed model computations that thereby enable their use for the analysis of extremely large genome-wide association studies for the first time. Besides algorithmic contributions we also present improvements to the statistical modeling part, that lead to an increase in power and better calibration over the traditional use of linear mixed models. Based on these improvements...

GENOSOJA - The Brazilian Soybean Genome Consortium: high throughput omics and beyond.

BENKO-ISEPPON, A. M.; NEPOMUCENO, A. L.; ABDELNOOR, R. V.
Fonte: Genetics and Molecular Biology, Ribeirão Preto, v. 35, n. 1, suppl., p. i-iv, May 2012. Publicador: Genetics and Molecular Biology, Ribeirão Preto, v. 35, n. 1, suppl., p. i-iv, May 2012.
Tipo: Artigo em periódico indexado (ALICE)
EN
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35.91%
Plant genomes are among the most complex and large ones of our planet, with high levels of redundancy when compared to other eukaryotic groups, leading to intricate processes for gene regulation and evolution. Such a complexity demands interdisciplinary and multidimensional approaches in order to allow a better understanding of the processes able to exploit the whole potential of the existing genes in different species, including crop plants. Among cultivated plants, soybean [Glycine max (L.) Merr.] occupies an outstanding position due to its importance as source of protein and oil that may also be converted into biodiesel. The seeds are rarely consumed in natura, but many traditional food products have been consumed, as soymilk, and tofu, as well as fermented products as soy sauce, and soy paste among others, besides its wide use for animal feed. Soybean cultivation has been highly concentrated geographically, with only four countries (USA, Brazil, Argentina and China) accounting for almost 90% of world output. Asia (excluding China) and Africa, the two regions where most of the food insecure countries are located, account for only 5% of production. Among countries classified as 'undernourished', only India and Bolivia are significant producers of soybeans (FAO...

Genome-Wide Joint Meta-Analysis of SNP and SNP-by-Smoking Interaction Identifies Novel Loci for Pulmonary Function

Hancock, Dana B.; Artigas, María Soler; Gharib, Sina A.; Henry, Amanda; Manichaikul, Ani; Ramasamy, Adaikalavan; Loth, Daan W.; Imboden, Medea; Koch, Beate; McArdle, Wendy L.; Smith, Albert V.; Smolonska, Joanna; Sood, Akshay; Tang, Wenbo; Zhai, Guangju;
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
35.89%
Genome-wide association studies have identified numerous genetic loci for spirometic measures of pulmonary function, forced expiratory volume in one second \((FEV_1)\), and its ratio to forced vital capacity \((FEV_1/FVC)\). Given that cigarette smoking adversely affects pulmonary function, we conducted genome-wide joint meta-analyses (JMA) of single nucleotide polymorphism (SNP) and SNP-by-smoking (ever-smoking or pack-years) associations on \(FEV_1\) and \(FEV_1/FVC\) across 19 studies (total N = 50,047). We identified three novel loci not previously associated with pulmonary function. SNPs in or near DNER (smallest \(P_{JMA} = 5.00×10^{−11})\), HLA-DQB1 and HLA-DQA2 (smallest \(P_{JMA} = 4.35×10^{−9})\), and KCNJ2 and SOX9 (smallest \(P_{JMA} = 1.28×10^{−8})\) were associated with \(FEV_1/FVC\) or \(FEV_1\) in meta-analysis models including SNP main effects, smoking main effects, and SNP-by-smoking (ever-smoking or pack-years) interaction. The HLA region has been widely implicated for autoimmune and lung phenotypes, unlike the other novel loci, which have not been widely implicated. We evaluated DNER, KCNJ2, and SOX9 and found them to be expressed in human lung tissue. DNER and SOX9 further showed evidence of differential expression in human airway epithelium in smokers compared to non-smokers. Our findings demonstrated that joint testing of SNP and SNP-by-environment interaction identified novel loci associated with complex traits that are missed when considering only the genetic main effects.

easyGWAS: An Integrated Computational Framework for Advanced Genome-Wide Association Studies

Grimm, Dominik Gerhard
Fonte: Universität Tübingen Publicador: Universität Tübingen
Tipo: Dissertation; info:eu-repo/semantics/doctoralThesis
EN
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35.89%
Recent advances in sequencing technologies have made it possible for the first time to sequence and analyse the genomes of whole populations of individuals in both a cost-effective manner and in a reasonable amount of time. One of the primary applications of this data is to better understand and investigate the genetic basis of common traits or diseases. For this purpose, genome-wide association studies (GWASs) are often used to find loci that are associated with a phenotype of interest. However, conducting GWASs is a challenging endeavour: first, different types of hidden confounding factors, such as population structure, environmental or technical influences, could lead to spurious associations. Second, it has been shown in several studies that associated loci often fail to explain much of the phenotypic variability — a phenomenon referred to as the problem of missing heritability. Many tools have been developed to partly address these challenges. The large diversity of these tools, however, have led to a highly fragmented and confusing landscape of tools. In addition, most of these tools do not share a common data format and do not provide straightforward solutions to visualise and annotate their results. In this thesis...

Design and Characterization of a 52K SNP Chip for Goats

Tosser-Klopp, Gwenola; Bardou, Philippe; Bouchez, Olivier; Cabau, Cédric; Crooijmans, Richard; Dong, Yang; Donnadieu-Tonon, Cécile; Eggen, André; Heuven, Henri C. M.; Jamli, Saadiah; Johari Jiken, Abdullah; Klopp, Christophe; Lawley, Cynthia T.; McEwan
Fonte: Universidade Autônoma de Barcelona Publicador: Universidade Autônoma de Barcelona
Tipo: Artigo de Revista Científica Formato: application/pdf
Publicado em //2014 ENG
Relevância na Pesquisa
35.88%
The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50–60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina...