Relevant bibliographies by topics / Non-Coding variants

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Non-Coding variants'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "Non-Coding variants"

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Bronstein, Revital, Elizabeth E. Capowski, Sudeep Mehrotra, et al. "A combined RNA-seq and whole genome sequencing approach for identification of non-coding pathogenic variants in single families." Human Molecular Genetics 29, no. 6 (2020): 967–79. http://dx.doi.org/10.1093/hmg/ddaa016.

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Abstract Inherited retinal degenerations (IRDs) are at the focus of current genetic therapeutic advancements. For a genetic treatment such as gene therapy to be successful, an accurate genetic diagnostic is required. Genetic diagnostics relies on the assessment of the probability that a given DNA variant is pathogenic. Non-coding variants present a unique challenge for such assessments as compared to coding variants. For one, non-coding variants are present at much higher number in the genome than coding variants. In addition, our understanding of the rules that govern the non-coding regions of the genome is less complete than our understanding of the coding regions. Methods that allow for both the identification of candidate non-coding pathogenic variants and their functional validation may help overcome these caveats allowing for a greater number of patients to benefit from advancements in genetic therapeutics. We present here an unbiased approach combining whole genome sequencing (WGS) with patient-induced pluripotent stem cell (iPSC)-derived retinal organoids (ROs) transcriptome analysis. With this approach, we identified and functionally validated a novel pathogenic non-coding variant in a small family with a previously unresolved genetic diagnosis.
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Makrythanasis, P., and SE Antonarakis. "Pathogenic variants in non-protein-coding sequences." Clinical Genetics 84, no. 5 (2013): 422–28. http://dx.doi.org/10.1111/cge.12272.

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Pei, Guangsheng, Ruifeng Hu, Peilin Jia, and Zhongming Zhao. "DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner." Nucleic Acids Research 49, W1 (2021): W131—W139. http://dx.doi.org/10.1093/nar/gkab429.

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Abstract More than 90% of the genetic variants identified from genome-wide association studies (GWAS) are located in non-coding regions of the human genome. Here, we present a user-friendly web server, DeepFun (https://bioinfo.uth.edu/deepfun/), to assess the functional activity of non-coding genetic variants. This new server is built on a convolutional neural network (CNN) framework that has been extensively evaluated. Specifically, we collected chromatin profiles from ENCODE and Roadmap projects to construct the feature space, including 1548 DNase I accessibility, 1536 histone mark, and 4795 transcription factor binding profiles covering 225 tissues or cell types. With such comprehensive epigenomics annotations, DeepFun expands the functionality of existing non-coding variant prioritizing tools to provide a more specific functional assessment on non-coding variants in a tissue- and cell type-specific manner. By using the datasets from various GWAS studies, we conducted independent validations and demonstrated the functions of the DeepFun web server in predicting the effect of a non-coding variant in a specific tissue or cell type, as well as visualizing the potential motifs in the region around variants. We expect our server will be widely used in genetics, functional genomics, and disease studies.
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Vervier, Kévin, and Jacob J. Michaelson. "TiSAn: estimating tissue-specific effects of coding and non-coding variants." Bioinformatics 34, no. 18 (2018): 3061–68. http://dx.doi.org/10.1093/bioinformatics/bty301.

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Zhou, Xin, Jian Wang, Jaimin Patel, et al. "Exploration of Coding and Non-coding Variants in Cancer Using GenomePaint." Cancer Cell 39, no. 1 (2021): 83–95. http://dx.doi.org/10.1016/j.ccell.2020.12.011.

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Wu, Zhenqin, Nilah M. Ioannidis, and James Zou. "Predicting target genes of non-coding regulatory variants with IRT." Bioinformatics 36, no. 16 (2020): 4440–48. http://dx.doi.org/10.1093/bioinformatics/btaa254.

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Abstract Summary Interpreting genetic variants of unknown significance (VUS) is essential in clinical applications of genome sequencing for diagnosis and personalized care. Non-coding variants remain particularly difficult to interpret, despite making up a large majority of trait associations identified in genome-wide association studies (GWAS) analyses. Predicting the regulatory effects of non-coding variants on candidate genes is a key step in evaluating their clinical significance. Here, we develop a machine-learning algorithm, Inference of Connected expression quantitative trait loci (eQTLs) (IRT), to predict the regulatory targets of non-coding variants identified in studies of eQTLs. We assemble datasets using eQTL results from the Genotype-Tissue Expression (GTEx) project and learn to separate positive and negative pairs based on annotations characterizing the variant, gene and the intermediate sequence. IRT achieves an area under the receiver operating characteristic curve (ROC-AUC) of 0.799 using random cross-validation, and 0.700 for a more stringent position-based cross-validation. Further evaluation on rare variants and experimentally validated regulatory variants shows a significant enrichment in IRT identifying the true target genes versus negative controls. In gene-ranking experiments, IRT achieves a top-1 accuracy of 50% and top-3 accuracy of 90%. Salient features, including GC-content, histone modifications and Hi-C interactions are further analyzed and visualized to illustrate their influences on predictions. IRT can be applied to any VUS of interest and each candidate nearby gene to output a score reflecting the likelihood of regulatory effect on the expression level. These scores can be used to prioritize variants and genes to assist in patient diagnosis and GWAS follow-up studies. Availability and implementation Codes and data used in this work are available at https://github.com/miaecle/eQTL_Trees. Supplementary information Supplementary data are available at Bioinformatics online.
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Pérez-Agustín, Adrian, Mel·lina Pinsach-Abuin, and Sara Pagans. "Role of Non-Coding Variants in Brugada Syndrome." International Journal of Molecular Sciences 21, no. 22 (2020): 8556. http://dx.doi.org/10.3390/ijms21228556.

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Brugada syndrome (BrS) is an inherited electrical heart disease associated with a high risk of sudden cardiac death (SCD). The genetic characterization of BrS has always been challenging. Although several cardiac ion channel genes have been associated with BrS, SCN5A is the only gene that presents definitive evidence for causality to be used for clinical diagnosis of BrS. However, more than 65% of diagnosed cases cannot be explained by variants in SCN5A or other genes. Therefore, in an important number of BrS cases, the underlying mechanisms are still elusive. Common variants, mostly located in non-coding regions, have emerged as potential modulators of the disease by affecting different regulatory mechanisms, including transcription factors (TFs), three-dimensional organization of the genome, or non-coding RNAs (ncRNAs). These common variants have been hypothesized to modulate the interindividual susceptibility of the disease, which could explain incomplete penetrance of BrS observed within families. Altogether, the study of both common and rare variants in parallel is becoming increasingly important to better understand the genetic basis underlying BrS. In this review, we aim to describe the challenges of studying non-coding variants associated with disease, re-examine the studies that have linked non-coding variants with BrS, and provide further evidence for the relevance of regulatory elements in understanding this cardiac disorder.
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Sen, Rituparno, Gero Doose, and Peter Stadler. "Rare Splice Variants in Long Non-Coding RNAs." Non-Coding RNA 3, no. 3 (2017): 23. http://dx.doi.org/10.3390/ncrna3030023.

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Koch, Linda. "Triaging risk variants in the non-coding genome." Nature Reviews Genetics 15, no. 12 (2014): 779. http://dx.doi.org/10.1038/nrg3862.

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Khurana, Ekta, Yao Fu, Dimple Chakravarty, Francesca Demichelis, Mark A. Rubin, and Mark Gerstein. "Role of non-coding sequence variants in cancer." Nature Reviews Genetics 17, no. 2 (2016): 93–108. http://dx.doi.org/10.1038/nrg.2015.17.

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Dissertations / Theses on the topic "Non-Coding variants"

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Alston, Jessica Shea. "Genetic and Functional Studies of Non-Coding Variants in Human Disease." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10515.

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Genome-wide association studies (GWAS) of common diseases have identified hundreds of genomic regions harboring disease-associated variants. Translating these findings into an improved understanding of human disease requires identifying the causal variants(s) and gene(s) in the implicated regions which, to date, has only been accomplished for a small number of associations. Several factors complicate the identification of mutations playing a causal role in disease. First, GWAS arrays survey only a subset of known variation. The true causal mutation may not have been directly assayed in the GWAS and may be an unknown, novel variant. Moreover, the regions identified by GWAS may contain several genes and many tightly linked variants with equivalent association signals, making it difficult to decipher causal variants from association data alone. Finally, in many cases the variants with strongest association signals map to non-coding regions that we do not yet know how to interpret and where it remains challenging to predict a variants likely phenotypic impact. Here, we present a framework for the genetic and functional study of intergenic regions identified through GWAS and describe application of this framework to chromosome 9p21: a non-coding region with associations to type 2 diabetes (T2D), myocardial infarction (MI), aneurysm, glaucoma, and multiple cancers. First, we compare methods for genetic fine-mapping of GWAS associations, including methods for creating a more comprehensive catalog of variants in implicated regions and methods for capturing these variants in case- control cohorts. Next, we describe an approach for using massively parallel reporter assays (MPRA) to systematically identify regulatory elements and variants across disease-associated regions. On chromosome 9p21, we fine-map the T2D and MI associations and identify, for each disease, a collection of common variants with equivalent association signals. Using MPRA, we identify hundreds of regulatory elements on chromosome 9p21 and multiple variants (including MI- and T2D-associated variants) with evidence for allelic effects on regulatory activity that can serve as a foundation for further study. More generally, the methods presented here have broad potential application to the many intergenic regions identified through GWAS and can help to uncover the mechanisms by which variants in these regions influence human disease.
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Pozojevi´c, Jelena [Verfasser]. "Functional and genetic analyses of coding and non-coding variants causing Cornelia de Lange Syndrome (CdLS) / Jelena Pozojevi´c." Lübeck : Zentrale Hochschulbibliothek Lübeck, 2019. http://d-nb.info/1174774908/34.

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Gusic, Mirjana [Verfasser], Thomas [Akademischer Betreuer] Meitinger, Thomas [Gutachter] Meitinger, and Julien [Gutachter] Gagneur. "Role of coding and non-coding variants in mitochondrial disease genes / Mirjana Gusic ; Gutachter: Thomas Meitinger, Julien Gagneur ; Betreuer: Thomas Meitinger." München : Universitätsbibliothek der TU München, 2021. http://d-nb.info/1241740232/34.

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Santana, dos santos Elizabeth. "Contribution of the Missense and Non-Coding BRCA1/2 Variants for the Hereditary Predisposition and Response to Treatment of Breast and Ovarian Cancers Assessment of the Functional Impact of Germline BRCA1/2 Variants Located in Non- Coding Regions in Families with Breast and/or Ovarian Cancer Predisposition Non-Coding Variants in BRCA1 and BRCA2 Genes: Potential Impact on Breast and Ovarian Cancer Predisposition." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASS027.

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Les cancers de l'ovaire et du sein sont définis par les principales voies impliquées dans la tumorigénèse. Dans les cancers héréditaires du sein/ovaire (HBOC), les tumeurs présentant des variants pathogènes (PV) de BRCA1/2 présentent une altération de la réparation de l'ADN par recombinaison homologue (RH). Des années après la découverte des gènes BRCA1/2, les PV ont été uniquement recherchés sur l'ADN constitutionnel. Aujourd’hui, cette information est également recherchée au niveau tumoral car en plus de leur utilité pour améliorer le conseil génétique, elle est aussi impliquée dans le choix thérapeutique. Cependant, les données recueillies indiquent que les PV inactivant la protéine ne seraient pas l’unique mécanisme d’inactivation de la voie de réparation de l’ADN par RH. Dans ce contexte, l'objectif principal de cette thèse est d'identifier des mécanismes alternatifs d'inactivation de la voie HR pour améliorer à la fois: le conseil génétique et la prise en charge thérapeutique. À cette fin, nous avons tenté de contribuer à la classification de variants non-codants et faux-sens (autre que provoquant un stop prématuré) de BRCA1/2 et également recherché de nouveaux biomarqueurs de réponse thérapeutique dans d’autres gènes de la voie de HR.Nous avons décrit des variants constitutionnels dans des régions potentiellement importantes de régulation des gènes BRCA1 et BRCA2, et démontré qu'une partie d'entre eux étaient fonctionnellement actifs à mettre en lien avec la pathogénicité. Nous avons également exploré les caractéristiques moléculaires des tumeurs du sein et de l'ovaire des porteurs des variants BRCA1 et observé une prédominance de la perte de l'allèle sauvage pour les tumeurs des porteurs de variants pathogènes. Etant donné ces résultats, nous proposons d’intégrer les informations de LOH dans le modèle multifactoriel de classification des variants BRCA1. Enfin, nous avons mis en évidence des mécanismes alternatifs d'inactivation de la voie RH, dans une cohorte de patientes avec un cancer de l'ovaire présentant une excellente réponse aux platines, y compris des mutations constitutionnelles et somatiques des gènes BRCA1/2, l'hyperméthylation du promoteur BRCA1 ainsi que des mutations dans d'autres gènes de la voie RH
Ovarian and breast cancers are currently defined by the main pathways involved in the tumorigenesis. In hereditary breast/ovarian cancers (HBOC), tumors with BRCA1/2 pathogenic variants (PV) present an impairment of DNA repair by homologous recombination (HR). For many years, BRCA1/2 PV were only searched on germline DNA. Currently, this information is also searched at tumor level to personalize treatment. Even so, the reason of the inactivation of this pathway remains uncertain for most cases, even in the presence of HR deficient signature.Gathered evidence indicates that protein inactivating PV may not be the only mechanism of HR dysfunction. In this context, the main objective of this thesis is to identify alternative mechanisms of HR inactivation to improve both: genetic counseling and therapeutic response. For this purpose, we have attempted to contribute to non-coding and missense (other than premature stop codon) BRCA1/2 variant classification and searched for new biomarkers of therapeutic response to DNA damage agents in other HR genes.We identified germline variants in key transcriptional regulatory elements of BRCA1 and BRCA2, and demonstrated that part of them were functionally active and had additional arguments suggesting pathogenicity. We also explored molecular features of breast and ovarian tumors from BRCA1 variant carriers and observed a predominance of loss of the wild-type allele. Conforming to this evidence, we propose to incorporate LOH information, into the multifactorial model for BRCA1 variant classification. Finally, besides the enrichment of BRCA1/2 germline and somatic PV, we described alternative mechanisms of HR inactivation in a OC population presenting optimal response to platinum-based chemotherapy, including BRCA1 promoter hypermethylation and also mutations in other genes of HR pathway
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Pinsach, Abuin Mel·lina. "Regulome-seq: a novel approach for the identification of non-coding variants associated with human disease. Assessment of its applicability in 89 Brugada syndrome individuals." Doctoral thesis, Universitat de Girona, 2019. http://hdl.handle.net/10803/666922.

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Brugada syndrome (BrS) is a cardiac electrical disease with high susceptibility to sudden cardiac death. Approximately 25-30% of BrS patients are explained by pathogenic variants in coding sequences of cardiac ion channels, especially in the cardiac sodium channel gene SCN5A. However, the role of genetic variants in regulatory elements affecting cardiac ion channels remains largely unknown. We integrated ENCODE information of topological organization, chromatin accessibility, histone marks, and transcription factor binding in human cardiac cells to define 1,293 putative regulatory regions of six BrS-associated genes (SCN5A, SCN2B, SCN3B, CACNA1C, CACNB2 and CACNA2D). We selectively captured and sequenced these regions in 89 BrS patients and compared the genetic variation identified to that present in a cohort of 200 healthy-aging individuals. Finally, we scored the variants based on the tolerance to variation and other parameters, allowing us to propose candidate regulatory variants that may explain the molecular basis of some BrS cases
La síndrome de Brugada (SBr) és una malaltia elèctrica cardíaca associada a mort sobtada cardíaca. Aproximadament un 25-30% dels pacients amb SBr s’expliquen per variants patogèniques en les seqüències codificants dels canals iònics cardíacs, especialment en el gen del canal de sodi cardíac SCN5A. Tot i així, els paper de les variants genètiques en els elements reguladors dels canals iònics cardíacs és encara desconegut. Utilitzant informació sobre l’organització topològica, accessibilitat de la cromatina i unió de factors de transcripció en cèl·lules cardíaques humanes, hem definit 1.293 regions reguladores de sis gens associats a SBr (SCN5A, SCN2B, SCN3B, CACNA1C, CACNB2 i CACNA2D). Hem seqüenciat aquestes regions en 89 pacients amb SBr i hem comparat les variants identificades amb les variants presents en 200 individus sans. Finalment, hem anotat les variants segons la tolerància a la variació i altres paràmetres, permetent-nos proposar variants reguladores candidates que podrien explicar alguns casos amb SBr
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Jayaram, N. "Improving the prediction of transcription factor binding sites to aid the interpretation of non-coding single nucleotide variants." Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/1556214/.

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Single nucleotide variants (SNVs) that occur in transcription factor binding sites (TFBSs) can disrupt the binding of transcription factors and alter gene expression which can cause inherited diseases and act as driver SNVs in cancer. The identification of SNVs in TFBSs has historically been challenging given the limited number of experimentally characterised TFBSs. The recent ENCODE project has resulted in the availability of ChIP-Seq data that provides genome wide sets of regions bound by transcription factors. These data have the potential to improve the identification of SNVs in TFBSs. However, as the ChIP-Seq data identify a broader range of DNA in which a transcription factor binds, computational prediction is required to identify the precise TFBS. Prediction of TFBSs involves scanning a DNA sequence with a Position Weight Matrix (PWM) using a pattern matching tool. This thesis focusses on the prediction of TFBSs by: (a) evaluating a set of locally-installable pattern-matching tools and identifying the best performing tool (FIMO), (b) using the ENCODE ChIP-Seq data to evaluate a set of de novo motif discovery tools that are used to derive PWMs which can handle large volumes of data, (c) identifying the best performing tool (rGADEM), (d) using rGADEM to generate a set of PWMs from the ENCODE ChIP-Seq data and (e) by finally checking that the selection of the best pattern matching tool is not unduly influenced by the choice of PWMs. These analyses were exploited to obtain a set of predicted TFBSs from the ENCODE ChIP-Seq data. The predicted TFBSs were utilised to analyse somatic cancer driver, and passenger SNVs that occur in TFBSs. Clear signals in conservation and therefore Shannon entropy values were identified, and subsequently exploited to identify a threshold that can be used to prioritize somatic cancer driver SNVs for experimental validation.
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Kremer, Laura Sophie [Verfasser], Thomas [Akademischer Betreuer] Floss, Bernhard [Gutachter] Küster, Thomas [Gutachter] Floss, and Johannes [Gutachter] Mayr. "Discovery and validation of coding and non-coding pathogenic variants in mitochondrial disorders / Laura Sophie Kremer ; Gutachter: Bernhard Küster, Thomas Floss, Johannes Mayr ; Betreuer: Thomas Floss." München : Universitätsbibliothek der TU München, 2017. http://d-nb.info/1152006525/34.

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Kremer, Laura Sophie Verfasser], Thomas [Akademischer Betreuer] [Floß, Bernhard [Gutachter] Küster, Thomas [Gutachter] Floss, and Johannes [Gutachter] Mayr. "Discovery and validation of coding and non-coding pathogenic variants in mitochondrial disorders / Laura Sophie Kremer ; Gutachter: Bernhard Küster, Thomas Floss, Johannes Mayr ; Betreuer: Thomas Floss." München : Universitätsbibliothek der TU München, 2017. http://nbn-resolving.de/urn:nbn:de:bvb:91-diss-20171219-1364275-1-5.

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Calvert-Joshua, Tracey. "Integrating regulatory and methylome data for the discovery of clear cell Renal Cell Carcinoma (ccRCC) variants." University of the Western Cape, 2015. http://hdl.handle.net/11394/5022.

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>Magister Scientiae - MSc
Kidney cancers, of which clear cell renal cell carcinoma comprises an estimated 70%, have been placed amongst the top ten most common cancers in both males and females. With a mortality rate that exceeds 40%, kidney cancer is considered the most lethal cancer of the genitourinary system. Despite advances in its treatment, the mortality- and incidence rates across all stages of the disease have continued to climb. Since the release of the Human Genome Project in the early 2000’s, most genetics studies have focused on the protein coding region of the human genome, which accounts for a mere 2% of the entire genome. It has been suggested that diverting our focus to the other 98% of the genome, which was previously dismissed as non-functional “junk DNA”, could possibly contribute significantly to our understanding of the underlying mechanisms of complex diseases.In this study a whole genome sequencing somatic mutation data set from the International Cancer Genome Consortium was used. The non-coding somatic mutations within the promoter, intronic, 5-prime untranslated and 3-prime untranslated regions of clear cell renal cell carcinoma-implicated genes were extracted and submitted to RegulomDB for their functional annotation.As expected, most of the variants were located within the intronic regions and only a small subset of identified variants was predicted to be deleterious. Although the variants all belonged to a selected subset of kidney cancer-associated genes, the genes frequently mutated in the non-coding regions were not the same genes that were frequently mutated in the whole exome studies (where the focus is on the coding sequences). This indicates that with whole genome sequencing studies a new set of genes/variants previously unassociated with the clear cell renal cell carcinoma could be identified. In addition, most of the non-coding somatic variants fell within multiple transcriptions factor binding sites. Since many of these variants were also deleterious (as predicted by RegulomDB), this suggests that mutations in the non-coding regions could contribute to disease due to their role in transcription factor binding site disruptions and their subsequent impact on transcriptional regulation. The substantial overlap between the genes with the most aberrantly methylated variants and the genes with the most transcription factor binding site disruptions signifies a potential link between differential methylation and transcription factor binding site affinities. In contrast to the upregulated DNA methylation generally seen in promoter methylation studies, all of the significant hits in this study were hypomethylated, with the subsequent up-regulation of the genes of interest, suggesting that in the clear cell renal cell carcinoma, aberrant methylation may play a role in activating proto-oncogenes, rather than the silencing of genes. When a cross-analysis was carried out between the gene expression patterns and the transcription factor binding site disruptions, the non-coding somatic variants and differential methylation profiles, the genes affected again showed a clear overlap. Interestingly, most of the variants were not present in the 1000genomes data and thus represent novel mutations, which possibly occurred as a result of genomic instability. However, identifying novel variants are always promising, since they epitomise the possibility of developing pioneering ways to target diseases. The numerous detrimental effects a single non-coding mutation can have on other genomic processes have been demonstrated in this study and therefore validate the inclusion of non-coding regions of the genome in genetic studies in order to study complex multifactorial diseases.
National Research Foundation (NRF) and DAAD
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Wang, Leyi. "STUDY TOWARD THE DEVELOPMENT OF ADVANCED INFLUENZA VACCINES." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1249332969.

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Book chapters on the topic "Non-Coding variants"

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Nückel, Holger, Erick C. Castelli, Philippe Moreau, Crista Ochsenfarth, Peter A. Horn, and Vera Rebmann. "Simple Methods for the Detection of HLA-G Variants in Coding and Non-coding Regions." In Methods in Molecular Biology™. Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-842-9_7.

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Zhao, Jingkang, Dongshunyi Li, Jungkyun Seo, Andrew S. Allen, and Raluca Gordân. "Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding." In Lecture Notes in Computer Science. Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-56970-3_21.

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Ramdas, Shweta, and Jun Z. Li. "Next-Generation Sequencing in Genetic Studies of Psychiatric Disorders." In Psychiatric Genetics. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780190221973.003.0015.

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Next-generation sequencing (NGS) technologies make it possible to efficiently detect DNA variants in either entire genomes or any subsets of the genome, and have dramatically enhanced our ability to search for genetic risk factors of complex psychiatric diseases. While genotyping-based association studies focus on common variants that track extended genomic segments, NGS provides unbiased identification of both common and rare variants, including those that are functionally important but appear in very few families or sporadic cases. Thus NGS directly highlights plausible causal variants, even if such variants are extremely heterogeneous in the population. Meanwhile, such heterogeneity requires new analytical approaches that can aggregate rare variant burden over predefined functional unit such as a gene or a segment of non-coding region with presumed function. Rapid application of NGS technologies also underscored other limits in psychiatric genetics research, including the need for detailed phenotyping and multi-scale integration of diverse data types.
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Schulze-Bahr, Eric. "Basic principles of genetic disease." In ESC CardioMed. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198784906.003.0148.

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The human genome consists of approximately 3 billion (3 × 109) base pairs of DNA (around 20,000 genes), organized as 23 chromosomes (diploid parental set), and a small mitochondrial genome (37 genes, including 13 proteins; 16,589 base pairs) of maternal origin. Most human genetic variation is natural, that is, common or rare (minor allele frequency >0.1%) and does not cause disease—apart from every true disease-causing (bona fide) mutation each individual genome harbours more than 3.5 million single nucleotide variants (including >10,000 non-synonymous changes causing amino acid substitutions) and 200–300 large structural or copy number variants (insertions/deletions, up to several thousands of base-pairs) that are non-disease-causing variations and scattered throughout coding and non-coding genomic regions.
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Cloninger, C. Robert. "Genetics of personality disorders." In New Oxford Textbook of Psychiatry, edited by John R. Geddes, Nancy C. Andreasen, and Guy M. Goodwin. Oxford University Press, 2020. http://dx.doi.org/10.1093/med/9780198713005.003.0120.

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Family, twin, and adoption studies have shown that personality disorders are moderately heritable, but most of the variability is the result of non-additive interactions among many genetic variants and environmental events acting in concert. Consequently, the pathway from genotype to phenotype is complex—individuals with the same genotype may have different features of personality disorder, or none (multifinality, also called pleiotropy), and individuals with different genotypes may have the same personality disorder (equifinality, also called heterogeneity). The same genetic and environmental variants cause normal and abnormal personality, so personality disorders are the result of quantitative trait variation and are not discrete disease entities. Human character traits, such as self-directedness and co-operativeness, allow people to self-regulate their emotional drives, and recent person-centred genome-wide association studies have revealed that these character traits are strongly influenced by regulatory gene variants, such as long non-coding RNAs, that influence adaptive functioning and neuroplasticity by epigenetic mechanisms.
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Lucchesi, John C. "Aging, cellular senescence and cancer: epigenetic alterations and nuclear remodeling." In Epigenetics, Nuclear Organization & Gene Function. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198831204.003.0021.

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Epigenetic modifications correlated with aging and oncogenesis are changes in the pattern of DNA methylation and of histone modifications, and changes in the level of histone variants (H3.3, macroH2A, H2A.Z) and gene mutations. The sirtuins are a set of highly conserved protein deacetylases of particular significance to the aging process. Many cancer types are found to carry mutations in chromatin-modifying genes such as those encoding methyl or acetyl transferases, affecting the histone modifications of promoters and enhancers. The aging process and oncogenesis present a number of changes in the nuclear architecture. Mutations in the lamina-coding genes lead to premature aging syndromes. Mutations in remodeling complexes are found in different cancers. Modifications that affect the architectural protein binding sites at topologically associating domain (TAD) borders can cause the merging of neighboring TADs. The levels of short non-coding RNAs (sncRNAs) are altered in model organisms and are associated with cancer. Changes in the position of chromosome territories often occur in tumor cells. Nevertheless, cellular senescence, due mostly to the absence of telomerase, represents a mechanism of tumor suppression.
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Lucchesi, John C. "Epigenetic chromatin changes and the transcription cycle." In Epigenetics, Nuclear Organization & Gene Function. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198831204.003.0005.

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In order to allow transcription to occur, the association of DNA with histone octamers and the compacted physical state of the chromatin fiber must be modified by the opportunistic binding of pioneer transcription factors to their cognate DNA binding sites. Once bound, pioneer factors recruit chromatin remodelers and histone-modifying enzymes for the purpose of repositioning nucleosomes and exposing regulatory regions (enhancers and gene promoters) to the components necessary for the initiation of transcription. Histone modifications, such as acetylation, methylation and ubiquitination, and the dynamic phosphorylation of specific amino acids on the major RNA polymerase II subunit activate transcription and attract the factors necessary to eliminate the pausing that normally occurs soon after initiation. Further histone modifications and the replacement of certain core histones by histone variants facilitate transcript elongation and termination. Two additional major epigenetic modifications that impact the process of transcription consist of the action of non-coding RNAs and DNA methylation.
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Lucchesi, John C. "Maintenance of the active and inactive states." In Epigenetics, Nuclear Organization & Gene Function. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198831204.003.0007.

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The maintenance of a gene in an active or inactive state is carried out by epigenetic modifications of the histones and of the DNA itself. Two major classes of complexes (PRC1 and PRC2), containing Polycomb group (PcG) proteins mediate transcriptional repression. PRC2 trimethylates histone H3 at lysine 27, a modification that attracts PRC1 leading to the ubiquitination of histone H2A. Variant PRC1 complexes can be targeted first, and mono-ubiquitinated histone H2A recruits PRC2 complexes that serve as the target for canonical PRC1 complexes. PRC2 can be targeted to sites of repression by associating with long non-coding RNAs. Trithorax group (TrxG) proteins form complexes that counteract PcG-mediated repression. Some subunits of these complexes maintain and enhance transcription by carrying out different lysine methylations (H3K4me, H3K36me and H3K79me) that are associated with active gene function; other subunits remodel chromatin by displacing and repositioning nucleosomes. Additional effects on transcription are transvections, whereby somatic pairing allows the regulatory region of one allele of a gene to influence the activity of the promoter of the allele on the homologous chromosome
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Lucchesi, John C. "Inheritance of chromatin modifications through the cell cycle." In Epigenetics, Nuclear Organization & Gene Function. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198831204.003.0016.

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Following mitosis, the particular transcriptional landscape of the parent cell must be faithfully transmitted to daughter cells. Although transcription ceases, not all transcription factors are displaced. DNA methylation has been implicated in the inheritance of chromatin characteristics because maintenance DNA methyl transferases methylate CpG dinucleotides on the newly replicated strand if the corresponding GpC on the parent strand is methylated. Nucleosomes that are deposited on the newly synthesized DNA strands are made up of old and new histones, and some marks present on the old histones are maintained. The proper distribution of nucleosomes and the topological organization of the genome into topologically associating domains (TADs) must be transmitted to daughter cells. Following DNA replication, centromeres must be specified on the daughter chromatids. In most eukaryotes, centromeres are identified by the presence of nucleosomes bearing the histone H3 variant CENP-A. An additional number of proteins and non-coding RNAs originating from centric and pericentromeric DNA repeats associate with centromeres and appear to play a role in centromere function.
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Conference papers on the topic "Non-Coding variants"

1

Stamoulis, C. "Estimation of correlations between copy-number variants in non-coding DNA." In 2011 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2011. http://dx.doi.org/10.1109/iembs.2011.6091345.

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Chuang, Kai-Wen, and Chien-Yu Chen. "Predicting Pathogenic Non-coding Variants on Imbalanced Data Set using Cluster Ensemble Sampling." In 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2019. http://dx.doi.org/10.1109/bibe.2019.00158.

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Ching, Travers, and Lana X. Garmire. "Pan-cancer analysis of expressed somatic nucleotide variants in long intergenic non-coding RNA." In Pacific Symposium on Biocomputing 2018. WORLD SCIENTIFIC, 2017. http://dx.doi.org/10.1142/9789813235533_0047.

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Liu, Yunhao, Shaoliang Peng, Wenjie Shu, Bin Jiang, Chao Yang, and Kun Xie. "Predicting functional elements and variants effects in non-coding regions based on deep learning." In 2020 IEEE International Conference on E-health Networking, Application & Services (HEALTHCOM). IEEE, 2021. http://dx.doi.org/10.1109/healthcom49281.2021.9398970.

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Sellers, Thomas A., Brett M. Reid, Y. Ann Chen, et al. "Abstract 4633: Evidence that long non-coding RNA variants associate with epithelial ovarian cancer risk." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-4633.

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Yang, Hongbo, Hui Zhang, Yu Luan, et al. "Abstract 2118: Non-coding germline GATA3 variants alter chromatin topology and contribute to pathogenesis of acute lymphoblastic leukemia." In Proceedings: AACR Annual Meeting 2021; April 10-15, 2021 and May 17-21, 2021; Philadelphia, PA. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1538-7445.am2021-2118.

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Kim, Taewan, and Carlo M. Croce. "Abstract 1830: Cancer-associated variants at 8q24 are correlated with expression of adjacent long non-coding RNAs involved in cell cycle regulation." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-1830.

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Al Khatib, Hebah A., Fatiha M. Benslimane, Israa El Bashir, Asmaa A. Al Thani, and Hadi M. Yassine. "Within-Host Diversity of SARS-Cov-2 in COVID-19 Patients with Variable Disease Severities." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0280.

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Background: The ongoing pandemic of SARS-COV-2 has already infected more than eight million people worldwide. The majority of COVID-19 patients are either asymptomatic or have mild symptoms. Yet, about 15% of the cases experience severe complications and require intensive care. Factors determining disease severity are not yet fully characterized. Aim: Here, we investigated the within-host virus diversity in COVID-19 patients with different clinical manifestations. Methods: We compared SARS-COV-2 genetic diversity in 19 mild and 27 severe cases. Viral RNA was extracted from nasopharyngeal samples and sequenced using Illumina MiSeq platform. This was followed by deep-sequencing analyses of SARS-CoV-2 genomes at both consensus and sub-consensus sequence levels. Results: Consensus sequences of all viruses were very similar, showing more than 99·8% sequence identity regardless of the disease severity. However, the sub-consensus analysis revealed significant differences in within-host diversity between mild and severe cases. Patients with severe symptoms exhibited a significantly (p-value 0.001) higher number of variants in coding and non-coding regions compared to mild cases. Analysis also revealed higher prevalence of some variants among severe cases. Most importantly, severe cases exhibited significantly higher within-host diversity (mean= 13) compared to mild cases (mean=6). Further, higher within-host diversity was observed in patients above the age of 60 compared to the younger age group. Conclusion: These observations provided evidence that within-host diversity might play a role in the development of severe disease outcomes in COVID19 patients; however, further investigations is required to elucidate this association.
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Liu, Qiao, Chen Chen, Annie Gao, Hang Hang Tong, and Lei Xie. "VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in genome-wide association studies: Applied to Alzheimer's disease." In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2017. http://dx.doi.org/10.1109/bibm.2017.8217995.

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Chen, Yian Ann, Zhihua Chen, Jennifer Permuth-Wey, et al. "Abstract 4579: Variants in long non-coding RNAs are associated with epithelial ovarian cancer risk in a pooled analysis of three genome-wide association studies." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-4579.

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