subject:( next generation sequencing)

Université de Neuchâtel

1. Geiser, Céline. Genome evolution and mechanisms underlying reproductive isolation in the polyploid "Biscutella laevigata".

Degree: 2014, Université de Neuchâtel

URL: http://doc.rero.ch/record/257452

► Malgré des avancées phénoménales en biologie évolutive, les mécanismes qui mènent à la spéciation, le berceau de la biodiversité, ne sont toujours pas complètement déchiffrés.… (more)

▼ Malgré des avancées phénoménales en biologie évolutive, les mécanismes qui mènent à la spéciation, le berceau de la biodiversité, ne sont toujours pas complètement déchiffrés. La polyploïdie, c’est-à-dire la multiplication du patrimoine chromosomique (par exemple doublé pour la tétraploïdie), est un phénomène récurrent, en particulier chez les plantes. Toutes les plantes à fleurs actuelles, avec leur incroyable diversité, ont connu au moins deux événements de polyploïdie dans leur histoire évolutive. Malgré cela il n’a jamais été possible de formellement associer la polyploïdie à des capacités adaptives accrues et son rôle dans la diversification des espèces reste controversé. Un mécanisme qui pourrait amener à des nouveautés chez le polyploïde est lié à de nouvelles fonctions émergentes des gènes dupliqués. C’est à ce mécanisme que je m’intéresse dans la première partie de ma thèse. En recomposant des séquences transcrites grâce aux nouvelles technologies de séquençage profond j’ai étudié les différents événements de polyploïdie qui ont influencé l’évolution d’une espèce alpine, la lunetière lisse tétraploïde (<i>Biscutella laevigata</i>). En analysant les forces sélectives agissant sur les gènes dupliqués j’ai pu déterminer des groupes fonctionnels potentiellement importants dans l’évolution de cette espèce. D’une part une partie des groupes fonctionnels préférentiellement retenus en deux copies, après un événement de polyploïdie récent, sont liés à l’écologie. D’autre part des copies de gènes sous sélection positive, c’est-à-dire probablement impliqués dans un processus de diversification, ont été mis en évidence. Ces gènes sont liés au cytosquelette et pourraient être associés à une adaptation à la polyploïdie ou au stress. Dans la deuxième partie de ma thèse je me suis intéressée aux divers mécanismes impliqués dans la spéciation commençante entre deux groupes d’une même population alpine de lunetière lisse tétraploïde (<i>Biscutella laevigata</i>). L’étude de la spéciation consiste à étudier les mécanismes qui conduisent à une cessation de flux de gènes entre deux groupes taxonomiques, c’est-à-dire l’isolement reproductif. Pour déchiffrer les divers mécanismes qui sous-tendent l’isolement reproductif, les suivis en population naturelle ainsi que des approches expérimentales sur le terrain se sont avérés être des outils essentiels. Tout d’abord la stucture génétique de cette population a révélé une zone hybride entre deux groupes. J’ai pu démontrer qu’une barrière principale qui sous-tend la divergence génétique est un décalage de floraison entre les deux groupes. Ces deux groupes semblent être adaptés à deux environnements distincts ce qui pourrait participer à l’isolement reproductif. Néanmoins, il n’a pas été possible de démontrer l’adaptation locale expérimentalement. Advisors/Committee Members: Christian (Dir.), Félix (Codir.).

Subjects/Keywords: next generation sequencing

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APA (6^th Edition):

Geiser, C. (2014). Genome evolution and mechanisms underlying reproductive isolation in the polyploid "Biscutella laevigata". (Thesis). Université de Neuchâtel. Retrieved from http://doc.rero.ch/record/257452

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Geiser, Céline. “Genome evolution and mechanisms underlying reproductive isolation in the polyploid "Biscutella laevigata".” 2014. Thesis, Université de Neuchâtel. Accessed April 12, 2021. http://doc.rero.ch/record/257452.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Geiser, Céline. “Genome evolution and mechanisms underlying reproductive isolation in the polyploid "Biscutella laevigata".” 2014. Web. 12 Apr 2021.

Vancouver:

Geiser C. Genome evolution and mechanisms underlying reproductive isolation in the polyploid "Biscutella laevigata". [Internet] [Thesis]. Université de Neuchâtel; 2014. [cited 2021 Apr 12]. Available from: http://doc.rero.ch/record/257452.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Geiser C. Genome evolution and mechanisms underlying reproductive isolation in the polyploid "Biscutella laevigata". [Thesis]. Université de Neuchâtel; 2014. Available from: http://doc.rero.ch/record/257452

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Sydney

2. Nafisinia, Michael. Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics .

Degree: 2017, University of Sydney

URL: http://hdl.handle.net/2123/16867

► The focus of this thesis was the identification of the genetic bases of Mendelian and mitochondrial respiratory chain disorders in a cohort of paediatric patients,… (more)

▼ The focus of this thesis was the identification of the genetic bases of Mendelian and mitochondrial respiratory chain disorders in a cohort of paediatric patients, to better understand their pathogenesis. Genetic disorders are caused by mutations in the mitochondrial or nuclear genomes and may be influenced to a lesser or greater degree by environmental factors. To date, nearly 3000 genes have been implicated in ~ 4,400 Mendelian phenotypes. However, despite this, the genetic bases for almost 50% of all known Mendelian phenotypes remains to be definitively elucidated. Mitochondrial respiratory chain disorders are the most common group of inborn errors of metabolism and can be caused by mutations in either mitochondrial DNA or nuclear DNA. The genetic heterogeneity of these disorders makes diagnosis challenging, adding distress to families already dealing with the trauma of an extremely ill family member. Mutations in mitochondrial DNA or nuclear DNA genes can result in impaired function of the respiratory chain causing broad symptoms including neuropathy, cardiomyopathy, muscle weakness, fatigue, cognitive impairment, visual and auditory impairment, to name a few. Despite the advances in gene screening techniques, the genetic bases of many respiratory chain disorders remains unidentified. This study had two phases: identification of the likely disease-causing variants in paediatric patients with suspected Mendelian or mitochondrial inherited disorders due to mitochondrial or nuclear DNA mutations, and implementation of functional studies to confirm pathogenicity and gain insights into possible disease mechanisms of the identified variants. Nine patients with suspected Mendelian disorders and two patients with a suspected mitochondrial disorder were studied in this project. Using whole exome sequencing (WES) in collaboration with other institutes or groups within Australia and overseas, we were able to efficiently identify the genetic basis of Mendelian and mitochondrial respiratory chain disorders in the majority of the paediatric patients studied in this project. In collaboration with bioinformaticians and clinician colleagues, we implemented sophisticated filtering pipelines, with candidate causative variants being narrowed down from the very expansive WES data. We then performed functional assays to determine the functional impact of the identified variants. These functional assays included immunoblotting and blue native polyacrylamide gel electrophoresis to measure protein expression and assembly. Further, in the case of the mitochondrial respiratory chain disorders, we measured the effect of the variant on the protein levels of mitochondrial respiratory chain complexes in patient fibroblast samples. We also measured respiratory chain complex enzyme activities using dipstick assays (for complex I and complex IV) or traditional spectrophotometric assays (for complexes I, II, III, and IV). In this PhD project, we have successfully identified four disease variants in NDUFV1 (OMIM: 161015), RARS…

Subjects/Keywords: Next generation sequencing

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APA (6^th Edition):

Nafisinia, M. (2017). Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics . (Thesis). University of Sydney. Retrieved from http://hdl.handle.net/2123/16867

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Nafisinia, Michael. “Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics .” 2017. Thesis, University of Sydney. Accessed April 12, 2021. http://hdl.handle.net/2123/16867.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Nafisinia, Michael. “Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics .” 2017. Web. 12 Apr 2021.

Vancouver:

Nafisinia M. Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics . [Internet] [Thesis]. University of Sydney; 2017. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/2123/16867.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Nafisinia M. Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics . [Thesis]. University of Sydney; 2017. Available from: http://hdl.handle.net/2123/16867

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Universiteit Utrecht

3. Hoek, G. van de. Identifying novel genes involved in congenital anomalies of the kidney and urinary tract.

Degree: 2013, Universiteit Utrecht

URL: http://dspace.library.uu.nl:8080/handle/1874/287149

► The recent collation of a large patient cohort encompassing the complete CAKUT spectrum, the advent of next generation sequencing (NGS) and progress in bioinformatic developmental… (more)

Subjects/Keywords: Kidney disease; next generation sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hoek, G. v. d. (2013). Identifying novel genes involved in congenital anomalies of the kidney and urinary tract. (Masters Thesis). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/287149

Chicago Manual of Style (16^th Edition):

Hoek, G van de. “Identifying novel genes involved in congenital anomalies of the kidney and urinary tract.” 2013. Masters Thesis, Universiteit Utrecht. Accessed April 12, 2021. http://dspace.library.uu.nl:8080/handle/1874/287149.

MLA Handbook (7^th Edition):

Hoek, G van de. “Identifying novel genes involved in congenital anomalies of the kidney and urinary tract.” 2013. Web. 12 Apr 2021.

Vancouver:

Hoek Gvd. Identifying novel genes involved in congenital anomalies of the kidney and urinary tract. [Internet] [Masters thesis]. Universiteit Utrecht; 2013. [cited 2021 Apr 12]. Available from: http://dspace.library.uu.nl:8080/handle/1874/287149.

Council of Science Editors:

Hoek Gvd. Identifying novel genes involved in congenital anomalies of the kidney and urinary tract. [Masters Thesis]. Universiteit Utrecht; 2013. Available from: http://dspace.library.uu.nl:8080/handle/1874/287149

University of Rochester

4. Glass, Carolyn. Identifying a Potential Molecular Therapeutic Target for MLL-AF9 Leukemia.

Degree: PhD, 2014, University of Rochester

URL: http://hdl.handle.net/1802/28976

► Leukemia is the most common form of cancer among children and adolescents, and approximately 2,000 infants per year are diagnosed within their first year of… (more)

▼ Leukemia is the most common form of cancer among children and adolescents, and approximately 2,000 infants per year are diagnosed within their first year of life. Infant survival rates are poor, reaching only 25-45% with current chemotherapy regimens. The Mixed Lineage Leukemia (MLL) gene translocation is present in 70-80% of infant leukemia cases and is the most significant biomarker for poor prognosis. MLL-gene translocations produce oncogenic fusion proteins, such as MLL-AF9 that bind and overactivate transcription of genes involved in normal hematopoiesis. One such gene that the MLL-AF9 fusion protein directly binds is MDS1-EVI1 (Myelodysplastic Syndrome- Ecotropic Virus Integration Site 1), a transcription factor critical for normal hematopoiesis. For our first aim, we determined whether MDS1-EVI1 DNA binding via specific zinc finger domains is required for MLL-AF9 leukemogenesis and identified genome-wide target genes. We discovered that MDS1-EVI1 DNA binding via its Zinc Finger 1 domain, is necessary for the development of MLL-AF9 leukemia in a mouse model. Using highthroughput sequencing techniques we identified several interesting key genes involving embryogenesis and cellular proliferation to be markedly upregulated in MDS1-EVI1 positive MLL- infant leukemia cells from primary patients. Furthermore, we found several target genes to be significantly overexpressed that may serve as potential druggable targets for novel therapies, or even potentially existing drug compounds. Furthermore, we explored whether MDS1-EVI1 HMT activity contributes to MLL-leukemia. For our second aim, we examined whether MDS1-EVI1 PR-domain HMT activity was aberrant in MLL-leukemic cells. A histone methyltransferase (HMT) assay did not demonstrate a significant difference in HMT activity in the presence of the MDS1-EVI1 PR-domain, and thus is not likely the major driving force of the PR-domain that induces MLLleukemogenesis. In conclusion, we elucidated the one of the main mechanism by which MDS1-EVI1 contributes to malignant transformation in MLL-infant leukemic cells, and have identified critical molecular genes and pathways that may serve as future druggable targets.

Subjects/Keywords: Leukemia; Next Generation Sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Glass, C. (2014). Identifying a Potential Molecular Therapeutic Target for MLL-AF9 Leukemia. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/28976

Chicago Manual of Style (16^th Edition):

Glass, Carolyn. “Identifying a Potential Molecular Therapeutic Target for MLL-AF9 Leukemia.” 2014. Doctoral Dissertation, University of Rochester. Accessed April 12, 2021. http://hdl.handle.net/1802/28976.

MLA Handbook (7^th Edition):

Glass, Carolyn. “Identifying a Potential Molecular Therapeutic Target for MLL-AF9 Leukemia.” 2014. Web. 12 Apr 2021.

Vancouver:

Glass C. Identifying a Potential Molecular Therapeutic Target for MLL-AF9 Leukemia. [Internet] [Doctoral dissertation]. University of Rochester; 2014. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/1802/28976.

Council of Science Editors:

Glass C. Identifying a Potential Molecular Therapeutic Target for MLL-AF9 Leukemia. [Doctoral Dissertation]. University of Rochester; 2014. Available from: http://hdl.handle.net/1802/28976

Cornell University

5. Al Abri, Mohammed. Development Of Genomic Methods And Tools For An Equine Model.

Degree: PhD, Animal Science, 2015, Cornell University

URL: http://hdl.handle.net/1813/40974

► The advent of genomic analysis has identified regions of functional significance in several mammalian species. However, for horses, relatively little such work was done compared… (more)

▼ The advent of genomic analysis has identified regions of functional significance in several mammalian species. However, for horses, relatively little such work was done compared to other farm animals. The current archive of genetic variations in the horse is mostly based on the Thoroughbred mare upon which the reference sequence (EquCab2.0) was generated. Thus, more investigation of the equine genomic architecture is critical to better understand the equine genome. Chapter 2 of this dissertation represents an analyses of next generation sequencing data of six horses from a diverse genetic background. I have utilized the most advanced techniques to identify, and annotate genetic variants including single nucleotide polymorphism, copy number variations and structural variations pertaining to these horse breeds. The analysis discovered thousands of novel SNPs and INDELs and hundreds of CNVs and SVs in each of the horses. These newly identified variants where formatted as online tracks and should provide a foundational database for future studies in horse genomics. Chapter three of the thesis discusses a genome wide association study aimed at the discovery of QTLs affecting body size variation in horses. I used the Illumina Equine SNP50 BeadChip to genotype 48 horses from diverse breeds and representing the extremes in body size in horses. Unlike most association studies, I have utilized a dominant model to identify these QTLs. The analysis revealed an association in chromosome one at the ANKRD1 gene (involved in muscle myocytes and cardiomyocyte growth and differentiation). In chapter four, I represent the results of a genomic study in which 36 Egyptian Arabian horses were genotyped using the Illumina Equine SNP70 BeadChip. The study was conducted to elucidate the genetic background of the herd, relatedness within the herd and to estimate genomic inbreeding values. I was able to re-establish the genetic links between the horses and to confirm their Egyptian ancestry among other Arabian horse bloodlines. Genomic inbreeding values were highly correlated with the pedigree estimated ones. Altogether, our results signify the benefit of using this BeadChip technology to infer relationships within herds and ancestry of herds and to estimate inbreeding in herds lacking pedigree recording. Advisors/Committee Members: Brooks,Samantha A. (chair), Boyko,Adam R. (committee member), Booth,James (committee member), Mezey,Jason G. (committee member).

Subjects/Keywords: Horse; Genomics; Next generation sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Al Abri, M. (2015). Development Of Genomic Methods And Tools For An Equine Model. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/40974

Chicago Manual of Style (16^th Edition):

Al Abri, Mohammed. “Development Of Genomic Methods And Tools For An Equine Model.” 2015. Doctoral Dissertation, Cornell University. Accessed April 12, 2021. http://hdl.handle.net/1813/40974.

MLA Handbook (7^th Edition):

Al Abri, Mohammed. “Development Of Genomic Methods And Tools For An Equine Model.” 2015. Web. 12 Apr 2021.

Vancouver:

Al Abri M. Development Of Genomic Methods And Tools For An Equine Model. [Internet] [Doctoral dissertation]. Cornell University; 2015. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/1813/40974.

Council of Science Editors:

Al Abri M. Development Of Genomic Methods And Tools For An Equine Model. [Doctoral Dissertation]. Cornell University; 2015. Available from: http://hdl.handle.net/1813/40974

6. Ortogero, Nicole. Identification and Characterization of Novel Somatic and Germ Cell Small RNA Species.

Degree: 2014, University of Nevada – Reno

URL: http://hdl.handle.net/11714/2832

► Small non-protein-coding RNAs are essential, ubiquitous molecules found in every cell. Their functions range from post-transcriptional regulation of mRNA expression to epigenetic control of the… (more)

▼ Small non-protein-coding RNAs are essential, ubiquitous molecules found in every cell. Their functions range from post-transcriptional regulation of mRNA expression to epigenetic control of the genome. Small noncoding RNAs also have crucial functions in the ribosome and spliceosome. Block of small RNA biogenesis and inactivation of effector complex proteins lead to embryonic lethality and loss of cell function. Because of their necessity in biological processes, they are of great interest in current research. Although small RNA research is in full throttle, many ambiguities and obstacles in this field still need to be addressed. This work resolves some of these roadblocks and expands our knowledge of existing small RNAs and their expression in somatic and germ cells. To properly characterize the function of small RNAs in a cell, it is essential to define the small RNA transcriptome. This can be accomplished through next-generation sequencing of small RNA. Unfortunately, current work in small RNA tends to concentrate on only one type of small RNA, predominantly miRNA, due to their already defined function, biogenesis, and structure. In addition, next-generation sequencing data generate millions of reads, and it is complicated to consider the entire small RNA transcriptome, as no comprehensive annotation pipeline is currently available. To further this field, we set out to define a small RNA annotation pipeline. To aid in this effort, we developed a graphic user interface program for small RNA data processing and annotation. We validated this pipeline by defining the Sertoli small RNA transcriptome with next-generation sequencing data. Sertoli cells represent the predominant somatic cell type within the testis and are considered "nurse cells" to developing male germ cells. Male gametes, sperm, are produced through spermatogenesis in the testis. Sertoli cells are in direct contact with all developing germ cells during spermatogenesis and normal Sertoli cell functions are required for normal germ cell development. Small RNAs help regulate dynamic transcriptomes, and we hypothesized that the Sertoli small RNA transcriptome needs to be dynamic due to the different germ cell stages Sertoli cells support. Indeed, all small RNA classes were found within the Sertoli cell and many novel RNAs were also identified in this study. Altogether, we successfully defined the entire small RNA transcriptome of Sertoli cells and developed a small RNA annotation pipeline for the comprehensive annotation of known and novel small RNAs. In our research of small RNAs, we identified a class of somatic small RNAs approximately 30 nucleotides long. In the male gonad a similar population has been defined as PIWI-interacting RNAs or piRNAs. piRNAs are approximately 30 nucleotides long and associate with PIWI proteins. Because PIWI proteins are germ cell exclusive, the somatic counterparts discovered cannot be considered piRNAs. Instead we termed them piRNA-like or pilRNA for their similarities to piRNAs. Our aims of this… Advisors/Committee Members: Yan, Wei (advisor), Hennig, Grant (committee member), Singer, Cherie (committee member), Zeh, David (committee member), Lu, Minggen (committee member).

Subjects/Keywords: Next Generation Sequencing; Small RNA

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APA (6^th Edition):

Ortogero, N. (2014). Identification and Characterization of Novel Somatic and Germ Cell Small RNA Species. (Thesis). University of Nevada – Reno. Retrieved from http://hdl.handle.net/11714/2832

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Ortogero, Nicole. “Identification and Characterization of Novel Somatic and Germ Cell Small RNA Species.” 2014. Thesis, University of Nevada – Reno. Accessed April 12, 2021. http://hdl.handle.net/11714/2832.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Ortogero, Nicole. “Identification and Characterization of Novel Somatic and Germ Cell Small RNA Species.” 2014. Web. 12 Apr 2021.

Vancouver:

Ortogero N. Identification and Characterization of Novel Somatic and Germ Cell Small RNA Species. [Internet] [Thesis]. University of Nevada – Reno; 2014. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/11714/2832.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Ortogero N. Identification and Characterization of Novel Somatic and Germ Cell Small RNA Species. [Thesis]. University of Nevada – Reno; 2014. Available from: http://hdl.handle.net/11714/2832

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Minnesota

7. Cradic, Kendall. Next Generation Sequencing: Applications for the Clinic.

Degree: PhD, Biomedical Informatics and Computational Biology, 2016, University of Minnesota

URL: http://hdl.handle.net/11299/182252

► Genomic information from the patient is becoming increasingly important for diagnosis of many diseases. Next Generation Sequencing (NGS), while commonly used as a research tool,… (more)

Subjects/Keywords: haplotyping; next generation sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cradic, K. (2016). Next Generation Sequencing: Applications for the Clinic. (Doctoral Dissertation). University of Minnesota. Retrieved from http://hdl.handle.net/11299/182252

Chicago Manual of Style (16^th Edition):

Cradic, Kendall. “Next Generation Sequencing: Applications for the Clinic.” 2016. Doctoral Dissertation, University of Minnesota. Accessed April 12, 2021. http://hdl.handle.net/11299/182252.

MLA Handbook (7^th Edition):

Cradic, Kendall. “Next Generation Sequencing: Applications for the Clinic.” 2016. Web. 12 Apr 2021.

Vancouver:

Cradic K. Next Generation Sequencing: Applications for the Clinic. [Internet] [Doctoral dissertation]. University of Minnesota; 2016. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/11299/182252.

Council of Science Editors:

Cradic K. Next Generation Sequencing: Applications for the Clinic. [Doctoral Dissertation]. University of Minnesota; 2016. Available from: http://hdl.handle.net/11299/182252

University of Melbourne

8. Orlowski, Christian. Epigenetic responses to external stimuli in murine embryonic stem cells.

Degree: 2012, University of Melbourne

URL: http://hdl.handle.net/11343/37286

► The epigenetic mechanisms underlying the nuclear plasticity of embryonic stem cells have been a focus of intensive research in the past several years. The emergence… (more)

▼ The epigenetic mechanisms underlying the nuclear plasticity of embryonic stem cells have been a focus of intensive research in the past several years. The emergence of massively parallel sequencing technology has enabled investigators to examine epigenetic responses to stimuli such as signals that trigger stem cell differentiation on a genome-wide scale. Histone modifications represent an essential mechanism that defines the chromatin architecture responsible for regulating the global transcriptional profile of a cell. Though our understanding of the role of histone modifications in stem cell differentiation has grown substantially over the last decade, many of their mechanisms remain elusive, particularly in terms of defining the many multiple developmental lineages a stem cell may take during the course of differentiation. Every lineage and cell type has a unique global epigenetic signature, but this signature is often highly dynamic and comprised of a complex interplay encompassing multiple levels of epigenetic regulation. Histone H3 lysine monomethylation (H3K4me1) represents a class of histone modifications that is typically associated with transcriptional activation. Histone H3 lysine trimethylation (H3K4me3), for instance, is tightly associated with gene transcription. H3K4me1’s role in the transcriptional status of genes has been less clear than H3K4me3, though it is known that H3K4me1 is a distinctive marker of distal regulatory regions such as transcriptional enhancer elements. H3K4me1 is to a comparatively lesser extent important to and associated with proximal regulatory promoter activation, as has been demonstrated in particular cases such as insulin gene activation and myogenesis. The histone lysine methyltransferase (HKMT) Set7/9 is capable of catalyzing monomethylation of histone H3 lysine 4 at gene promoters. It is not certain whether Set7/9 has any regulatory role in the deposition of H3K4me1 at distal regulatory elements. This study investigated the global epigenetic effects of inducing early vascular differentiation in pluripotent murine embryonic stem cells (mESCs) with respect to H3K4me1 and its relationship to the changing transcriptome, principally by utilizing mRNA-sequencing and ChIP-sequencing technology. Furthermore, this study addressed the role of Set7/9 in regulating the genome-wide distribution of H3K4me1 in Sca-1+ vascular progenitor cells (VPCs) using an RNA interference technique. Through the determination of the genome-wide distribution of H3K4me1 at the proximal as well as distal regulatory regions associated with genes, this study identified that differentiation-induced H3K4me1 changes were often defined by a large proportion of promoter regions exhibiting a distinctive gain in H3K4me1, whereas Sca-1+ VPCs with ablated Set7/9 function demonstrated the reverse. In both scenarios, putative enhancers identified by H3K4me1 enrichment were also identified as having undergone substantial changes…

Subjects/Keywords: bioinformatics; next generation sequencing; epigenetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Orlowski, C. (2012). Epigenetic responses to external stimuli in murine embryonic stem cells. (Doctoral Dissertation). University of Melbourne. Retrieved from http://hdl.handle.net/11343/37286

Chicago Manual of Style (16^th Edition):

Orlowski, Christian. “Epigenetic responses to external stimuli in murine embryonic stem cells.” 2012. Doctoral Dissertation, University of Melbourne. Accessed April 12, 2021. http://hdl.handle.net/11343/37286.

MLA Handbook (7^th Edition):

Orlowski, Christian. “Epigenetic responses to external stimuli in murine embryonic stem cells.” 2012. Web. 12 Apr 2021.

Vancouver:

Orlowski C. Epigenetic responses to external stimuli in murine embryonic stem cells. [Internet] [Doctoral dissertation]. University of Melbourne; 2012. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/11343/37286.

Council of Science Editors:

Orlowski C. Epigenetic responses to external stimuli in murine embryonic stem cells. [Doctoral Dissertation]. University of Melbourne; 2012. Available from: http://hdl.handle.net/11343/37286

University of New South Wales

9. Deveson, Ira. Three (largely unrelated) experiments in the age of next-generation sequencing.

Degree: Biotechnology & Biomolecular Sciences, 2017, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/58940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:48001/SOURCE02?view=true

► Next generation sequencing (NGS) enables researchers to identify instances of genetic variation and measure gene expression in an unbiased, global fashion. In this thesis I… (more)

▼ Next generation sequencing (NGS) enables researchers to identify instances of genetic variation and measure gene expression in an unbiased, global fashion. In this thesis I describe three experiments that apply NGS in quite distinct contexts. Together these illustrate the strengths and broad utility of this revolutionary technology.Experiment 1. I have developed a set of synthetic DNA standards – termed sequins – that emulate human genetic features and constitute qualitative and quantitative spike- in controls for NGS. I have used this approach to represent common and clinically relevant genetic variation, ranging from single nucleotide variants to large structural rearrangements. Here I describe the design and validation of sequin controls, and demonstrate their capacity to measure and mitigate biases during NGS analysis.Experiment 2. In many vertebrates sex is determined by external environmental cues rather than by sex chromosomes. In reptiles, for instance, temperature-dependent sex determination (TSD) is common. I have used the Australian central bearded dragon, in which chromosomal sex determination is overridden at high temperatures to produce sex-reversed female offspring, as a unique model to identify TSD-specific features of the transcriptome. Here I show that an intron is retained in mature transcripts from each of two Jumonji-family chromatin modifier genes, JARID2 and JMJD3, in female dragons that have been sex-reversed by temperature, but not in normal chromosomal females or males. I also observed sex-associated differential retention of the equivalent introns expressed in alligators and turtles, indicative of a reptile-wide mechanism that may control TSD.Experiment 3. The human transcriptome is so large, diverse and dynamic that, even after a decade of investigation by RNA sequencing (RNA-Seq), we are yet to resolve its true dimensions. I have performed targeted single-molecule and short-read RNA- Seq to survey the transcriptional landscape of a single human chromosome (Hsa21) at unprecedented resolution. This analysis identifies a fundamental distinction between the architecture of protein-coding and noncoding gene content. Unlike their coding counterparts, noncoding exons undergo universal alternative splicing to produce a seemingly limitless variety of isoforms. I propose that noncoding exons are functionally modular, with combinatorial alternative splicing generating an enormous repertoire of potential regulatory RNAs and a rich transcriptional reservoir for gene evolution. Advisors/Committee Members: Mattick, John, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW, Janitz, Michael, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW, Timothy, Mercer, Clinical School - St Vincent's Hospital, Faculty of Medicine, UNSW.

Subjects/Keywords: Next-generation sequencing; Genomics; Transcriptomics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Deveson, I. (2017). Three (largely unrelated) experiments in the age of next-generation sequencing. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/58940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:48001/SOURCE02?view=true

Chicago Manual of Style (16^th Edition):

Deveson, Ira. “Three (largely unrelated) experiments in the age of next-generation sequencing.” 2017. Doctoral Dissertation, University of New South Wales. Accessed April 12, 2021. http://handle.unsw.edu.au/1959.4/58940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:48001/SOURCE02?view=true.

MLA Handbook (7^th Edition):

Deveson, Ira. “Three (largely unrelated) experiments in the age of next-generation sequencing.” 2017. Web. 12 Apr 2021.

Vancouver:

Deveson I. Three (largely unrelated) experiments in the age of next-generation sequencing. [Internet] [Doctoral dissertation]. University of New South Wales; 2017. [cited 2021 Apr 12]. Available from: http://handle.unsw.edu.au/1959.4/58940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:48001/SOURCE02?view=true.

Council of Science Editors:

Deveson I. Three (largely unrelated) experiments in the age of next-generation sequencing. [Doctoral Dissertation]. University of New South Wales; 2017. Available from: http://handle.unsw.edu.au/1959.4/58940 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:48001/SOURCE02?view=true

10. Wong, Wallace K. Utilization Analysis of Reagents Used in Next Generation DNA Sequencing .

Degree: 2013, California State University – San Marcos

URL: http://hdl.handle.net/10211.8/438

► Building on the Nobel Prize winning work of Dr. Fredrick Sanger, DNA sequencing has evolved into a high-throughput, massive parallel experimental system called Next Generation… (more)

▼ Building on the Nobel Prize winning work of Dr. Fredrick Sanger, DNA sequencing has evolved into a high-throughput, massive parallel experimental system called Next Generation DNA Sequencing (NGS). NGS is critical in today???s laboratory in both research and clinical settings. With progressive innovations and refined methods in molecular biology, genetic research is becoming faster and more robust; contributing to more precise academic research and target specific clinical treatments. Local biotechnology companies specializing in Next Generation Sequencing, such as Illumina, Inc., are considered one of the leaders at the fore front of NGS DNA Sequencing. The success of Illumina???s DNA sequencing platform can be attributed to its proprietary sequencing properties known as TruSeq v3 chemistry through sequencing by synthesis (SBS) technologies. Recently, post experimental observations have indicated several reagents have more than adequate volumes needed to conduct the advertised 209 cycle sequencing experiments. Based on our current observations in reagent utilization, this reagent overfill may represent lost profit margin, increased overhead and environmental impact. We have conducted an SBS reagent audit with hopes of determining new optimal reagent volumes needed to maximize company profit margins as well as minimize environmental impacts and overhead. Using random sampling from the Genomic Services lab at Illumina Inc., we monitored over 220 experiments for approximately 30 weeks. From our measurements, we were able to calculate lost-bottle ratios from our current reagent fills and propose new reagent volumes based on our observed fluidic threshold. In comparisons to the current volume fills, our proposed volumes would save approximately 53 SBS reagent bottles for every sixteen sequencing runs. This new volume implementation would reduce overhead cost, environmental impact, increase profit margins, and improve chemical handling. Advisors/Committee Members: Kern, Albert (advisor).

Subjects/Keywords: Next Generation Sequencing; Biotechnology; sequencing properties

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APA (6^th Edition):

Wong, W. K. (2013). Utilization Analysis of Reagents Used in Next Generation DNA Sequencing . (Thesis). California State University – San Marcos. Retrieved from http://hdl.handle.net/10211.8/438

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Wong, Wallace K. “Utilization Analysis of Reagents Used in Next Generation DNA Sequencing .” 2013. Thesis, California State University – San Marcos. Accessed April 12, 2021. http://hdl.handle.net/10211.8/438.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Wong, Wallace K. “Utilization Analysis of Reagents Used in Next Generation DNA Sequencing .” 2013. Web. 12 Apr 2021.

Vancouver:

Wong WK. Utilization Analysis of Reagents Used in Next Generation DNA Sequencing . [Internet] [Thesis]. California State University – San Marcos; 2013. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/10211.8/438.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Wong WK. Utilization Analysis of Reagents Used in Next Generation DNA Sequencing . [Thesis]. California State University – San Marcos; 2013. Available from: http://hdl.handle.net/10211.8/438

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Otago

11. Sutton, Jolene Theresa. Major histocompatibility complex and microsatellite genetic diversity in bottlenecked populations of New Zealand passerines .

Degree: 2013, University of Otago

URL: http://hdl.handle.net/10523/4335

► Theory predicts that rapid decreases in population size (“population bottlenecks”) will result in initial decreases in allelic diversity through a random sampling of individuals from… (more)

▼ Theory predicts that rapid decreases in population size (“population bottlenecks”) will result in initial decreases in allelic diversity through a random sampling of individuals from the source population, followed by subsequent losses through genetic drift (random sampling of alleles from one generation to the next) if population sizes remain small. Years of empirical research based on neutral genetic diversity (i.e. the diversity of alleles or loci for which mutations do not result in changes to fitness) supports this theory. However, it has been argued that selection will maintain diversity at functionally important genes, even through severe bottlenecks. The major histocompatibility complex (MHC) forms an integral component of the vertebrate immune response, and due to strong balancing selection, is one of the most polymorphic regions of the entire genome. Despite 20 years of research in natural populations, empirical studies offer highly contradictory explanations of the relative roles of selection and genetic drift in shaping MHC variation during population bottlenecks. Many studies conclude that “drift outweighs selection”, rendering MHC diversity effectively neutral during population declines, while several others have found evidence that balancing selection can maintain MHC diversity during these events, even while neutral diversity is lost. A few studies have concluded that in small populations, selection can accelerate the rate of loss for adaptive diversity. In this thesis, I test for signals of balancing selection and genetic drift in shaping post-bottleneck MHC diversity, in an effort to inform the debate in this research field. I also examine factors that influence the impact of population bottlenecks, and which may have led to the disparity among previous study results. I focus my research on threatened New Zealand passerines, which provide a model study system due to their bottleneck histories, as well as availability of both pre- and post-bottleneck samples. To achieve my goals, I compare genetic diversity at MHC class II B loci and at microsatellite loci. I first synthesise the results of previous studies that examined MHC and neutral genetic diversity in bottlenecked populations for multiple vertebrate taxa. Based on meta-analytical techniques, I conclude that bottleneck events generally result in loss of both MHC and neutral genetic diversity, and that MHC diversity can be lost at a faster rate than neutral diversity in natural populations. I find that a key factor in shaping genetic diversity is bottleneck duration, with prolonged bottlenecks resulting in the greatest impacts. In a subsequent chapter, I go on to characterise MHC class II B diversity in contemporary populations of New Zealand South Island and North Island saddlebacks. I find evidence of historic balancing selection, which helps to identify classical MHC allele sequences (under strong selection) from those of non-classical loci (not under strong selection). I also find that South Island saddlebacks have less MHC diversity than… Advisors/Committee Members: Jamieson, Ian G (advisor).

Subjects/Keywords: Philesturnus; Petroica; next generation sequencing; immunogenetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sutton, J. T. (2013). Major histocompatibility complex and microsatellite genetic diversity in bottlenecked populations of New Zealand passerines . (Doctoral Dissertation). University of Otago. Retrieved from http://hdl.handle.net/10523/4335

Chicago Manual of Style (16^th Edition):

Sutton, Jolene Theresa. “Major histocompatibility complex and microsatellite genetic diversity in bottlenecked populations of New Zealand passerines .” 2013. Doctoral Dissertation, University of Otago. Accessed April 12, 2021. http://hdl.handle.net/10523/4335.

MLA Handbook (7^th Edition):

Sutton, Jolene Theresa. “Major histocompatibility complex and microsatellite genetic diversity in bottlenecked populations of New Zealand passerines .” 2013. Web. 12 Apr 2021.

Vancouver:

Sutton JT. Major histocompatibility complex and microsatellite genetic diversity in bottlenecked populations of New Zealand passerines . [Internet] [Doctoral dissertation]. University of Otago; 2013. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/10523/4335.

Council of Science Editors:

Sutton JT. Major histocompatibility complex and microsatellite genetic diversity in bottlenecked populations of New Zealand passerines . [Doctoral Dissertation]. University of Otago; 2013. Available from: http://hdl.handle.net/10523/4335

University of California – Riverside

12. Cacho, Ashley. Base-Calling of High-Throughput Sequencing Data Using a Random Effects Mixture Model.

Degree: Applied Statistics, 2016, University of California – Riverside

URL: http://www.escholarship.org/uc/item/98x9v8rn

► The emergence of high-throughput sequencing (HTS) technology has greatly influenced research in biological sciences including clinical applications such as in the understanding of disease etiology… (more)

Subjects/Keywords: Statistics; Bioinformatics; base-calling; next-generation sequencing

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APA (6^th Edition):

Cacho, A. (2016). Base-Calling of High-Throughput Sequencing Data Using a Random Effects Mixture Model. (Thesis). University of California – Riverside. Retrieved from http://www.escholarship.org/uc/item/98x9v8rn

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Cacho, Ashley. “Base-Calling of High-Throughput Sequencing Data Using a Random Effects Mixture Model.” 2016. Thesis, University of California – Riverside. Accessed April 12, 2021. http://www.escholarship.org/uc/item/98x9v8rn.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Cacho, Ashley. “Base-Calling of High-Throughput Sequencing Data Using a Random Effects Mixture Model.” 2016. Web. 12 Apr 2021.

Vancouver:

Cacho A. Base-Calling of High-Throughput Sequencing Data Using a Random Effects Mixture Model. [Internet] [Thesis]. University of California – Riverside; 2016. [cited 2021 Apr 12]. Available from: http://www.escholarship.org/uc/item/98x9v8rn.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Cacho A. Base-Calling of High-Throughput Sequencing Data Using a Random Effects Mixture Model. [Thesis]. University of California – Riverside; 2016. Available from: http://www.escholarship.org/uc/item/98x9v8rn

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Vanderbilt University

13. Hutchinson, Katherine Emily. Identification of Novel Targets for Therapy in Solid Tumors.

Degree: PhD, Cancer Biology, 2015, Vanderbilt University

URL: http://hdl.handle.net/1803/15255

► Solid tumor treatment paradigms have drastically improved in recent decades through direct targeting of the protein products of somatic, constitutively active “driver” mutations and their… (more)

▼ Solid tumor treatment paradigms have drastically improved in recent decades through direct targeting of the protein products of somatic, constitutively active “driver” mutations and their effector signaling pathways. Prior to these advances, metastatic solid tumors were primarily managed through administration of traditional cytotoxic chemotherapy. A prime example of this success is evident in melanomas expressing alterations at codon V600 of the serine-threonine kinase, BRAF. Compared to the chemotherapeutic standard-of-care in metastatic melanoma, dacarbazine, patients with BRAF V600E/K/M/R/D-mutated tumors exhibit significantly higher response and survival rates when treated with V600-variant specific small molecule inhibitors, vemurafenib and dabrafenib. However, potential driver mutations have not been identified for all tumors, and a large fraction of tumors are still “driver negative”. Herein, we sought to uncover new ‘drivers’ in pan-negative melanoma and pancreatic acinar cell carcinoma (PACC). While approximately 70% of melanomas harbor actionable driver alterations, the remaining one-third of patients are considered pan-negative. No driver alterations have yet been identified in patients with PACC, likely due to the rarity of this tumor type. Through whole-genome sequencing (WGS), we identified BRAF non-V600 alterations (L597, K601) in pan-negative melanomas that activate the mitogen-activation protein kinase (MAPK) signaling pathway and confer sensitivity to MEK1/2 inhibitors. Using comprehensive targeted, next-generation sequencing platforms, we identified MAPK-pathway activating RAF fusions in both pan-negative melanomas and PACCs. Finally, efforts to distinguish further pan-negative melanomas from one another revealed that a subset of pan-negative melanomas exhibit baseline activation of the ERBB family receptor tyrosine kinases (RTKs) EGFR, HER2 and HER3, suggesting a potential avenue for ERBB kinase inhibition in this disease. Collectively, this work describes the identification of novel and clinically actionable targets in previously un-druggable cancer subtypes. Advisors/Committee Members: Graham Carpenter (committee member), Jeffrey A. Sosman (committee member), Ann Richmond (committee member), William Pao (committee member), Jin Chen (Committee Chair).

Subjects/Keywords: next-generation sequencing; targeted therapy; cancer; melanoma

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hutchinson, K. E. (2015). Identification of Novel Targets for Therapy in Solid Tumors. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/15255

Chicago Manual of Style (16^th Edition):

Hutchinson, Katherine Emily. “Identification of Novel Targets for Therapy in Solid Tumors.” 2015. Doctoral Dissertation, Vanderbilt University. Accessed April 12, 2021. http://hdl.handle.net/1803/15255.

MLA Handbook (7^th Edition):

Hutchinson, Katherine Emily. “Identification of Novel Targets for Therapy in Solid Tumors.” 2015. Web. 12 Apr 2021.

Vancouver:

Hutchinson KE. Identification of Novel Targets for Therapy in Solid Tumors. [Internet] [Doctoral dissertation]. Vanderbilt University; 2015. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/1803/15255.

Council of Science Editors:

Hutchinson KE. Identification of Novel Targets for Therapy in Solid Tumors. [Doctoral Dissertation]. Vanderbilt University; 2015. Available from: http://hdl.handle.net/1803/15255

Penn State University

14. Zhang, Zhenhai. DATAMINING OF GENOME-WIDE NUCLEOSOME DATA GENERATED BY NEXT-GENERATION SEQUENCING .

Degree: 2011, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/11443

► The fundamental building block of eukaryotic genomes is the nucleosome, which consists of 147 base pairs DNA sequence and four core histones with possible exchange… (more)

▼ The fundamental building block of eukaryotic genomes is the nucleosome, which consists of 147 base pairs DNA sequence and four core histones with possible exchange of histone variants, such as H2Av. Both the position and composition of nucleosomes provide important roles during genome compaction and gene regulation. MNase Chromatin ImmunoPrecipitation followed by next-generation sequencing (ChIP-Seq) allows scientists to investigate genome-wide nucleosome positions in a near base pair resolution. Chapter 2 summarizes principles, concepts, and philosophies in producing computer scripts, which I developed to process and analyze genomic MNase ChIP-seq data. The resulting pipelines and script toolkits led to the successful analysis in Chapter 3, 4, and 5. For example, while MNase ChIP-seq has revealed that the H2Av histone variant preferentially marks euchromatin promoter regions in fly, thus far no parallel study has been conducted on heterochromatic regions. In chapter 3 of this thesis, I compared the H2Av nucleosome patterns around same genomic features between euchromatin and heterochromatin. I found that different genomic features have each have a unique H2Av nucleosome organization. This study provided insight into the how nucleosomes are organized in the framework of the typically more compact and transcriptionally silent heterochromatin. High-throughput sequencing efforts in yeast also showed that nucleosomes are organized in a uniformly spaced array at 5’ end of genes. The mechanism underlying this array formation is far from understood and remains controversial. In chapter 4 of this thesis, I investigated the contributions of DNA sequence, statistical positioning, and ATP-dependent trans-acting factors to genome-wide nucleosome positioning. The genomic DNA sequence defines the thermo-dynamic landscape for nucleosome occupancy and this study shows that the position of the first nucleosome in the array is most dependent on DNA sequence. In collaboration with others I discovered a novel ATP-driven packing mechanism against a genomic barrier that drives nucleosome organization at the 5’ end of most genes. Poly (dA:dT) tracks in 5’ nucleosome-free promoter regions (NFRs) generally excluded nucleosome binding, thereby forming one genomic barrier. ATP-dependent chromatin remodelers pack nucleosomes against this barrier to form regularly spaced arrays. The effect of chromatin remodelers lasts for about four nucleosomes into each genic array, after which the underlying DNA sequence directs nucleosome placement. This new mechanism replaces three other prevailing mechanisms of nucleosome organization (DNA-encoded, statistical positioning, and transcription), and suggests that the packing mechanism creates nucleosome organizing centers that function to buffer nucleosome density and positioning against transient changes in nucleosome level that might occur during transcription and DNA replication. Advisors/Committee Members: Benjamin Franklin Pugh, Dissertation Advisor/Co-Advisor, Benjamin Franklin Pugh, Committee Chair/Co-Chair, David Scott Gilmour, Committee Member, Debashis Ghosh, Committee Member, Yu Zhang, Committee Member.

Subjects/Keywords: Next-generation sequencing; data mining; ChIP-Seq

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Zhang, Z. (2011). DATAMINING OF GENOME-WIDE NUCLEOSOME DATA GENERATED BY NEXT-GENERATION SEQUENCING . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/11443

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zhang, Zhenhai. “DATAMINING OF GENOME-WIDE NUCLEOSOME DATA GENERATED BY NEXT-GENERATION SEQUENCING .” 2011. Thesis, Penn State University. Accessed April 12, 2021. https://submit-etda.libraries.psu.edu/catalog/11443.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zhang, Zhenhai. “DATAMINING OF GENOME-WIDE NUCLEOSOME DATA GENERATED BY NEXT-GENERATION SEQUENCING .” 2011. Web. 12 Apr 2021.

Vancouver:

Zhang Z. DATAMINING OF GENOME-WIDE NUCLEOSOME DATA GENERATED BY NEXT-GENERATION SEQUENCING . [Internet] [Thesis]. Penn State University; 2011. [cited 2021 Apr 12]. Available from: https://submit-etda.libraries.psu.edu/catalog/11443.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zhang Z. DATAMINING OF GENOME-WIDE NUCLEOSOME DATA GENERATED BY NEXT-GENERATION SEQUENCING . [Thesis]. Penn State University; 2011. Available from: https://submit-etda.libraries.psu.edu/catalog/11443

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Guelph

15. Taidi, Saina. Biodiversity Assessment of Insect from Environmental Samples Using qPCR and Next-Generation Parallelized Sequencing of DNA Barcodes.

Degree: MS, Department of Integrative Biology, 2012, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3951

► This thesis employs three bioindicator species of mayfly (Insecta: Ephemeroptera) and three of caddisfly (Insecta: Trichoptera) as models to develop a reliable biodiversity and biomonitoring… (more)

Subjects/Keywords: Next generation sequencing; DNA barcoding; Biomonitoring

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Taidi, S. (2012). Biodiversity Assessment of Insect from Environmental Samples Using qPCR and Next-Generation Parallelized Sequencing of DNA Barcodes. (Masters Thesis). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3951

Chicago Manual of Style (16^th Edition):

Taidi, Saina. “Biodiversity Assessment of Insect from Environmental Samples Using qPCR and Next-Generation Parallelized Sequencing of DNA Barcodes.” 2012. Masters Thesis, University of Guelph. Accessed April 12, 2021. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3951.

MLA Handbook (7^th Edition):

Taidi, Saina. “Biodiversity Assessment of Insect from Environmental Samples Using qPCR and Next-Generation Parallelized Sequencing of DNA Barcodes.” 2012. Web. 12 Apr 2021.

Vancouver:

Taidi S. Biodiversity Assessment of Insect from Environmental Samples Using qPCR and Next-Generation Parallelized Sequencing of DNA Barcodes. [Internet] [Masters thesis]. University of Guelph; 2012. [cited 2021 Apr 12]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3951.

Council of Science Editors:

Taidi S. Biodiversity Assessment of Insect from Environmental Samples Using qPCR and Next-Generation Parallelized Sequencing of DNA Barcodes. [Masters Thesis]. University of Guelph; 2012. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3951

University of Edinburgh

16. Emelianova, Katie. Using next generation sequencing to investigate the generation of diversity in the genus Begonia.

Degree: PhD, 2017, University of Edinburgh

URL: http://hdl.handle.net/1842/29584

► Begonia is one of the most diverse genera on the planet, with a species count approaching 2000 and a distribution across tropics in South America,… (more)

▼ Begonia is one of the most diverse genera on the planet, with a species count approaching 2000 and a distribution across tropics in South America, Africa and South East Asia. The genus has occupied a vast range of niches; many highly variable growth forms can be found across the distribution, and species exhibit very diverse morphologies, even in closely related species. A recent study has revealed a putative whole genome duplication (WGD) event in the evolutionary history of Begonia, which has prompted an interest in investigating the impact gene and genome duplication has had on the diversification of Begonia. To answer questions about phenotypic and ecological diversification in Begonia, two species from South America, B. conchifolia and B. plebeja were chosen as study species based on their close phylogenetic relationship and divergent ecology and phenotype. RNA-seq data for six tissues from B. conchifolia and B. plebeja was generated using the Illumina sequencing platform, and normalised relative expression data was obtained by mapping reads to transcripts predicted from the B. conchifolia draft genome. A bioinformatics pipeline was devised to compare expression profiles across 6 different tissues between duplicated gene pairs shared between B. conchifolia and B. plebeja. Gene duplicate pairs were selected as candidates if they showed divergent expression in one species but not in another. Such duplicate pairs are suggestive of neofunctionalization in one species, providing evidence of a potential basis for phenotypic divergence and diversification between B. conchifolia and B. plebeja. Two duplicate pairs were identified as showing such divergent expression patterns as well as being functionally ecologically relevant, Chalcone Synthase and 3-Ketoacyl-CoA synthase, involved in anthocyanin biosynthesis and wax biosynthesis respectively. Investigation of expression and duplication patterns in both gene families showed the candidate gene families to be strikingly different. While 3-Ketoacyl-CoA synthase showed deeper duplications shared with outgroup taxa, Chalcone Synthase appeared to be expanded very recently, with a burst of duplications specific to the genus. 3-Ketoacyl-CoA synthase showed examples of partitioned expression by tissue for different gene family members, with at least five members of the gene family being highly expressed in one or two tissues only. Chalcone Synthase, however, showed dominance of one basal gene family member. Other Chalcone Synthase members, though expressed at lower levels, showed some evidence of reciprocal silencing in B. plebeja, though this pattern was not observed in B. conchifolia. Further investigation of the Chalcone Synthase gene family revealed lineage specific duplication in B. plebeja, and more extensive differential duplication patterns were found across other South American Begonias. Additionally, signals of positive selection were found in two branches on the Chalcone Synthase phylogeny.

Subjects/Keywords: 583; Begonia; plant evolution; next generation sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Emelianova, K. (2017). Using next generation sequencing to investigate the generation of diversity in the genus Begonia. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/29584

Chicago Manual of Style (16^th Edition):

Emelianova, Katie. “Using next generation sequencing to investigate the generation of diversity in the genus Begonia.” 2017. Doctoral Dissertation, University of Edinburgh. Accessed April 12, 2021. http://hdl.handle.net/1842/29584.

MLA Handbook (7^th Edition):

Emelianova, Katie. “Using next generation sequencing to investigate the generation of diversity in the genus Begonia.” 2017. Web. 12 Apr 2021.

Vancouver:

Emelianova K. Using next generation sequencing to investigate the generation of diversity in the genus Begonia. [Internet] [Doctoral dissertation]. University of Edinburgh; 2017. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/1842/29584.

Council of Science Editors:

Emelianova K. Using next generation sequencing to investigate the generation of diversity in the genus Begonia. [Doctoral Dissertation]. University of Edinburgh; 2017. Available from: http://hdl.handle.net/1842/29584

Erasmus University Rotterdam

17. L.C. Chaitanya (Lakshmi). Genetic Approaches to Appearance and Ancestry: Improving Forensic DNA Analysis.

Degree: 2016, Erasmus University Rotterdam

URL: http://hdl.handle.net/1765/94499

► Traditionally, routine forensic casework is based on comparative grounds. DNA profiles obtained from crime-scenes are compared with those of potential suspects or DNA profiles deposited… (more)

Subjects/Keywords: Phenotyping; HIrisPlex; Next Generation Sequencing; Mitochondrial DNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

(Lakshmi), L. C. (2016). Genetic Approaches to Appearance and Ancestry: Improving Forensic DNA Analysis. (Thesis). Erasmus University Rotterdam. Retrieved from http://hdl.handle.net/1765/94499

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

(Lakshmi), L.C. Chaitanya. “Genetic Approaches to Appearance and Ancestry: Improving Forensic DNA Analysis.” 2016. Thesis, Erasmus University Rotterdam. Accessed April 12, 2021. http://hdl.handle.net/1765/94499.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

(Lakshmi), L.C. Chaitanya. “Genetic Approaches to Appearance and Ancestry: Improving Forensic DNA Analysis.” 2016. Web. 12 Apr 2021.

Vancouver:

(Lakshmi) LC. Genetic Approaches to Appearance and Ancestry: Improving Forensic DNA Analysis. [Internet] [Thesis]. Erasmus University Rotterdam; 2016. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/1765/94499.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

(Lakshmi) LC. Genetic Approaches to Appearance and Ancestry: Improving Forensic DNA Analysis. [Thesis]. Erasmus University Rotterdam; 2016. Available from: http://hdl.handle.net/1765/94499

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

18. Davey, Susan Rosemary. A novel genotyping approach to improve transfusion support for patients with HLA and/or HPA alloantibodies.

Degree: Thesis (D.B.M.S.), 2018, University of the West of England, Bristol

URL: https://uwe-repository.worktribe.com/output/864032 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.737794

► Patients who require platelet transfusion support but have become sensitised to Human Leucocyte Antigens (HLA) or Human Platelet Antigens (HPA) require suitably matched or selected… (more)

▼ Patients who require platelet transfusion support but have become sensitised to Human Leucocyte Antigens (HLA) or Human Platelet Antigens (HPA) require suitably matched or selected products to avoid adverse transfusion reactions resulting from antibodies reacting with the transfused product. Provision of compatible products for these patients is often challenging, and requires significant resources from the blood service. This study set out to develop and implement next generation sequencing (NGS) technology to enhance the HLA and HPA definition of both platelet donors and recipients. An NGS based method was designed and developed for high throughput, allele level HLA class I genotyping and used to evaluate the impact of NGS technology on the selection of platelet donors using HLA epitope matching (HEM). In addition, an alternative NGS approach was designed to simultaneously sequence the six genes that code for glycoproteins expressing HPA in order to define all known HPA systems in both donor and patient samples. Allele level HLA-A, -B and –C genotypes were generated for 519 platelet donors by NGS. A critical evaluation of algorithms used to predict alleles from low to medium resolution HLA types demonstrated that NGS was more accurate when determining HLA epitopes for the selection of platelets by HEM. The HLA genotyping data obtained was used to establish previously undefined HLA allele and haplotype frequencies at third field resolution in the English platelet donor population. This thesis also includes the first reported NGS based method for the simultaneous genotyping of HPA-1 to HPA-29, with the additional capability of novel HPA detection. NGS has been shown to significantly improve the definition of both HLA and HPA genetic systems and will provide a number of future benefits for laboratories and the patients they support, including provision of well matched transfusion products, the detection of rare or novel polymorphisms and increased knowledge of HLA and HPA frequencies.

Subjects/Keywords: 615.3; Next Generation Sequencing; HPA; Genotyping; HLA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Davey, S. R. (2018). A novel genotyping approach to improve transfusion support for patients with HLA and/or HPA alloantibodies. (Doctoral Dissertation). University of the West of England, Bristol. Retrieved from https://uwe-repository.worktribe.com/output/864032 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.737794

Chicago Manual of Style (16^th Edition):

Davey, Susan Rosemary. “A novel genotyping approach to improve transfusion support for patients with HLA and/or HPA alloantibodies.” 2018. Doctoral Dissertation, University of the West of England, Bristol. Accessed April 12, 2021. https://uwe-repository.worktribe.com/output/864032 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.737794.

MLA Handbook (7^th Edition):

Davey, Susan Rosemary. “A novel genotyping approach to improve transfusion support for patients with HLA and/or HPA alloantibodies.” 2018. Web. 12 Apr 2021.

Vancouver:

Davey SR. A novel genotyping approach to improve transfusion support for patients with HLA and/or HPA alloantibodies. [Internet] [Doctoral dissertation]. University of the West of England, Bristol; 2018. [cited 2021 Apr 12]. Available from: https://uwe-repository.worktribe.com/output/864032 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.737794.

Council of Science Editors:

Davey SR. A novel genotyping approach to improve transfusion support for patients with HLA and/or HPA alloantibodies. [Doctoral Dissertation]. University of the West of England, Bristol; 2018. Available from: https://uwe-repository.worktribe.com/output/864032 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.737794

19. Al Turki, Saeed. Integrated approaches to elucidate the genetic architecture of congenital heart defects.

Degree: PhD, 2014, University of Cambridge

URL: https://doi.org/10.17863/CAM.16352 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.590265

► Congenital heart defects (CHD) are structural anomalies affecting the heart, are found in 1% of the population and arise during early stages of embryo development.… (more)

▼ Congenital heart defects (CHD) are structural anomalies affecting the heart, are found in 1% of the population and arise during early stages of embryo development. Without surgical and medical interventions, most of the severe CHD cases would not survive after the first year of life. The improved health care for CHD patients has increased CHD prevalence significantly, and it has been estimated that the population of adults with CHD is growing ~5% per year. Understanding the causes of CHD would greatly help improve our knowledge of the pathophysiology, family counseling and planning and possibly prevention and treatment in the future. The aim of my thesis was to identify novel or known CHD genes enriched for rare coding genetic variants in isolated CHD cases and learn about the relative performance of different study designs. High-throughput next generation sequencing (NGS) was used to sequence all coding genes (whole exome) coupled with various analytical pipelines and tools to identify candidate genes in different family-based study designs. Since there is no general consensus on the underlying genetic model of isolated CHD, I developed a suite of software tools to enable different family-based exome analyses of de novo and inherited variants (chapter 2) and then piloted these tools in several gene discovery projects where the mode of inheritance was already known to identify previously described and novel pathogenic genes, before applying them to an analysis of families with two or more siblings with CHD. Based on the tools developed in chapter 2, I designed a two-stage study to investigate isolated parent-offspring trios with Tetralogy of Fallot (chapter 3). In the first stage, I used whole exome sequence data from 30 trios to identify genes with de novo coding variants. This analysis identified six de novo loss-of-function and 13 de novo missense variants. Only one gene showed recurrent de novo mutations in NOTCH1, a well known CHD gene that has mostly been associated with left ventricle outflow tract malformations (LVOT). Besides NOTCH1, the de novo analysis identified several possibly pathogenic novel genes such as ZMYM2 and ARHGAP35, that harbor de novo loss-of-function variants (frameshift and stop gain, respectively). In the second stage of the study, I designed custom baits to capture 122 candidate genes for additional sequencing using NGS in a larger sample size of 250 parent-offspring trios with isolated Tetralogy of Fallot and identified six de novo variants in four genes, half of them are loss-of-function variants. Both of NOTCH1 and its ligand JAG1 harbor two additional de novo mutations (two stop gains in NOTCH1 and one missense and a splice donor in JAG1). The analysis showed a strongly significant over-representation of de novo loss-of-function variants in NOTCH1 (P=3.8 ×10-9). To assess alternative family-based study design in CHD, I combined the analysis from 13 isolated parent-offspring trios with 112 unrelated index cases of isolated atrioventricular septal defects (AVSD) in chapter 4.…

Subjects/Keywords: 616.1; Congenital heart defects; Next generation sequencing

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APA (6^th Edition):

Al Turki, S. (2014). Integrated approaches to elucidate the genetic architecture of congenital heart defects. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.16352 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.590265

Chicago Manual of Style (16^th Edition):

Al Turki, Saeed. “Integrated approaches to elucidate the genetic architecture of congenital heart defects.” 2014. Doctoral Dissertation, University of Cambridge. Accessed April 12, 2021. https://doi.org/10.17863/CAM.16352 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.590265.

MLA Handbook (7^th Edition):

Al Turki, Saeed. “Integrated approaches to elucidate the genetic architecture of congenital heart defects.” 2014. Web. 12 Apr 2021.

Vancouver:

Al Turki S. Integrated approaches to elucidate the genetic architecture of congenital heart defects. [Internet] [Doctoral dissertation]. University of Cambridge; 2014. [cited 2021 Apr 12]. Available from: https://doi.org/10.17863/CAM.16352 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.590265.

Council of Science Editors:

Al Turki S. Integrated approaches to elucidate the genetic architecture of congenital heart defects. [Doctoral Dissertation]. University of Cambridge; 2014. Available from: https://doi.org/10.17863/CAM.16352 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.590265

Boston College

20. Indap, Amit R. Discovering rare variants from populations to families.

Degree: PhD, Biology, 2013, Boston College

URL: http://dlib.bc.edu/islandora/object/bc-ir:101399

► Partitioning 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… (more)

▼ Partitioning 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… Advisors/Committee Members: Gabor T. Marth (Thesis advisor).

Subjects/Keywords: bioinformatics; human genetics; next generation sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Indap, A. R. (2013). Discovering rare variants from populations to families. (Doctoral Dissertation). Boston College. Retrieved from http://dlib.bc.edu/islandora/object/bc-ir:101399

Chicago Manual of Style (16^th Edition):

Indap, Amit R. “Discovering rare variants from populations to families.” 2013. Doctoral Dissertation, Boston College. Accessed April 12, 2021. http://dlib.bc.edu/islandora/object/bc-ir:101399.

MLA Handbook (7^th Edition):

Indap, Amit R. “Discovering rare variants from populations to families.” 2013. Web. 12 Apr 2021.

Vancouver:

Indap AR. Discovering rare variants from populations to families. [Internet] [Doctoral dissertation]. Boston College; 2013. [cited 2021 Apr 12]. Available from: http://dlib.bc.edu/islandora/object/bc-ir:101399.

Council of Science Editors:

Indap AR. Discovering rare variants from populations to families. [Doctoral Dissertation]. Boston College; 2013. Available from: http://dlib.bc.edu/islandora/object/bc-ir:101399

21. Al Turki, Saeed. Integrated approaches to elucidate the genetic architecture of congenital heart defects.

Degree: PhD, 2014, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/245178https://www.repository.cam.ac.uk/bitstream/1810/245178/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/245178/6/sa9_thesis_corrected_13Jan2014.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/7/sa9_thesis_corrected_13Jan2014.pdf.jpg

► Congenital heart defects (CHD) are structural anomalies affecting the heart, are found in 1% of the population and arise during early stages of embryo development.… (more)

▼ Congenital heart defects (CHD) are structural anomalies affecting the heart, are found in 1% of the population and arise during early stages of embryo development. Without surgical and medical interventions, most of the severe CHD cases would not survive after the first year of life. The improved health care for CHD patients has increased CHD prevalence significantly, and it has been estimated that the population of adults with CHD is growing ~5% per year. Understanding the causes of CHD would greatly help improve our knowledge of the pathophysiology, family counseling and planning and possibly prevention and treatment in the future. Several lines of evidence from humans and animal models have supported a substantial genetic component for CHD. However, gene discovery in CHD has been difficult due to the extreme locus heterogeneity and the lack of a distinct genotype–phenotype correlation. Currently, genetic causes are identified in fewer than 20-‐30% of the cases, most of which are syndromic while the isolated CHD cases remain largely without explanation. The aim of my thesis was to identify novel or known CHD genes enriched for rare coding genetic variants in isolated CHD cases and learn about the relative performance of different study designs. High-throughput next generation sequencing (NGS) was used to sequence all coding genes (whole exome) coupled with various analytical pipelines and tools to identify candidate genes in different family-based study designs. Since there is no general consensus on the underlying genetic model of isolated CHD, I developed a suite of software tools to enable different family-based exome analyses of de novo and inherited variants (chapter 2) and then piloted these tools in several gene discovery projects where the mode of inheritance was already known to identify previously described and novel pathogenic genes, before applying them to an analysis of families with two or more siblings with CHD. Based on the tools developed in chapter 2, I designed a two-stage study to investigate isolated parent-offspring trios with Tetralogy of Fallot (chapter 3). In the first stage, I used whole exome sequence data from 30 trios to identify genes with de novo coding variants. This analysis identified six de novo loss-of-function and 13 de novo missense variants. Only one gene showed recurrent de novo mutations in NOTCH1, a well known CHD gene that has mostly been associated with left ventricle outflow tract malformations (LVOT). Besides NOTCH1, the de novo analysis identified several possibly pathogenic novel genes such as ZMYM2 and ARHGAP35, that harbor de novo loss-of-function variants (frameshift and stop gain, respectively). In the second stage of the study, I designed custom baits to capture 122 candidate genes for additional sequencing using NGS in a larger sample size of 250 parent-offspring trios with isolated Tetralogy of Fallot and identified six de novo variants in four genes, half of them are loss-of-function variants. Both of NOTCH1 and its ligand JAG1 harbor two…

Subjects/Keywords: Congenital heart defects; Next generation sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Al Turki, S. (2014). Integrated approaches to elucidate the genetic architecture of congenital heart defects. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/245178https://www.repository.cam.ac.uk/bitstream/1810/245178/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/245178/6/sa9_thesis_corrected_13Jan2014.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/7/sa9_thesis_corrected_13Jan2014.pdf.jpg

Chicago Manual of Style (16^th Edition):

Al Turki, Saeed. “Integrated approaches to elucidate the genetic architecture of congenital heart defects.” 2014. Doctoral Dissertation, University of Cambridge. Accessed April 12, 2021. https://www.repository.cam.ac.uk/handle/1810/245178https://www.repository.cam.ac.uk/bitstream/1810/245178/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/245178/6/sa9_thesis_corrected_13Jan2014.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/7/sa9_thesis_corrected_13Jan2014.pdf.jpg.

MLA Handbook (7^th Edition):

Al Turki, Saeed. “Integrated approaches to elucidate the genetic architecture of congenital heart defects.” 2014. Web. 12 Apr 2021.

Vancouver:

Al Turki S. Integrated approaches to elucidate the genetic architecture of congenital heart defects. [Internet] [Doctoral dissertation]. University of Cambridge; 2014. [cited 2021 Apr 12]. Available from: https://www.repository.cam.ac.uk/handle/1810/245178https://www.repository.cam.ac.uk/bitstream/1810/245178/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/245178/6/sa9_thesis_corrected_13Jan2014.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/7/sa9_thesis_corrected_13Jan2014.pdf.jpg.

Council of Science Editors:

Al Turki S. Integrated approaches to elucidate the genetic architecture of congenital heart defects. [Doctoral Dissertation]. University of Cambridge; 2014. Available from: https://www.repository.cam.ac.uk/handle/1810/245178https://www.repository.cam.ac.uk/bitstream/1810/245178/2/license.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/3/license_rdf ; https://www.repository.cam.ac.uk/bitstream/1810/245178/6/sa9_thesis_corrected_13Jan2014.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/245178/7/sa9_thesis_corrected_13Jan2014.pdf.jpg

University of Manitoba

22. Xu, Minqi. Using next generation sequencing to detect clinically relevant oncogene mutations in lung cancer.

Degree: Pathology, 2017, University of Manitoba

URL: http://hdl.handle.net/1993/32390

► Introduction: Modern care of patients with lung cancer requires rapid and accurate diagnosis leading to personalized therapies for individual patients based on molecular characteristics of… (more)

▼ Introduction: Modern care of patients with lung cancer requires rapid and accurate diagnosis leading to personalized therapies for individual patients based on molecular characteristics of their tumour. Detecting mutations that predict response to drug quickly and accurately is an essential part of this process. Next generation sequencing (NGS) technologies provide an alternative approach for detecting mutated oncogenes in cancer. We hypothesize that NGS is equal if not superior to standard methods for identifying targetable mutations in the EGFR and ALK genes in lung cancer. Methods: DNA and RNA from 38 formalin fixed paraffin embedded lung cancer samples (37 non-small cell lung cancer (NSCLC) and one small cell lung cancer (SCLC)) archived in Diagnostic Services Manitoba were collected and analyzed using gene enrichment methods from Archer Diagnostics followed by sequencing on the Illumina MiSeq NGS machine. Targeted DNA sequencing to detect the EGFR mutation was performed on 19 samples while targeted RNA sequencing was applied to 20 samples to identify the ALK gene rearrangement. The NGS results were compared with and confirmed by current clinical standard molecular tests for EGFR (real-time PCR) and ALK (immunohistochemistry and FISH). Results: Three cases were positive for the EGFR mutation and two other samples harbored the EML4-ALK fusion genes as determined by NGS. The concordance between NGS and real-time PCR for EGFR mutation detection was 88.9%. Additionally, the NGS methodology also provided profiles of other genes commonly mutated in NSCLC including KRAS and TP53. The consistency for ALK fusion testing was 100% between NGS and FISH. Conclusion: This study provides support that NGS is a promising diagnostic tool for mutation detection in NSCLC and holds strong potential for an alternative approach to identifying clinically relevant targets such as EGFR and ALK. Furthermore, NGS provides more information on cancer driven gene mutations than other traditional methods. Advisors/Committee Members: Qing, Gefei (Pathology) (supervisor), Myal, Yvonne (Pathology).

Subjects/Keywords: next generation sequencing; lung cancer; ALK; EGFR

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Xu, M. (2017). Using next generation sequencing to detect clinically relevant oncogene mutations in lung cancer. (Masters Thesis). University of Manitoba. Retrieved from http://hdl.handle.net/1993/32390

Chicago Manual of Style (16^th Edition):

Xu, Minqi. “Using next generation sequencing to detect clinically relevant oncogene mutations in lung cancer.” 2017. Masters Thesis, University of Manitoba. Accessed April 12, 2021. http://hdl.handle.net/1993/32390.

MLA Handbook (7^th Edition):

Xu, Minqi. “Using next generation sequencing to detect clinically relevant oncogene mutations in lung cancer.” 2017. Web. 12 Apr 2021.

Vancouver:

Xu M. Using next generation sequencing to detect clinically relevant oncogene mutations in lung cancer. [Internet] [Masters thesis]. University of Manitoba; 2017. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/1993/32390.

Council of Science Editors:

Xu M. Using next generation sequencing to detect clinically relevant oncogene mutations in lung cancer. [Masters Thesis]. University of Manitoba; 2017. Available from: http://hdl.handle.net/1993/32390

University College Cork

23. O'Sullivan, Daniel. The application of next generation sequencing to profile microbe related cheese quality defects.

Degree: 2015, University College Cork

URL: http://hdl.handle.net/10468/2809

► High throughput next generation sequencing, together with advanced molecular methods, has considerably enhanced the field of food microbiology. By overcoming biases associated with culture dependant… (more)

▼ High throughput next generation sequencing, together with advanced molecular methods, has considerably enhanced the field of food microbiology. By overcoming biases associated with culture dependant approaches, it has become possible to achieve novel insights into the nature of food-borne microbial communities. In this thesis, several different sequencing-based approaches were applied with a view to better understanding microbe associated quality defects in cheese. Initially, a literature review provides an overview of microbe-associated cheese quality defects as well as molecular methods for profiling complex microbial communities. Following this, 16S rRNA sequencing revealed temporal and spatial differences in microbial composition due to the time during the production day that specific commercial cheeses were manufactured. A novel Ion PGM sequencing approach, focusing on decarboxylase genes rather than 16S rRNA genes, was then successfully employed to profile the biogenic amine producing cohort of a series of artisanal cheeses. Investigations into the phenomenon of cheese pinking formed the basis of a joint 16S rRNA and whole genome shotgun sequencing approach, leading to the identification of Thermus species and, more specifically, the pathway involved in production of lycopene, a red coloured carotenoid. Finally, using a more traditional approach, the effect of addition of a facultatively heterofermentative Lactobacillus (Lactobacillus casei) to a Swiss-type cheese, in which starter activity was compromised, was investigated from the perspective of its ability to promote gas defects and irregular eye formation. X-ray computed tomography was used to visualise, using a non-destructive method, the consequences of the undesirable gas formation that resulted. Ultimately this thesis has demonstrated that the application of molecular techniques, such as next generation sequencing, can provide a detailed insight into defect-causing microbial populations present and thereby may underpin approaches to optimise the quality and consistency of a wide variety of cheeses. Advisors/Committee Members: Giblin, Linda, McSweeney, Paul L. H., Cotter, Paul D., Sheehan, Diarmuid, Teagasc.

Subjects/Keywords: Microbiology; Next generation sequencing; Cheese defects

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

O'Sullivan, D. (2015). The application of next generation sequencing to profile microbe related cheese quality defects. (Thesis). University College Cork. Retrieved from http://hdl.handle.net/10468/2809

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

O'Sullivan, Daniel. “The application of next generation sequencing to profile microbe related cheese quality defects.” 2015. Thesis, University College Cork. Accessed April 12, 2021. http://hdl.handle.net/10468/2809.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

O'Sullivan, Daniel. “The application of next generation sequencing to profile microbe related cheese quality defects.” 2015. Web. 12 Apr 2021.

Vancouver:

O'Sullivan D. The application of next generation sequencing to profile microbe related cheese quality defects. [Internet] [Thesis]. University College Cork; 2015. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/10468/2809.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

O'Sullivan D. The application of next generation sequencing to profile microbe related cheese quality defects. [Thesis]. University College Cork; 2015. Available from: http://hdl.handle.net/10468/2809

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

24. Whitaker, Briana Kathleen. Host Specificity, Negative Feedbacks, and Pathogen Defense in the Plant Phyllosphere Microbiome .

Degree: 2018, Indiana University

URL: http://hdl.handle.net/2022/22316

► My dissertation research spans several topics in plant microbial ecology. In two research projects, I have explored whether host specificity influences fungal endophyte community structure… (more)

▼ My dissertation research spans several topics in plant microbial ecology. In two research projects, I have explored whether host specificity influences fungal endophyte community structure in plant leaves across several ecotypes of switchgrass (Panicum virgatum) and across 19 plant species within the Asteraceae family. In these works, I found contrasting results for the importance of host specificity, where fungal endophytes did not preferentially colonize specific host ecotypes within a single species, but did preferentially colonize specific host species within a single family. Additionally, I also found that more phylogenetically related host species within the Asteraceae family shared more similar fungal endophyte communities than more phylogenetically distant hosts. In another portion of my research, I applied a novel extension of the plant-soil feedback framework to microbiota associated with aboveground tissues, termed “plant-phyllosphere feedback”. In this work, I found that all four species tested experienced strong negative plant-phyllosphere feedback suggesting that phyllosphere, like rhizosphere (belowground), microbiota can potentially mediate plant species coexistence via negative feedbacks. In a final work, I tested whether traits displayed by bacterial endophytes in vitro can be used to reliably predict disease reduction outcomes in planta across variable climatic conditions using wheat plants and the fungal pathogen Fusarium graminearum. I did not ultimately find that in vitro trait assessments were good predictors of disease reduction outcomes in planta. However, my analyses did reveal differences among bacterial endophytes in their resilience to variable climatic conditions and degree of pathogen antagonism, emphasizing the importance of considering the abiotic environment for studies of putatively beneficial plant microbiota. Through my dissertation research, I have provided evidence for the extent and limitations of host specificity in the aboveground plant microbiome, the potential role of aboveground plant microbes in mediating species coexistence, and their role in reducing pathogenic outcomes in an agriculturally relevant host. Advisors/Committee Members: Clay, Keith (advisor).

Subjects/Keywords: fungal endophytes; next generation sequencing; crops

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APA (6^th Edition):

Whitaker, B. K. (2018). Host Specificity, Negative Feedbacks, and Pathogen Defense in the Plant Phyllosphere Microbiome . (Thesis). Indiana University. Retrieved from http://hdl.handle.net/2022/22316

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Whitaker, Briana Kathleen. “Host Specificity, Negative Feedbacks, and Pathogen Defense in the Plant Phyllosphere Microbiome .” 2018. Thesis, Indiana University. Accessed April 12, 2021. http://hdl.handle.net/2022/22316.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Whitaker, Briana Kathleen. “Host Specificity, Negative Feedbacks, and Pathogen Defense in the Plant Phyllosphere Microbiome .” 2018. Web. 12 Apr 2021.

Vancouver:

Whitaker BK. Host Specificity, Negative Feedbacks, and Pathogen Defense in the Plant Phyllosphere Microbiome . [Internet] [Thesis]. Indiana University; 2018. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/2022/22316.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Whitaker BK. Host Specificity, Negative Feedbacks, and Pathogen Defense in the Plant Phyllosphere Microbiome . [Thesis]. Indiana University; 2018. Available from: http://hdl.handle.net/2022/22316

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Toronto

25. Tam, Shirley. miRNA Analysis by Next-generation Sequencing and its Prognostic Importance in Non-small Cell Lung Cancer.

Degree: PhD, 2015, University of Toronto

URL: http://hdl.handle.net/1807/71354

► Lung cancer is the leading cause of cancer death worldwide, with an estimated 1.8 million new cases diagnosed each year. Non-small cell lung cancer (NSCLC)… (more)

▼ Lung cancer is the leading cause of cancer death worldwide, with an estimated 1.8 million new cases diagnosed each year. Non-small cell lung cancer (NSCLC) is the predominant histological type, accounting for approximately 85% of all lung cancers. Despite significant advances in smoking cessation, early detection and genetic understanding of the disease, the 5-year overall survival has remained at ~15% over the past few decades. Post-surgical chemotherapy has been shown to improve the survival of some early-stage NSCLC patients, but the overall benefit is modest. To optimize the toxicity/benefit ratio, better diagnostic tools are needed to identify low-risk individuals who can be spared from unnecessary intervention, while avoiding undertreating high-risk patients. Over the past decade, a multitude of prognostic gene signatures has been published, however, none are currently used in the clinical setting to guide therapeutic decision-making. It is hypothesized that the integration of multidimensional high-throughput molecular data may better capture the molecular heterogeneity of lung cancer patients, resulting in more robust biomarkers for patient classification. To aid in the prediction of patient outcome using multidimensional molecular data, I have worked on different stages of the process of biomarker development with respect to microRNAs (miRNA) and their potential added prognostic value to gene signatures. First, I conducted a comprehensive comparison of miRNA profiling technologies, including next-generation sequencing, a microarray platform and the NanoString nCounter System. Next, data preprocessing methods were evaluated to develop a standardized pipeline for the preprocessing of small RNA-seq data, with the end-goal of retrieving miRNA count abundance profiles. Finally, miRNA profiling was performed on tumour specimen resected from early-stage NSCLC patients and combined with gene expression profiling data for the development of an integrated miRNA-mRNA risk classifier for predicting prognosis. The knowledge gained from these studies provides technical insights for the analysis of miRNAs and biological insights for the development of more robust prognostic classifiers. Advisors/Committee Members: Tsao, Ming-Sound, McPherson, John D, Medical Biophysics.

Subjects/Keywords: Lung Cancer; miRNA; Next-generation sequencing; 0307

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APA (6^th Edition):

Tam, S. (2015). miRNA Analysis by Next-generation Sequencing and its Prognostic Importance in Non-small Cell Lung Cancer. (Doctoral Dissertation). University of Toronto. Retrieved from http://hdl.handle.net/1807/71354

Chicago Manual of Style (16^th Edition):

Tam, Shirley. “miRNA Analysis by Next-generation Sequencing and its Prognostic Importance in Non-small Cell Lung Cancer.” 2015. Doctoral Dissertation, University of Toronto. Accessed April 12, 2021. http://hdl.handle.net/1807/71354.

MLA Handbook (7^th Edition):

Tam, Shirley. “miRNA Analysis by Next-generation Sequencing and its Prognostic Importance in Non-small Cell Lung Cancer.” 2015. Web. 12 Apr 2021.

Vancouver:

Tam S. miRNA Analysis by Next-generation Sequencing and its Prognostic Importance in Non-small Cell Lung Cancer. [Internet] [Doctoral dissertation]. University of Toronto; 2015. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/1807/71354.

Council of Science Editors:

Tam S. miRNA Analysis by Next-generation Sequencing and its Prognostic Importance in Non-small Cell Lung Cancer. [Doctoral Dissertation]. University of Toronto; 2015. Available from: http://hdl.handle.net/1807/71354

University of Minnesota

26. Palani, Nagendra Prasad. Molecular multiplexing methods for genome-scale measurements.

Degree: PhD, Plant and Microbial Biology, 2018, University of Minnesota

URL: http://hdl.handle.net/11299/209124

► I present the utility of unique DNA barcodes to tag distinct genotypes and subsequently link them to phenotypes. Such molecular tagging allowed us to perform… (more)

Subjects/Keywords: functional genomics; high throughput; next generation sequencing

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APA (6^th Edition):

Palani, N. P. (2018). Molecular multiplexing methods for genome-scale measurements. (Doctoral Dissertation). University of Minnesota. Retrieved from http://hdl.handle.net/11299/209124

Chicago Manual of Style (16^th Edition):

Palani, Nagendra Prasad. “Molecular multiplexing methods for genome-scale measurements.” 2018. Doctoral Dissertation, University of Minnesota. Accessed April 12, 2021. http://hdl.handle.net/11299/209124.

MLA Handbook (7^th Edition):

Palani, Nagendra Prasad. “Molecular multiplexing methods for genome-scale measurements.” 2018. Web. 12 Apr 2021.

Vancouver:

Palani NP. Molecular multiplexing methods for genome-scale measurements. [Internet] [Doctoral dissertation]. University of Minnesota; 2018. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/11299/209124.

Council of Science Editors:

Palani NP. Molecular multiplexing methods for genome-scale measurements. [Doctoral Dissertation]. University of Minnesota; 2018. Available from: http://hdl.handle.net/11299/209124

University of Melbourne

27. Garsed, Dale William. Genomic alterations in well- and de-differentiated liposarcoma.

Degree: 2013, University of Melbourne

URL: http://hdl.handle.net/11343/38387

► Well- and de-differentiated liposarcomas (WD/DDLPS) are tumours that arise from fat cells (adipocytes) and are characterised by the presence of supernumerary ring or ‘giant-rod’ marker… (more)

▼ Well- and de-differentiated liposarcomas (WD/DDLPS) are tumours that arise from fat cells (adipocytes) and are characterised by the presence of supernumerary ring or ‘giant-rod’ marker chromosomes (neochromosomes; NCs). NCs are associated with several cancer types and are thought to harbour oncogenic mutations in the form of amplified oncogenes or fusion genes. However, knowledge of their structure and oncogenic properties is limited. The aim of this thesis is to comprehensively map genomic alterations in WD/DDLPS NCs, and to identify the mechanisms of pathogenesis in this disease. This report describes the first sequence-level map of cancer-associated NCs. A unique targeted genomics approach was developed, in which flow cytometry was used to isolate giant marker NCs from a panel of WD/DDLPS cell lines, and their content and structure was mapped using single nucleotide polymorphism mapping arrays and next-generation sequencing analyses. The NCs have a complex spatial architecture, with over 900 structural variations, the majority of which were formed by DNA translocations showing evidence of nonhomologous end-joining repair. I developed a novel classification system defining distinct patterns of breakpoints and fusions, which formed the basis for detailed analysis of this complex structure. In-depth characterisation of DNA fusions revealed the molecular history of NC evolution. Different patterns of rearrangement were observed, including evidence of localised shattering and random repair (chromothripsis) on the long arm of chromosome 12, which may be a fundamental mechanism in NC formation. Following initial assembly, DNA amplification occurs by breakage-fusion-bridge cycles in the ring conformation, a phase terminated by linearization and the acquisition of functional telomeres from normal chromosomal counterparts. A genome-wide survey of copy number variations (CNVs) was carried out in primary WD/DDLPS, to define regions most likely to harbour oncogenes and tumour suppressors. The most significant regions of CNV were determined by measuring the frequency of occurrence and amplitude of DNA gain or loss. The genes identified in these candidate regions were then triaged to a list of candidate genes suitable for functional validation, by (i) testing for copy number correlation with matched mRNA expression data, (ii) identifying biologically significant genes based on the literature, and (iii) comparing these findings to a previously published independent data set. A number of novel copy number alterations were identified, including amplification of NUP107, OS9 and CYP27B1, and deletion of DDX6, HRAS, and OTUB1. In order to refine the list of candidate oncogenes, a functional validation screen was performed using RNA interference (RNAi) to determine which amplified genes are necessary for WD/DDLPS cell growth. Short interfering RNA…

Subjects/Keywords: liposarcoma; genomics; neochromosome; NUP107; next-generation sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Garsed, D. W. (2013). Genomic alterations in well- and de-differentiated liposarcoma. (Doctoral Dissertation). University of Melbourne. Retrieved from http://hdl.handle.net/11343/38387

Chicago Manual of Style (16^th Edition):

Garsed, Dale William. “Genomic alterations in well- and de-differentiated liposarcoma.” 2013. Doctoral Dissertation, University of Melbourne. Accessed April 12, 2021. http://hdl.handle.net/11343/38387.

MLA Handbook (7^th Edition):

Garsed, Dale William. “Genomic alterations in well- and de-differentiated liposarcoma.” 2013. Web. 12 Apr 2021.

Vancouver:

Garsed DW. Genomic alterations in well- and de-differentiated liposarcoma. [Internet] [Doctoral dissertation]. University of Melbourne; 2013. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/11343/38387.

Council of Science Editors:

Garsed DW. Genomic alterations in well- and de-differentiated liposarcoma. [Doctoral Dissertation]. University of Melbourne; 2013. Available from: http://hdl.handle.net/11343/38387

28. Wang, Yi. Genome Assembly and Annotation of Isochrysis Galbana .

Degree: 2014, California State University – San Marcos

URL: http://hdl.handle.net/10211.3/120851

► Isochrysis Galbana is a species of cocoolithophores, which is a main factor of forming ocean's interior and sediments, and influencing the global cycles of carbon… (more)

Subjects/Keywords: Next-Generation Sequencing; Genome Assembly; Genome Annotation

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APA (6^th Edition):

Wang, Y. (2014). Genome Assembly and Annotation of Isochrysis Galbana . (Thesis). California State University – San Marcos. Retrieved from http://hdl.handle.net/10211.3/120851

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Wang, Yi. “Genome Assembly and Annotation of Isochrysis Galbana .” 2014. Thesis, California State University – San Marcos. Accessed April 12, 2021. http://hdl.handle.net/10211.3/120851.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Wang, Yi. “Genome Assembly and Annotation of Isochrysis Galbana .” 2014. Web. 12 Apr 2021.

Vancouver:

Wang Y. Genome Assembly and Annotation of Isochrysis Galbana . [Internet] [Thesis]. California State University – San Marcos; 2014. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/10211.3/120851.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Wang Y. Genome Assembly and Annotation of Isochrysis Galbana . [Thesis]. California State University – San Marcos; 2014. Available from: http://hdl.handle.net/10211.3/120851

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Universitat de Valencia

29. García-García, Gema. Usher syndrome : molecular analysis of USH2 genes and development of a next-generation sequencing platform .

Degree: 2013, Universitat de Valencia

URL: http://hdl.handle.net/10550/29081

► El síndrome de Usher (USH) es una enfermedad hereditaria autosómica recesiva, caracterizada por la asociación de hipoacusia neurosensorial, retinosis pigmentaria y, en ocasiones, alteración de… (more)

▼ El síndrome de Usher (USH) es una enfermedad hereditaria autosómica recesiva, caracterizada por la asociación de hipoacusia neurosensorial, retinosis pigmentaria y, en ocasiones, alteración de la función vestibular. Clínicamente, el USH se puede clasificar en tres tipos (USH1, USH2 y USH3), principalmente en base a la gravedad y progresión de la hipoacusia y presencia o no de disfunción vestibular. El USH es heterogéneo tanto a nivel clínico como genético y, hasta la fecha, se han descrito 11 genes implicados en la enfermedad. El USH2 es la forma más común y tres son los genes responsables conocidos: USH2A (72 exones), GPR98 (90 exones) y DFNB31 (12 exones). USH2A es responsable de más del 70% de los casos USH2, teniendo una menor implicación los otros dos genes. Hasta esta tesis, no se había realizado un análisis exhaustivo de estos tres genes en pacientes españoles con síndrome de Usher. Por ello, uno de los objetivos fue el análisis molecular de los tres genes USH2 en una cohorte inicial de 88 pacientes con síndrome de Usher. El estudio consintió en el análisis de los exones, más las regiones intrónicas flanqueantes, mediante amplificación por PCR y secuenciación directa por Sanger. El estudio no se limitó a la detección de mutaciones puntuales, las variantes detectadas fueron analizadas con varios programas bioinformáticos para predecir su posible patogenicidad y, cuando fue necesario, se realizaron estudios funcionales para comprobar los efectos predichos. Además también se realizaron análisis de CGH-array (comparative genome hibrydization array) para detectar posibles grandes inserciones/deleciones, que no identifican los típicos análisis por PCR. El estudio se inició con USH2A,y en los pacientes en los que no se encontraron mutaciones en este gen, se continuó con el análisis de GPR98 y DFNB31. Treinta y siete (23 nuevas) mutaciones diferentes se detectaron en USH2A y 7 (5 nuevas) en GPR98. No se detectaron mutaciones en DFNB31. Las mutaciones detectadas fueron de naturaleza muy diversa (cambios de aminoácido, isocodificantes, codones de parada prematuro directos, pequeñas deleciones e inserciones) y en la mayoría de casos las mutaciones fueron privadas, demostrando la elevada heterogeneidad alélica de esta enfermedad. Además, se identificaron dos grandes deleciones gracias al uso de la técnica de CGH-array. En el desarrollo de este estudio se describió por primera vez en el USH, la presencia de una mutación intrónica profunda en el gen USH2A que produce la activación de un pseudoexon. Esta variante fue detectada en 4 pacientes españoles, completando y mejorando de esta forma el diagnóstico molecular del USH. Esta parte del estudio nos permitió estimar la prevalencia de los genes USH2 en población española. USH2A está implicado en un 76% de los casos USH2, seguido de GPR98 con un 5,2%. DFNB31 tiene una menor implicación en nuestra población. CLRN1,es el único gen responsable del USH3 conocido. Sin embargo, se ha publicado que este gen también puede estar implicado en pacientes con USH1 o USH2. El… Advisors/Committee Members: Aller Mañas, Elena (advisor).

Subjects/Keywords: next generation sequencing; usher syndrome; genetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

García-García, G. (2013). Usher syndrome : molecular analysis of USH2 genes and development of a next-generation sequencing platform . (Doctoral Dissertation). Universitat de Valencia. Retrieved from http://hdl.handle.net/10550/29081

Chicago Manual of Style (16^th Edition):

García-García, Gema. “Usher syndrome : molecular analysis of USH2 genes and development of a next-generation sequencing platform .” 2013. Doctoral Dissertation, Universitat de Valencia. Accessed April 12, 2021. http://hdl.handle.net/10550/29081.

MLA Handbook (7^th Edition):

García-García, Gema. “Usher syndrome : molecular analysis of USH2 genes and development of a next-generation sequencing platform .” 2013. Web. 12 Apr 2021.

Vancouver:

García-García G. Usher syndrome : molecular analysis of USH2 genes and development of a next-generation sequencing platform . [Internet] [Doctoral dissertation]. Universitat de Valencia; 2013. [cited 2021 Apr 12]. Available from: http://hdl.handle.net/10550/29081.

Council of Science Editors:

García-García G. Usher syndrome : molecular analysis of USH2 genes and development of a next-generation sequencing platform . [Doctoral Dissertation]. Universitat de Valencia; 2013. Available from: http://hdl.handle.net/10550/29081

University of New South Wales

30. Roth Schulze, Alexandra Jazmin. Functional diversity and host-specificity of macroalgal surface-associated marine bacteria.

Degree: Biotechnology & Biomolecular Sciences, 2015, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/55414 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37505/SOURCE02?view=true

► Multicellular eukaryotic organisms live in constant interaction with microorganisms thatcolonise their surfaces. In the marine environment, macroalgae are colonised bycomplex communities of bacteria, however the… (more)

▼ Multicellular eukaryotic organisms live in constant interaction with microorganisms thatcolonise their surfaces. In the marine environment, macroalgae are colonised bycomplex communities of bacteria, however the mechanisms that drive the assembly andstability of those bacterial communities are poorly understood. This thesis exploresbacterial communities associated to diverse macroalgal species by using 16S rRNAamplicon sequencing and metagenomics to access their taxonomic composition andfunctionality.To understand the influence of biogeography on bacterial community composition,samples of three green macroalgal species belonging to the genus Ulva (U. australis, U.rigida and U. ohnoi) and seawater collected from different locations were analysed. Ahigh taxonomic variability was detected between the communities associated withdifferent individuals of the same host-species, but despite this, a core of functions wasconsistently present and enriched in all communities. This indicated that taxonomicallydistinct bacteria are providing the same set of functions in different macroalgal species.Local and host-specific conditions also played a role in the selection and assembly ofcommunities on Ulva.To define how community composition is influenced by different kind of surfaces, thetaxonomic and functional composition of planktonic and various surface-associatedbacterial communities were compared. A partitioning of the diversity revealed a hightaxonomic variability between samples, but also showed that most of the functionaldiversity could be found in any given surface. This shows that the functionality to live on a surface can be contained in any given community and that selection occurs onspecific aspects of the surface.In order to define the stability of a macroalgal holobiont during environmental changes,individuals of the green alga Caulerpa taxifolia was exposed to low pH and hightemperature conditions. The bacterial community composition was found to berelatively stable, with only one bacterium increasing in abundance. Moreover, themacroalgal host had an increased growth rate, which suggested that this particularholobiont can resist changing conditions associated to future climate change scenarios.This thesis has contributed to the understanding of mechanisms and factors that drivethe selection and assembly of bacterial communities on marine surfaces. Advisors/Committee Members: Thomas, Torsten, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW.

Subjects/Keywords: Next-generation sequencing; Microbial communities; Macroalgae

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APA (6^th Edition):

Roth Schulze, A. J. (2015). Functional diversity and host-specificity of macroalgal surface-associated marine bacteria. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/55414 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37505/SOURCE02?view=true

Chicago Manual of Style (16^th Edition):

Roth Schulze, Alexandra Jazmin. “Functional diversity and host-specificity of macroalgal surface-associated marine bacteria.” 2015. Doctoral Dissertation, University of New South Wales. Accessed April 12, 2021. http://handle.unsw.edu.au/1959.4/55414 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37505/SOURCE02?view=true.

MLA Handbook (7^th Edition):

Roth Schulze, Alexandra Jazmin. “Functional diversity and host-specificity of macroalgal surface-associated marine bacteria.” 2015. Web. 12 Apr 2021.

Vancouver:

Roth Schulze AJ. Functional diversity and host-specificity of macroalgal surface-associated marine bacteria. [Internet] [Doctoral dissertation]. University of New South Wales; 2015. [cited 2021 Apr 12]. Available from: http://handle.unsw.edu.au/1959.4/55414 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37505/SOURCE02?view=true.

Council of Science Editors:

Roth Schulze AJ. Functional diversity and host-specificity of macroalgal surface-associated marine bacteria. [Doctoral Dissertation]. University of New South Wales; 2015. Available from: http://handle.unsw.edu.au/1959.4/55414 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37505/SOURCE02?view=true

Open Access Theses and Dissertations