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Author:
Publisher:
ISBN: 9781339160511
Category :
Languages : en
Pages : 173
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Book Description
In the last century cancer has become increasingly prevalent and is the second largest killer in the United States, estimated to afflict 1 in 4 people during their life. Despite our long history with cancer and our herculean efforts to thwart the disease, in many cases we still do not understand the underlying causes or have successful treatments. In my graduate work, I've developed two approaches to the study of cancer genomics and applied them to the whole genome sequencing data of cancer patients from The Cancer Genome Atlas (TCGA). In collaboration with Dr. Ewing, I built a pipeline to detect retrotransposon insertions from paired-end high-throughput sequencing data and found somatic retrotransposon insertions in a fifth of cancer patients.
Author:
Publisher:
ISBN: 9781339160511
Category :
Languages : en
Pages : 173
Get Book Here
Book Description
In the last century cancer has become increasingly prevalent and is the second largest killer in the United States, estimated to afflict 1 in 4 people during their life. Despite our long history with cancer and our herculean efforts to thwart the disease, in many cases we still do not understand the underlying causes or have successful treatments. In my graduate work, I've developed two approaches to the study of cancer genomics and applied them to the whole genome sequencing data of cancer patients from The Cancer Genome Atlas (TCGA). In collaboration with Dr. Ewing, I built a pipeline to detect retrotransposon insertions from paired-end high-throughput sequencing data and found somatic retrotransposon insertions in a fifth of cancer patients.
Author: Andrew William McPherson
Publisher:
ISBN:
Category :
Languages : en
Pages : 176
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Book Description
Genome rearrangements are important mutational events in many cancers, and their detection and characterization has the potential to improve treatment options for cancer patients. Evidence of genome rearrangement is available in the sequence of affected DNA and RNA molecules of tumour cells. The development of high-throughput sequencing has drastically increased the efficiency with which researchers can sequence DNA and RNA molecules, though the new technologies have resulted in an increased computational burden, requiring solutions to novel algorithmic problems. In this thesis we describe novel algorithms for detection and characterization of genome rearrangements with specific focus on rearrangements that reshape tumour genomes and impact cancer biology. We describe a method for detecting gene fusions from RNA sequence data (RNA-Seq). Given both RNA-Seq and Whole Genome Sequence (WGS) data, we describe an integrated method for detection of expressed rearrangements, and subsequently extend this method to account for complex genomic rearrangements. Finally, we describe a method for detecting rearrangements existing in subpopulations of tumour cells, and determining the impact on the content of the genome in those subpopulations. The described methods each formulate a maximum parsimony or likelihood optimization problem, and propose combinatorial algorithms to solve these problems. A common theme for the described methods is the benefits of integrating multiple and diverse data-types. We demonstrate using simulated and real data that principled methods for joint analysis of multiple data-types frequently out-perform independent analyses of each data-type. We apply our methods to the detection and characterization of rearrangements in tumour samples, and provide novel examples of events relevant to the biology of each tumour.
Author: Katayoon Kasaian
Publisher: Elsevier Inc. Chapters
ISBN: 0128061065
Category : Medical
Languages : en
Pages : 52
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Book Description
Advances in high-throughput sequencing technologies have enabled cost-effective sequencing of a single human genome at an unprecedented rate, facilitating scientific endeavours never imagined possible before. These improvements have transformed the field of cancer genomics, allowing the complete molecular characterization of individual cancer genomes. However, the promise of unveiling the complexity of cancer has lent itself to yet another level of complexity, the task of managing and integrating the massive amount of data that is generated as part of such experiments. There is a need to manage and store large sequence datasets such that they can be accessed and shared readily but, more importantly, there is a need for their thorough and efficient analysis. Developments and improvements in computer hardware and processing power have eliminated the data storage and access issues. Additionally, bioinformatic algorithms and software, designed specifically for the analysis of cancer genomic data, are now able comprehensively to profile the mutations in a cancer sample, to provide a probability score for their role as disease drivers and to identify potential actionable targets. Although the functional validation of putative driver mutations will remain a necessity, continued improvements in sequencing technologies and analysis tools promise to provide increasingly reliable computational analysis of cancer genomes.
Author: Wei Wu
Publisher: Springer Science & Business Media
ISBN: 1461476453
Category : Medical
Languages : en
Pages : 383
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Book Description
This volume provides an interdisciplinary perspective of applying Next Generation Sequencing (NGS) technology to cancer research. It aims to systematically introduce the concept of NGS, a variety of NGS platforms and their practical implications in cancer biology.This unique and comprehensive text will integrate the unprecedented NGS technology into various cancer research projects as opposed to most books which offer a detailed description of the technology. This volume will present true experimental results with concrete data processing pipelines, discuss the bottleneck of each platform for real project in cancer research. In additional, single cancer cell sequencing as the proof of concept will be introduced in this book, along with cutting-edge information provided will help the intended audience to develop a comprehensive understanding of the NGS technology and practical whole genome sequencing data analysis and rapidly translate into their own research, specifically in the field of cancer biology.
Author: Sameek Roychowdhury
Publisher: Springer Nature
ISBN: 3030236374
Category : Medical
Languages : en
Pages : 196
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Book Description
Genomic sequencing technologies have augmented the classification of cancer beyond tissue of origin and towards a molecular taxonomy of cancer. This has created opportunities to guide treatment decisions for individual patients with cancer based on their cancer’s unique molecular characteristics, also known as precision cancer medicine. The purpose of this text will be to describe the contribution and need for multiple disciplines working together to deliver precision cancer medicine. This entails a multi-disciplinary approach across fields including molecular pathology, computational biology, clinical oncology, cancer biology, drug development, genetics, immunology, and bioethics. Thus, we have outlined a current text on each of these fields as they work together to overcome various challenges and create opportunities to deliver precision cancer medicine. As trainees and junior faculty enter their respective fields, this text will provide a framework for understanding the role and responsibility for each specialist to contribute to this team science approach.
Author: Ryan D. Morin
Publisher: Elsevier Inc. Chapters
ISBN: 0128061006
Category : Medical
Languages : en
Pages : 47
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Book Description
Identifying gene expression changes in cancer provides opportunities to identify biomarkers that can be informative in regard to risk and in the choice of treatment options. In recent years, advances in sequencing have provided not only a quantitative measure of gene expression, but the resolution of diverse species of RNA, alternative transcripts and allele-specific expression. As well, such data have revealed novel sequences such as those from pathogens, mutations resulting in amino acid differences and fusion transcripts resulting from translocations and other structural alterations, each of which can inform the development of novel treatment strategies or potential preventive measures. In this chapter, we will discuss how transcriptome sequencing is conducted and analyzed and provide examples that illustrate its utility in studying cancer samples.
Author: Garima Kushwaha
Publisher:
ISBN:
Category :
Languages : en
Pages : 164
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Book Description
NGS data output has increased at a rate that outpaces Moore’s law, more than doubling each year since it was invented. Studying such high-throughput data has revealed limitless insight about the genome, transcriptome, and epigenome of many species. In this thesis, I contributed the research community with means to better study of such data along with leveraging a high-throughput biological data to better understand epigenetic regulation of a cell and their disease associations using computational methods. Firstly, I contributed towards building on and improving an existing software tool, PRIMEGENS used to design primers for polymerase chain reaction (PCR) which is one of the most breakthrough and highly used technology in the field of genetics. Apart from contributing towards releasing its new version, PRIMEGENSv2, I designed and made available its webversion PRIMEGENSw3 providing an interactive, easy-to-use and user-friendly online tool for high-throughput primer and probe designed. Next, I leverage the high-through sequencing data profiling genomic methylation, expression of genes and histone modifications. I conducted computational analysis of genomewide epigenetic modifications that play a key role in cancer development and cellular proliferation. We found evidences showing that hypomethylation changes at regions other than promoter region might also contribute to some significant deleterious effect that can result in malignant transformation or tumor progression and thus have higher biological significance. Also, this study contributes to our understanding about the relationship between methylation of different genic parts including exons and introns from 3’ and 5’ UTRs, with expression levels in chronic lymphocyte leukemia (CLL) samples. Next, a systems biology approach of independent network construction and preservation of 3’UTR methylation and expression data also revealed expression regulation by hypomethylation of 3’UTRs. Lastly, I validated the presence of widespread hypomethylation regions like 3’UTR, gen body and introns and expression regulation in other cancer types. Hence, I present this study as a new paradigm of looking at genome-wide DNA hypomethylation, in addition to hypermethylation, that can be very helpful to unveil their underlying synergistic mechanism regulating the disease. Overall, this dissertation focuses and present how scalability and specificity of the PCR based enrichment method, combined with the throughput and accuracy of the NGS technology, enable researchers to perform ultra-deep sequencing of regions of interest to better understand areas such as tumorigenesis, population diversity, microbial resistance, and disease susceptibility and thereby advance the scientific fields.
Author: Janet D. Rowley
Publisher: Springer
ISBN: 3319199838
Category : Medical
Languages : en
Pages : 486
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Book Description
This volume collates world experts’ insights into the molecular biology of cancer chromosomes, their abnormalities and the subsequent cellular consequences. Exploring themes involving oncogenes, such as by chromosomal translocations, other genome rearrangements and somatic mutations, this book is a review of the field of cancer genetics that presages a new era, as whole genome sequencing becomes more accessible. The work begins with a look at historical themes, such as the analysis of metaphase chromosomes using microscopy and staining techniques, advances in which provided our first broad glimpse into the genetic anatomy of a malignant cell. Readers will learn about the application of DNA molecular cloning techniques in the 1980s, that led to the identification of the genes involved in the Philadelphia and Burkitt's lymphoma chromosomal translocations, solidifying the role of oncogenes and tumour suppressor genes in cancer aetiology via chromosomal alterations and which launched a field in cancer genetics. Subsequent chapters bring the reader up to date by reviewing recent developments in the field, with dedicated sections on leukaemia/lymphoma, sarcomas and epithelial tumours. Contributions feature numerous colour tables and illustrations and this volume will provide a basis for understanding cancer chromosomes for many years to come.
Author: Institute of Medicine
Publisher: National Academies Press
ISBN: 0309224187
Category : Science
Languages : en
Pages : 354
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Book Description
Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.
Author: Hye-Jung E. Chun
Publisher: Elsevier Inc. Chapters
ISBN: 0128060999
Category : Medical
Languages : en
Pages : 48
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Book Description
Cancer results from accumulated mutations in the genome. Sequencing is an accurate method to detect mutations. Second-generation sequencing technology, commonly referred to as next-generation sequencing technology, enables rapid, efficient and affordable DNA sequencing, and is transforming the scale and scope of cancer research. The technology is sufficiently flexible and affordable to allow sequencing of many cancer genomes, and thus facilitates both sequencing of samples from large patient cohorts and during disease progression in individual cancer patients. The high depths of redundant sequence coverage that can be obtained using some second-generation sequencing technologies, along with sequencing reads amplified from single DNA molecules, facilitate detection of subclones of cells in tumors. Large-scale genome sequencing of hundreds or even thousands of cancer samples is being conducted by several groups that aim to identify and characterize cancer driver mutations. Goals of such work, previously infeasible with Sanger sequencing instruments, are to use this information to improve cancer prognosis, diagnosis and therapeutic decision-making. The speed of data analysis is rate limiting, and investigators are struggling to accommodate and interpret the data deluge produced by second-generation technologies. In this chapter, we discuss cancer properties that are revealed by sequencing and the implication of such properties in experimental design and data interpretation. We describe past, current and upcoming sequencing technologies and the application of second-generation sequencing technologies in cancer genomics. Finally, we discuss the impact of second-generation sequencing technology in shaping personalized medicine.
