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Cancer Genomics

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Cancer Genomics

Cancer Genomics Book
Author : Graham Dellaire,Robert J. Arceci
Publisher : Elsevier Inc. Chapters
Release : 2013-11-21
ISBN : 0128060980
Language : En, Es, Fr & De

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Book Description :

From the first descriptions of cancer in Egypt around 3000 BC to our current “one week” whole-genome sequence, the history of integrating new ideas into the practice of medicine has been unrelenting, although not without its failures as well its successes. This chapter represents a brief historical summary of some of the key success stories in our understanding of cancer that has led to our current age of cancer genomics. As the Chinese proverb states, “When you drink from the well, remember who dug it”, and reflecting on this rich and varied history, we conclude the chapter with a discussion of current and future challenges to the application of our new and developing understanding of cancer genomes to patient therapy.

Cancer Genomics and Proteomics

Cancer Genomics and Proteomics Book
Author : Narendra Wajapeyee
Publisher : Humana Press
Release : 2014-07-17
ISBN : 9781493909933
Language : En, Es, Fr & De

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Book Description :

Cancer Genomics and Proteomics: Methods and Protocols, Second Edition includes methods for the analyses of cancer genome and proteome that have illuminated us about the changes in cancer cells. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Cancer Genomics and Proteomics: Methods and Protocols, Second Edition seeks to aid scientists in the further study into various aspects of tumor initiation and progression.

Cancer Genomics

Cancer Genomics Book
Author : Zhaolin Xu
Publisher : Elsevier Inc. Chapters
Release : 2013-11-21
ISBN : 012806109X
Language : En, Es, Fr & De

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Book Description :

Lung cancer remains the leading cause of cancer-related death worldwide. Although surgical resections of these tumors are considered as one of the most effective treatments, most lung cancer patients present at an advanced stage of the disease at the time of diagnosis and are not candidates for surgical resection. Overall, the prognosis of lung cancer is very poor and the 5-year survival rate is only about 16 %, which has not significantly changed in the past several decades. Therefore, seeking new directions of treatment for this most deadly disease becomes crucial. Recent development in the understanding of the molecular pathogenesis of lung cancer has led to new strategies of treatment. Development of lung cancers is thought to be driven by gene mutations in most, if not all, cases. Detailed analysis at the molecular level to identify these gene mutations or alterations in lung cancer provides the insight for understanding the disease and is fundamental for establishment of personalized targeted therapy. Personalized targeted therapy based on particular gene mutations has shown to be effective and is believed to be one of the new directions of the treatment in dealing with this disease. In modern oncology, there is an increasing need to facilitate the development and implementation of biomarkers based on known gene mutations/alterations in clinical practice and identification of new gene mutations/alterations through high-throughput DNA sequencing technology to enter a new era of personalized targeted therapy for lung cancer patients.

Cancer Genomics and Proteomics

Cancer Genomics and Proteomics Book
Author : Eden Dennis
Publisher : Unknown
Release : 2015-03-09
ISBN : 9781632420664
Language : En, Es, Fr & De

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Book Description :

The book focuses on the field of cancer genomics and proteomics. It has been compiled with elaborative reviews of the most general cancers, from bench to bedside applications by an internationally renowned team of veterans and it will certainly contribute to the medical and scientific community by illustrating updated discoveries of oncogenomics and their potential applications in cancer translational research. This comprehensive book aims to serve as a useful resource for clinicians, students, oncologists, scientists and health professionals engaged in cancer research.

Cancer Genomics

Cancer Genomics Book
Author : Ryan D. Morin,Stephen B. Montgomery
Publisher : Elsevier Inc. Chapters
Release : 2013-11-21
ISBN : 0128061006
Language : En, Es, Fr & De

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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.

Collaborative Genomics Projects A Comprehensive Guide

Collaborative Genomics Projects  A Comprehensive Guide Book
Author : Margi Sheth,Julia Zhang,Jean C Zenklusen
Publisher : Academic Press
Release : 2016-02-24
ISBN : 0128023686
Language : En, Es, Fr & De

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Book Description :

Collaborative Genomics Projects: A Comprehensive Guide contains operational procedures, policy considerations, and the many lessons learned by The Cancer Genome Atlas Project. This book guides the reader through methods in patient sample acquisition, the establishment of data generation and analysis pipelines, data storage and dissemination, quality control, auditing, and reporting. This book is essential for those looking to set up or collaborate within a large-scale genomics research project. All authors are contributors to The Cancer Genome Atlas (TCGA) Program, a NIH- funded effort to generate a comprehensive catalog of genomic alterations in more than 35 cancer types. As the cost of genomic sequencing is decreasing, more and more researchers are leveraging genomic data to inform the biology of disease. The amount of genomic data generated is growing exponentially, and protocols need to be established for the long-term storage, dissemination, and regulation of this data for research. The book's authors create a complete handbook on the management of research projects involving genomic data as learned through the evolution of the TCGA program, a project that was primarily carried out in the US, but whose impact and lessons learned can be applied to international audiences. Establishes a framework for managing large-scale genomic research projects involving multiple collaborators Describes lessons learned through TCGA to prepare for potential roadblocks Evaluates policy considerations that are needed to avoid pitfalls Recommends strategies to make project management more efficient

Stochastic Methods in Cancer Research Applications to Genomics and Angiogenesis

Stochastic Methods in Cancer Research  Applications to Genomics and Angiogenesis Book
Author : Paola M. V. Rancoita
Publisher : Ledizioni
Release : 2011
ISBN : 8895994582
Language : En, Es, Fr & De

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Book Description :

In this thesis, I study three stochastic methods that can be applied for the analysis of data in cancer research and, in particular, to cancer genomic data and to images of angiogenic processes. Cancer is a multistep process where the accumulation of genomic lesions alters cell biology. The latter is under control of several pathways and thus, cancer can arise via different mechanisms affecting different pathways. Due to the general complexity of this disease and the different types of tumors, the efforts of cancer research cover several research areas such as, for example, immunology, genetics, cell biology, angiogenesis.

Cancer Genomics

Cancer Genomics Book
Author : Robert L. Strausberg
Publisher : IOS Press
Release : 2002
ISBN : 9781586032517
Language : En, Es, Fr & De

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Book Description :

This work states that we are no longer satisfied to study a gene or gene product in isolation, but rather we strive to view each gene within the complex circuitry of a cell. It states that as a family of diseases, all cancer results from changes in the genome.

Cancer Genomics

Cancer Genomics Book
Author : Graham Dellaire,Jason N Berman,Robert J. Arceci
Publisher : Academic Press
Release : 2013-11-21
ISBN : 0123972744
Language : En, Es, Fr & De

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Book Description :

Cancer Genomics addresses how recent technological advances in genomics are shaping how we diagnose and treat cancer. Built on the historical context of cancer genetics over the past 30 years, the book provides a snapshot of the current issues and state-of-the-art technologies used in cancer genomics. Subsequent chapters highlight how these approaches have informed our understanding of hereditary cancer syndromes and the diagnosis, treatment and outcome in a variety of adult and pediatric solid tumors and hematologic malignancies. The dramatic increase in cancer genomics research and ever-increasing availability of genomic testing are not without significant ethical issues, which are addressed in the context of the return of research results and the legal considerations underlying the commercialization of genomic discoveries. Finally, the book concludes with "Future Directions", examining the next great challenges to face the field of cancer genomics, namely the contribution of non-coding RNAs to disease pathogenesis and the interaction of the human genome with the environment. Tools such as sidebars, key concept summaries, a glossary, and acronym and abbreviation definitions make this book highly accessible to researchers from several fields associated with cancer genomics. Contributions from thought leaders provide valuable historical perspective to relate the advances in the field to current technologies and literature.

Cancer Genomics

Cancer Genomics Book
Author : Moamen Bydoun,Paola Marcato,Graham Dellaire
Publisher : Elsevier Inc. Chapters
Release : 2013-11-21
ISBN : 0128061103
Language : En, Es, Fr & De

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Book Description :

Breast cancer is the most common cancer in women worldwide and the second leading cause of cancer deaths. Although early diagnosis, outcome prediction and treatment options are the ultimate objectives when assessing breast cancer patients, the methodology behind this clinical assessment varies and has gradually evolved from using standard clinical criteria into incorporating high-throughput genome-wide analysis. Early methods involved evaluating tumor size and spread as well as histological assessment (tumor grade). Later, the expression of hormone/growth receptors (ER, PR, and HER2) was added to the standard stratification of breast cancer patients. More recently, molecular approaches, which are based on the expression of a well-defined set of genes, have subdivided patients into five clinically relevant subtypes which not only predict prognosis and dictate treatment choice but also complement standard assessment. The advent of genome-wide analysis has produced the most robust classification system of breast cancers by coupling specific genetic aberrations (single nucleotide mutations and gene copy number variations) with gene expression profiles. Although these genome-wide approaches offer a promising future for breast cancer prognosis and treatment options, they are still not clinically feasible for standard population-based screening. Nonetheless, these approaches are becoming faster and more reliable in understanding the molecular architecture of breast cancer and are slowly paving the way towards personalized treatments which are tailored to individual patients. In the light of a rapidly evolving field of breast cancer genomics, this chapter highlights key standard and upcoming approaches for diagnosis, prognosis and treatment and discusses the feasibility of genome-oriented personalized treatments.

Cancer Genomics

Cancer Genomics Book
Author : Katayoon Kasaian,Yvonne Y. Li,Steven J.M. Jones
Publisher : Elsevier Inc. Chapters
Release : 2013-11-21
ISBN : 0128061065
Language : En, Es, Fr & De

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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.

Cancer Genomics

Cancer Genomics Book
Author : Michael Fraser,Alejandro Berlin,Veronique Ouellet,Fred Saad,Robert G. Bristow
Publisher : Elsevier Inc. Chapters
Release : 2013-11-21
ISBN : 0128061111
Language : En, Es, Fr & De

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Book Description :

Prostate cancer (CaP) is the most commonly diagnosed malignancy in men in the Western world. In North America, more than 275000 men are diagnosed annually whereby approximately 1 in 6 men will be diagnosed with CaP in their lifetime, and 1 in 34 men will die from castrate-resistant metastatic disease. Unfortunately, current clinical prognostic factors explain only a proportion of the observed variation in clinical outcome from patient to patient. Furthermore, over-treatment of indolent and low-risk cancers leads to inappropriate morbidity following radiotherapy or surgery. As such, better predictors of individualized prognosis and treatment response are urgently needed to triage patients to customized and intensified CaP treatment. Recent developments in next-generation sequencing have made it possible to identify prognostic and predictive signatures based on genomic profiles. Herein, we review the recent genetic data pertaining to prostate cancer carcinogenesis, progression, castrate-resistance and metastases. We discuss the genetic basis of CaP progression from localized to systemic disease (e.g. point mutations, copy number alterations and structural variants) and important considerations for CaP biology including intra- and inter-prostatic heterogeneity, multifocality and multiclonality, TMPRSS2–ERG and other ETS-family gene fusions and the role of the tumor microenvironment (e.g. hypoxia and the contribution of caner-associated stroma). Finally, we focus on the use of genomic markers as prognostic factors for local failure and for systemic disease, as novel risk stratification tools, in triaging patients to existing treatment options and, ultimately, the potential of genomics for the identification of molecular targets for CaP therapy. We conclude by summarizing selected outstanding questions in CaP biology that can be addressed effectively through international cooperation between genome sequencing projects such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC).

Cancer Genomics

Cancer Genomics Book
Author : Hye-Jung E. Chun,Jaswinder Khattra,Martin Krzywinski,Samuel A. Aparicio,Marco A. Marra
Publisher : Elsevier Inc. Chapters
Release : 2013-11-21
ISBN : 0128060999
Language : En, Es, Fr & De

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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.

Cancer Genomics

Cancer Genomics Book
Author : Matthew Parker,Erin Hedlund,Jinghui Zhang
Publisher : Elsevier Inc. Chapters
Release : 2013-11-21
ISBN : 0128061073
Language : En, Es, Fr & De

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Book Description :

The vast amount of genomic data being produced by the research community is becoming readily accessible to biomedical researchers and clinicians to apply to their cancer(s) of interest. The major cancer genome projects, among others, The Cancer Genome Atlas (TCGA), the International Cancer Genome Consortium (ICGC) and the Pediatric Cancer Genome Project (PCGP) are contributing to this genomic data goldmine by sequencing hundreds to thousands of cancer genomes and supplementing these data with analyses such as gene expression and methylation. In addition to the raw data that are being made available through large data warehouses, “Data Portals” are becoming the norm for accessing and analyzing these data by third parties. We describe key features of some of these portals and other tools for the analysis of next-generation sequencing and other genomic data.

Cancer Genomics

Cancer Genomics Book
Author : Shile Zhang,Jun S. Wei,Javed Khan
Publisher : Elsevier Inc. Chapters
Release : 2013-11-21
ISBN : 0128061014
Language : En, Es, Fr & De

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Book Description :

The complexity of the transcriptome has been appreciated in recent years in light of the Encyclopedia of DNA Elements (ENCODE) project. While less than 3% of the genome is annotated with protein-coding genes, 62% of the genome is long RNA molecules (>200 nucleotides). With an increasing sequencing throughput and a decreasing cost, RNA sequencing (RNA-seq) is becoming a frequently used technology in transcriptome research. This chapter summarizes the advantages of RNA-seq compared to hybridization-based microarrays, the RNA-seq experiment workflow and reviews current applications of RNA-seq in the field of cancer research. With advantages in expression analysis of non-coding genes, fusion genes, investigation of expressed allelic imbalance, pseudogenes, viral integrated genes, and post-transcriptional regulation analysis including splicing, polyadenylation as well as RNA editing, RNA-seq technology has a tremendous potential to elucidate the complexity of the transcriptome and its working mechanisms in the initiation and development of cancer. Along with expression and pathway analysis, RNA-seq data can clarify the functional consequences of any potential genomic (DNA) variances and thus help to distinguish “driver” from “passenger” genomic events. In summary, RNA-seq allows a genome-wide interrogation of complex transcriptomes and will help elucidate important biological mechanisms linked to cancer phenotypes. In addition, the non-protein-coding transcriptome has the potential to provide novel biomarkers for early detection, diagnostics, prognostics and targets for therapy.

Cancer Genomics

Cancer Genomics Book
Author : Ulrich Pfeffer
Publisher : Springer Science & Business Media
Release : 2013-02-12
ISBN : 9400758421
Language : En, Es, Fr & De

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Book Description :

The combination of molecular biology, engineering and bioinformatics has revolutionized our understanding of cancer revealing a tight correlation of the molecular characteristics of the primary tumor in terms of gene expression, structural alterations of the genome, epigenetics and mutations with its propensity to metastasize and to respond to therapy. It is not just one or a few genes, it is the complex alteration of the genome that determines cancer development and progression. Future management of cancer patients will therefore rely on thorough molecular analyses of each single case. Through this book, students, researchers and oncologists will obtain a comprehensive picture of what the first ten years of cancer genomics have revealed. Experts in the field describe, cancer by cancer, the progress made and its implications for diagnosis, prognosis and treatment of cancer. The deep impact on the clinics and the challenge for future translational research become evident.

Cancer Genomics

Cancer Genomics Book
Author : Jason N. Berman,Priscilla P.L. Chiu,Graham Dellaire
Publisher : Elsevier Inc. Chapters
Release : 2013-11-21
ISBN : 0128061057
Language : En, Es, Fr & De

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Book Description :

Genome-wide association (GWA) studies and tumor-specific epigenome, transcriptome and genome sequencing projects are generating an ever-growing list of susceptibility alleles, as well as putative gain- and loss-of-function gene mutations associated with cancer. These genetic changes ultimately need to be validated to determine their contribution to the initiation, progression and likelihood of treatment response for various cancers. The bottle-neck is no longer obtaining sequence data or completion of the GWA studies, but rather the ability efficiently to validate candidate genes identified by these projects. In vivo studies in animal models are the “gold standard” for validation of these candidate drivers and modifiers of cancer. Furthermore, once a gene product or molecular pathway has been validated as playing an important role in the development or progression of cancer, animal models provide the necessary preclinical data for evaluation of the efficacy and toxicity of new therapeutics targeting that gene or pathway. As such, animal models play an essential role in cancer research by facilitating the translation of genomic discoveries into preclinical studies that precede new targeted therapies for cancer. In this chapter, we will discuss vertebrate and invertebrate animal models as they apply to cancer genomics, as well as key technologies employed. In particular, we will focus on the use of murine and zebrafish human tumor xenografts and transgenic models.

Cancer Genomics

Cancer Genomics Book
Author : Louise Parker
Publisher : Elsevier Inc. Chapters
Release : 2013-11-21
ISBN : 0128061235
Language : En, Es, Fr & De

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Book Description :

The number of people diagnosed with cancer each year will almost double to 21 million cases worldwide by 2030 because of the aging population. Studies of the human genome have demonstrated that as few as 5–10% of adult cancers are due to genetic inheritance. Over 90% of cancers are due to endogenous or exogenous exposure to chemicals and radiation; many of these carcinogenic exposures, to tobacco smoke, for example, are avoidable and thus the consequent disease is preventable. The “exposome” is the concept which captures all carcinogenic exposures across the lifetime, quantified by direct biomarker assessment. Exposomics is in its infancy, but if progress such as has occurred in the Human Genome project occurs in this field, it has the potential greatly to enhance our understanding of the complex interactions and mechanisms of action of environmental exposures. In particular, evidence is increasing that cancer is as much a disease of the epigenome as the genome and that many of these environmental factors act to alter gene expression through changes in the epigenome. Exposomics will enable us better to avoid carcinogenic exposures, to limit the carcinogenic effect of these exposures and to identify potential new targets for developmental therapeutics.

Novel Computational Methods for Cancer Genomics Data Analysis

Novel Computational Methods for Cancer Genomics Data Analysis Book
Author : Jinpeng Liu
Publisher : Unknown
Release : 2021
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Novel Computational Methods for Cancer Genomics Data Analysis book written by Jinpeng Liu, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Cancer Genomics

Cancer Genomics Book
Author : David Malkin
Publisher : Elsevier Inc. Chapters
Release : 2013-11-21
ISBN : 0128061081
Language : En, Es, Fr & De

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Book Description :

Cancer is the most common cause of disease-related death in children beyond the newborn period. Most cancers are thought to arise sporadically; however, classical studies of well-defined familial cancer associations, known as cancer predisposition syndromes (CPS), together with emerging work arising from new high-resolution genomic platforms have confirmed that at least 25% of childhood cancers result from hereditary factors. The spectrum of cancers found in the diverse array of known hereditary cancer syndromes is vast. Similarly, the number of genes linked to these syndromes continues to expand. This chapter explores the genotype:phenotype correlations in several defined cancer predisposition syndromes that primarily affect children. In particular, a selection of syndromes that are caused by germline mutations in classical tumor suppressor genes (RB1, TP53, WT1) and oncogenes (RET), syndromes associated with congenital developmental anomalies (Beckwith–Wiedemann syndrome, Gorlin syndrome) and an emerging syndrome associated with microRNA processing (DICER1) provide examples of the heterogeneity that these syndromes exhibit. The chapter concludes with a discussion of the clinical impact of genetic testing and clinical surveillance for early cancer detection.