Cancer Genomics for the Clinician

• Author : Ramaswamy Govindan, MD,Ashiq Masood, MD
• Publisher : Springer Publishing Company
• Release : 28 January 2019

Cancer Genomics for the Clinician is a practical guide to cancer genomics and its application to cancer diagnosis and care. The book begins with a brief overview of the various types of genetic alterations that are encountered in cancer, followed by accessible and applicable information on next generation sequencing technology and bioinformatics; tumor heterogeneity; whole genome, exome, and transcriptome sequencing; epigenomics; and data analysis and interpretation. Each chapter provides essential explanations of concepts, terminology, and methods. Also included are tips

• Author : Robert L. Strausberg
• Publisher : IOS Press
• Release : 28 March 2023

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.

• Author : Graham Dellaire,Jason N Berman,Robert J. Arceci
• Publisher : Academic Press
• Release : 21 November 2013

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

• Author : Moamen Bydoun,Paola Marcato,Graham Dellaire
• Publisher : Elsevier Inc. Chapters
• Release : 21 November 2013

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,

• Author : Katayoon Kasaian,Yvonne Y. Li,Steven J.M. Jones
• Publisher : Elsevier Inc. Chapters
• Release : 21 November 2013

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.

• Author : Michael Fraser,Alejandro Berlin,Veronique Ouellet,Fred Saad,Robert G. Bristow
• Publisher : Elsevier Inc. Chapters
• Release : 21 November 2013

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.

• Author : Hye-Jung E. Chun,Jaswinder Khattra,Martin Krzywinski,Samuel A. Aparicio,Marco A. Marra
• Publisher : Elsevier Inc. Chapters
• Release : 21 November 2013

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

• Author : Ulrich Pfeffer
• Publisher : Springer Science & Business Media
• Release : 12 February 2013

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

• Author : Matthew Parker,Erin Hedlund,Jinghui Zhang
• Publisher : Elsevier Inc. Chapters
• Release : 21 November 2013

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

• Author : Shile Zhang,Jun S. Wei,Javed Khan
• Publisher : Elsevier Inc. Chapters
• Release : 21 November 2013

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

• Author : Jason N. Berman,Priscilla P.L. Chiu,Graham Dellaire
• Publisher : Elsevier Inc. Chapters
• Release : 21 November 2013

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

• Author : Louise Parker
• Publisher : Elsevier Inc. Chapters
• Release : 21 November 2013

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

• Author : Daniel Gaston,Carman Giacomantonio
• Publisher : Elsevier Inc. Chapters
• Release : 21 November 2013

Colorectal cancer (CRC) is the third most common form of cancer and a leading cause of cancer-related mortality in both men and women, particularly in Western and developed nations. The high mortality rate has been attributed to the fact that colon cancer is often diagnosed at a late stage. Three primary subtypes of CRC have been described based on their molecular pathology and their underlying genetics: chromosomal instability (CIN), microsatellite instability (MSI), and CpG island hypermethylation. Over the last 30 years,

• Author : Hui Ling,George A. Calin
• Publisher : Elsevier Inc. Chapters
• Release : 21 November 2013

The discovery of microRNA (miRNA) involvement in cancer a decade ago, and the more recent findings of long non-coding RNAs in human diseases, challenged the long-standing view that RNAs without protein-coding potential are simply “junk” transcription within the human genome. These findings evidently changed the dogma that “DNA makes RNA makes protein” by showing that RNAs themselves can be essential regulators of cellular function and play key roles in cancer development. MiRNAs are evolutionarily conserved short single-stranded transcripts of 19–24 nucleotides

• Author : Branavan Manoranjan,Parvez Vora,Chitra Venugopal,Sheila K. Singh
• Publisher : Elsevier Inc. Chapters
• Release : 21 November 2013

The classification of brain tumors has evolved from a morphological and histological basis to one that is now in keeping with the advances of modern technology consisting of novel molecular subgroups rooted in clinical outcome and risk stratification. In this chapter, we discuss recent and emerging genomic findings that may be of clinical utility in the foreseeable future for adult and pediatric glioblastoma, pediatric medulloblastoma, ependymoma, and diffuse intrinsic pontine glioma. Moreover, limitations in the current molecular classification of these