BIOARRAYS FROM BASICS TO DIAGNOSTICS PDF

10 matches Bioarrays Bioarrays From Basics to Diagnostics Edited by. Krishnarao Appasani, PhD, MBA Founder and CEO GeneExpression Systems, Inc. Bioarrays: From Basics to Diagnostics provides an integrated and comprehensive collection of timely articles on the use of bioarray techniques. Bloarrays: From Basics to Diagnostics Krishnarao Appasani, PhD, MBA Humana Press: , pages ISBN & ISBN-1 3:

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From Basics to Diagnostics Home Bioarrays: From Basics to Diagnostics. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher.

All papers, comments, opinions, conclusions, or recommendations are those of the author sand do not necessarily reflect the views of the publisher. This publication is printed on acid-free paper. Oligoarray background was supplied by Dr. Fero of the Stanford Functional Genomics Facility. Droplet from the finger image was originally drawn by Dr. Brown of the Stanford University Biochemistry Department and reproduced here with permission.

Cover design by Raghu K. For those organizations that have been granted a photocopy license from the CCC, a separate system of payment has been arranged and is acceptable to Humana Press Inc. The fee code for users of the Transactional Reporting Service is: Printed in the United States of America.

Includes bibliographical references and index.

Oligonucleotide Array Sequence Analysis. QU B ] RB Burma Foreword It seems a while since it was possible frok one person to bioarrayz abreast of all aspects of microarrays. Early in the development of the technology there were few fabrication methods, the amount of data generated was small enough that a human could comprehend it without too much help from computers, and there was a handful of publications on the topic.

But that changed around ten years ago with the advent of the application of arrays to gene expression analysis. And now the field is so wide that it embraces a number of quite narrow specialisations; there are people whose careers are founded on array bioinformatics or whose working day ciagnostics largely filled in sample preparation for microarrays. The technology continues to advance along many paths. New modes of use, such as array CGH, appear frequently and spawn a range of applications.

There can be few areas of biology that do not use the technology. For those of us who have been in the field since its beginning, it is satisfying to see the technology producing research data that could not be obtained in any other way, buoarrays which is advancing so many fields.

Bioarrays : From Basics to Diagnostics (2007, Hardcover)

None is more satisfying than the advances in disease research, where the molecular characterisation of genetic and infectious diseases is laying the foundations for new diagnostics and treatments. From Basics to Diagnostics is a timely review of applications of arrays to human biology and to human disease. The articles illustrate the flexibility of the technology and its great potential. But reading these reviews makes it clear that array technology is only a part of the picture.

Some of the biological systems addressed by the technology, interacting networks of gene expression, for example, are complex and several chapters stress the need in such cases for careful experimental design and data interpretation. These are extremely important issues. These chapters are a timely reminder that the technology, if carelessly applied, can lead to poor data that may be difficult to correct.

Most of the experience with arrays has been with nucleic acids. The main reason for this is the simplicity of the relationship between analyte and probe molecules, which relies on the rules of Watson-Crick base pairing. There are easy ways to make probes by replicating clones, cDNA or genomic DNA, or by synthesising oligonucleotides using the efficient chemistry developed in the s: No simple relationship exists for any other type of analyte.

It is, of course, possible to make arrays from antibodies to proteins and examples are described in this volume, but the process is an empirical one and the rules of interaction between antibody and epitope are not so well understood.

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However, it is also clear that a description of proteins and their modifications is a necessary complement to the description of the genes and their RNA products. It is testament to the power and effectiveness of the array platform that this large investment in reagents for protein analysis is seen to be worthwhile.

The articles in this volume address these issues and make clear that microarrays have proven their value as research tools. Their future as diagnostic devices is also vii viii Foreword addressed; much effort is going into discovering reagents that can be used in routine testing.

However, it seems unlikely that the tests that will emerge from this research will be carried out on the discovery platform. Migration to diagnostics is well under way, but simpler, quicker and cheaper methods and devices will be needed to translate the technology to the point of care or to the testing laboratory. This, in turn, will feed back to improve the standard of work done in basic research settings. The technology has come a long way in the past decade.

It still has far to go. The chapters in Bioarrays: From Basics to Diagnostics present a fascinating view of the field at this interesting point in the journey. Edwin Southern Oxford, December Preface Molecular Biology was once considered to be a completely useless subject, remote from medical applications, and of only academic interest.

But now molecular biology may help create a new public health paradigm. Gene expression or genomics is the branch of molecular biology that describes the functional architecture of genes. The wealth of genetic information revealed from genome sequencing projects, in combination with the discovery of array technology, has paved the way for a new discipline—molecular diagnostics—within which scientists can dissect and understand the molecular pathogenesis of the biological cell.

The use of biological arrays became a routine practice in several molecular, cell biological, and toxicological laboratories around the globe, and the technology is collectively referred as BioArrays or BioChips. From Basics to Diagnostics is focused primarily on applications in molecular diagnostics, bioarrays have potential applications in biology, medicine, and agriculture.

From Basics to Diagnostics is mainly intended for readers in the molecular cell biology, genomics, and molecular diagnostics fields.

It will also be useful in advanced graduate level courses, as well as interesting to those in biotechnology and molecular medicine.

Although a number of books already cover array technology, Bioarrays: From Basics to Diagnostics differs from its ffom The book focuses on the concepts of oligonucleotide, cDNA, protein, antibody, and carbohydrate arrays, in 17 chapters, grouped into four parts.

The chapters are written by experts in the field, from both academic and industrial backgrounds. This book will serve as a reference for graduate students, postdoctoral researchers, and professors from academia and as an explanatory analysis for executives, and scientists in biotechnology and pharmaceutical companies.

My hope is that Bioarrays: From Basics to Diagnostics will provide both a prolog to bioarrays for newcomers and insight to those already active in the field.

Edwin Southern at the University of Oxford first baics a way to basice inkjet printing to show oligonucleotide sequences on glass slides in the late s. Subsequently, his group demonstrated the first array of all octapurines in a simple eight-step process by using in-house combinatorial chemistry approaches.

During the early s Stephan Fodor at Affymetrix, using photolithography-based methods, developed the miniaturized oligonucleotide array of eight nucleotides. At the same time, Patrick Brown at Stanford University devised an essentially different array fabrication method.

Brown proposed and demonstrated for the first time an arrangement ix x Preface of already-synthesized snippets of DNA placed at regular intervals on a glass surface by a robot. The same technology platform was extended later to development of protein arrays, glycoarrays, and tissue arrays, jointly referred to as bioarrays or biochips.

Before the discovery of this bioarray technology, only a limited number of techniques were available such as, differential display or serial analysis of gene expression for investigating gene expression and regulation.

Bioarrays : From Basics to Diagnostics (, Hardcover) | eBay

However, use of microarrays paved new avenues to study expression profiling the process of measuring simultaneously the expression of thousands of individual genes in a given biological sample. Use of microarrays became a routine practice for studying gene expression. Current bioarray platforms also allow the analysis of the function, expression, and disease involvement of several thousands of genes.

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However, in reality, the discovery of only a few good genes is enough for the routine clinical molecular diagnostics that have emerged recently. Use of bioarrays falls under the new subject of Systemomics, or the holistic study of expression profiling gene, protein, lipid, and drugfunction, physiological circuits, and developmental networks in human animal body systems.

Several innovators like Fodor envisioned these developments almost 15 years ago. Despite their proof-ofconcept papers, which are reviewed here, microarray-based diagnostics had to wait several more years to become a routine tool in the clinical diagnostics laboratories, a development hastened by studies of cancer prognosis, prediction, and classification.

In the last decade, DNA microarray research has provided a wealth of information on gene expression. From a simple technique to analyze gene expression patterns of relatively few genes, microarrays have evolved into indispensable tools for scientists in biomedicine.

Characterizing cancer-gene expression patterns from a systems perspective will also involve understanding the protein—protein networks and transcriptional regulatory programs. Protein chip technologies are helping academicians to better understand the basic research. Proteomics approaches are uniquely useful in biomarker discovery and subsequent immunoassay development.

Therefore, proteomics can be seen as a platform for identifying new analytes for the diagnostic industry, rather than just a tool. Antibody microarrays are also useful because they can measure protein abundance independently of gene expression, unlike the DNA microarrays.

It is known that changes in gene expression do not always correlate with protein expression. Patterns of protein expression can be used to diagnose disease or determine appropriate treatment for patients. In addition, antibody arrays can be used to study protein expression in tumor cells, phosphorylation states of cellular proteins, and posttranslational modifications of proteins.

In contrast, tissue microarrays will allow researchers to validate the targets identified from the DNA and protein arrays in a high-throughput manner by using immunohistochemistry and in situ hybridization methods.

The advantage conferred by tissue microarray validation is pivotal to rapid screening of several hundreds of different Dixgnostics xi types of tumors, where a specific protein is studied in different tumor histogenesis pathways. This approach is particularly useful in the screening of new genes and antibodies, and it is ideal for target-specific therapeutic development.

Many of the applications mentioned here are described in the four parts of Bioarrays: From Basics to Diagnostics, and a summary of each part can be found in the intro-duction on each part title page. In the near future, we will be able to use molecular signatures or panels of multiplexed biomarkers to identify whether a tumor is malignant or benign, its site of origin, its prognostic subtype, and even predict its response to therapy.

Clearly, high-throughput approaches and bioinformatics will have a primary role in future clinical oncology and pathology. To fully realize the potential of biomarkers to aid in drug development, industry must implement best practices for biomarker development, and promote translational research strategies.

However, the biggest obstacle to translating discovery from bench to bedside is not only technological but regulatory. It is possible that no single type of assay, DNA based or protein based, will be able to completely replace the biorrays type. However, in a nutshell, array technology indeed has the potential to accommodate all required assay formats on one testing platform, and to provide better reagents for pathological diagnosis in the future.

Many people have contributed to making my involvement in this project possible. I thank my teachers throughout my life for their excellent teaching, guidance, and mentoring, which led me to become a scientist, and to bring baaics educational enterprise of editing to readers.