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Integrated Molecular Analyses of Biological Samples on a Bead‑Based Microarray Platform

This chapter appears in the following book:

Integrated Biochips for DNA Analysis

Edited by: Robin Hui Liu and Abraham P. Lee
ISBN: 978-0-387-76758-1
» Get more information about this book at landesbioscience.com «

Chapter authors:
Joanne M. Yeakley, Daniel A. Peiffer, Marina Bibikova, Tim McDaniel, Kevin L. Gunderson, Richard Shen, Bahram G. Kermani, Lixin Zhou, Eugene Chudin, Shawn C. Baker, Kenneth M. Kuhn, Frank Steemers, Mark Hansen, Michael Graige , Celeste McBride, Steven Barnard, Bob Kain, David Barker and Jian-Bing Fan


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Molecular analyses of biological samples have traditionally been pursued in parallel, with those researchers studying genetic diversity having few technical approaches in common with those studying gene expression. Increasingly, scientists recognize the importance of integrating analytical technologies to further research, particularly into emerging fields such as epigenetics and the genetics of gene expression. In this chapter, we describe a suite of applications that take advantage of the Illumina® bead‑based microarrays, all of which are read out on a single analytical instrument. The integration of whole genome genotyping, high throughput focused genotyping, whole transcriptome expression profiling, focused expression profiling of fresh or preserved tissues, allele‑specific expression profiling and DNA methylation assays on the BeadArray™ Reader allows researchers to expand their perspectives, from whole genomes to single bases, from genetics to expression and on to epigenetics.

Joanne M. Yeakley
Illumina, Inc.

Daniel A. Peiffer
Illumina, Inc.

Marina Bibikova
Illumina, Inc.

Tim McDaniel
Illumina, Inc.

Kevin L. Gunderson
Illumina, Inc.

Richard Shen
Illumina, Inc.

Bahram G. Kermani
Illumina, Inc.

Lixin Zhou
Illumina, Inc.

Eugene Chudin
Illumina, Inc.

Shawn C. Baker
Illumina, Inc.

Kenneth M. Kuhn
Illumina, Inc.

Frank Steemers
Illumina, Inc.

Mark Hansen
Illumina, Inc.

Michael Graige
Illumina, Inc.

Celeste McBride
Illumina, Inc.

Steven Barnard
Illumina, Inc.

Bob Kain
Illumina, Inc.

David Barker
Illumina, Inc.

Jian-Bing Fan
Illumina, Inc.

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