Sample A: Cover Page of Thesis, Project, or Dissertation Proposal

Chapter 1: An Introduction to Microarrays
Gene expression Microarray technology is a high throughput capture detection assay that
produces a fairly complete representation of a sample’s genome-wide transcript complement [1,
2]. The assay has been predominately utilized for gene expression experiments, but
modifications in probe design allow the use of this platform for single nucleotide polymorphism
and comparative genome hybridization experiments [3-5]. The array concept is a capture
detection assay as developed from Northern and Southern blots [5, 6], and this detection method
has spawned analogous methods such as the immunological assays known as ELISAs (enzyme
linked immunosorbent assays) [7]. Unfortunately, for most platforms, rigorous experimental
design has been sacrificed in order to rapidly achieve high throughput genome-wide analysis, but
we have developed a number of assessment strategies for the individual probes that allow us to
ascertain the reliability of individual measurements.
Our focus here is upon gene expression analysis, and particularly those performed using the
Affymetrix platform [8], which has the benefits of sampling transcripts multiple times, and
having probes short enough to be sensitive to individual differences in sequence [8, 9]. For gene
expression Microarray analysis, mRNA transcripts are extracted from a collection of cells, which
can represent anything from a pure culture to a cryogenically preserved and laser-dissected tissue
sample. These mRNA samples can be sheared, transformed or otherwise amplified into cDNA or
cRNA ‘targets’, and at some part of the protocol they are labeled, most often with a fluorescent
dye [5].
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