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GeneChip® Exon Array Design
The primary objective for the design of
this first-generation GeneChip® Exon
Array is to interrogate each potential
exon with one probe set over the entire
genome on a single array. With this array,
researchers are able to cost-effectively
analyze gene expression at the level of
transcript diversity on a whole-genome
scale for the first time.
This Technical Note describes in detail
the implementation of the exon array
design concept and provides a summary
of the array content and probe selection
results using the GeneChip® Human
Exon 1.0 ST Array (Sense Target) as an
example. In particular, changes in this
design are compared and contrasted
with existing arrays, such as the
GeneChip® Human Genome U133 Plus
2.0 Array, in order to highlight the
implications and advantages of using
the Human Exon 1.0 ST Array for
expression analysis.
Technical Note
GeneChip® Exon Array Design
Introduction
On the GeneChip® Human Exon 1.0 ST
Array, 5,362,207 features are used to
interrogate one million exon clusters (col-
lections of overlapping exons) with over
1.4 million probe sets. Probe sequences
were selected using the high-quality
human genome assembly (July 2003,
hg16, build 34) and a variety of genome
annotations including those inferred from
human, mouse, and rat cDNAs (Appendix
1, Appendix 2, and Appendix 3). A number
of publicly available gene prediction sets
were also used (Appendix 4 and Appendix 5)
including Ensembl, GENSCAN, and Vega.
Implementation of the Exon
Array Design Concept
PROBE SELECTION REGIONS, EXON CLUSTERS,
TRANSCRIPT CLUSTERS, AND GENES
One significant feature of this exon array
design is that the various input sequences
and annotations were consolidated onto
the genome and then divided into probe
selection regions (PSRs). The PSRs are
contiguous and do not overlap in genomic
space. An example of PSRs resulting from
the consolidation process for the GeneChip®
Human Exon 1.0 ST Array is shown in
Figure 1.
The co