Shotgun Microarrays: High-throughput Validation of Gene Expression Changes Using Multiple Platforms
Roderick
V.
Jensen
Wesleyan
University
and
Brigham
and
Women's
Hospital/
Harvard
Medical
School
DNA
Microarrays
have
emerged
as
important
new
tools
for
the
large-scale
measurement
of
differential
gene
expression
in
a
wide
variety
of
biomedical
experiments,
comparing
normal
and
diseased
tissues,
different
states
of
biological
processes,
and
the
response
to
drugs
or
toxins.
A
single
cDNA
or
oligonucleotide
microarray
can
provide
detailed
quantitative
information
on
the
levels
of
expression
of
thousands
of
genes.
However,
as
with
any
laboratory
measurement,
this
data
is
subject
to
errors.
To
identify
real
changes
in
gene
expression
it
is
essential
to
understand
and
model
the
sources
of
errors
in
these
measurements.
Our
laboratory
has
performed
extensive
studies
of
microarray
data
from
multiple
microarray
platforms
including
homemade
cDNA
arrays,
Amersham/Motorola
CodeLink
arrays,
Agilent
in
situ
microarrays,
and
the
popular
Affymetrix
GeneChips.
The
comparison
of
differential
gene
expression
measurements
both
within
and
across
platforms
provides
the
basis
for
statistical
error
models
essential
for
the
useful
interpretation
of
the
data.
Our
"shotgun
microarray"
approach
has
successfully
identified
gene
expression
signatures
in
a
variety
of
different
applications
ranging
from
the
distinction
of
normal
human
tissues,
to
the
classification
of
cancer,
to
the
identification
of
genomic
differences
in
young
and
old
tissue
samples.