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The State of Microarrays
The Scientist: 2003
By: Hien Dang
A new “fab”

Microarrays
– What is Microarray?
– Microarray’s applications
– Great Challenges
– Everyone is doing it… why not you?
Microarrays… what is it?

Takes an array of orderly arrangement of
samples with thousands of florescent spots
that provides researchers information on
thousands of genes simultaneously
 A “fab” that’s going on today..
– Involves fast progress of collecting data
– Used for genomic research as well as many
others(proteomics, ecology,etc.)
Applications…

For DNA microarray…
– 1. Identification of sequence(gene/gene
mutation)
– 2. Determination of expression
level(abundance of genes)
Applications…

Protein Arrays
– Protein-to-protein interactions
– profiling antibody binding and specificity
Microarrays…

Accepted by many rapidly, technical
challenges remain
– 1. Universal Standardization Language
– 2. Data noise
– 3. Technological difficulties: Computers and
biologists don’t mix too well…
– 2. Probe length on specificity of oligo

Longer better, but cost more…
Universal Standardization
Language

Challenge: How do we understand global
microarray if its written in different
languages?
 Temporary Answer: MIAME(Minimal
Information About a Microarray
Experiment) adopted by MGEDS
Universal Standardization
Language

Conditional solution to
standardization issue
 For universal
interpretation of data
analysis
 However, not
everyone has adopted
this language
Data Noise



Challenge: Problem
persists base upon either
good or bad microarrays
Cross-hybridization and
significant use of RNA
during amplification
contribute to data noise
Temporary Answer:
None… Perhaps better
methods?
Computer Scientists vs.
Biologist

Challenge: Great
amount of data, where
to store? How to
analyze? What to do
with it? How to
share?
Computer Scientists vs.
Biologist

Temporary Answer:
GeneSifter.Net.
– Accessible to
everyone. Cost? Free.
Uses World Wide Web
to.
– Easy to use.
– Cheap. Easy.Excess
anywhere. what more
do you want?
Probe Length

Challenge: Affects of probe length on the
specificity of oligo microarrays generated
 Temporary Answer: Amersham Biosciences: A
new Array that eliminates hybridization problems.
– Putting oligo into a 3-D matrix using only a 30mer
sequence. Cheap

Affymetrix: 25-30mer put directly on chip using
comibatorial chemistry and photolithography
Everyone’s doing it…

The most rapid technology used in
molecular research today.
 Costs are high, however efficient.
 Many challenges yet to master.
 Fast data, beats traditional work.
Not really…






Many are skeptical about this new technology
“limited.. Results are hard to handle and interpret”
Results hard to understand
Just because you have result doesn’t mean you
know what it is
Blind researchers of an objective: A strong
hypothesis
just because everyone is doing it, I’m doing it
too…
Conclusion


The Scientist explores
many areas of microarrays
and allows the research
community to see the
good, bad and challenges
of microarrays.
How will this technology
affect you? Just about in
every aspect. This is a
“revolution” of research.
The Scientist 2003