Download Microarrays

What technique would we use to determine
whether a certain gene was transcribed
in cancer cells?
A Northern Blot
What technique would we use to determine
which of 10 different genes were transcribed
in cancer cells?
Lots of Northern Blots
What technique would we use to determine
which of 100 different genes were transcribed
in cancer cells?
A Microarray (Gene Chip)
Pages 208-211 in your book
What technique would we use to determine
the identity of unknown genes that were
transcribed in cancer cells?
A Microarray (Gene Chip)
Pages 208-211 in your book
Microarray
Bio Chip
Genome Chips
DNA Chip
DNA Array
Gene Chip
Gene Array
Can get 500,000 spots on
one slide (representing that
many different sequences)
Two basic kinds of microarrays:
Genomic & cDNA
Genomic Microarray
Each spot is a single-stranded oligonucleotide
(25 bases long) that represents part of the coding
region of a gene.
Robots are used to spot these DNA oligonucleotides
Click here to see a video showing this…..
cDNA Microarray
Each spot is a single-stranded cDNA
from a specific tissue or organ.
cDNA
Genomic Chip
Non-Cancer Cell
cDNA
cDNA
A
?
?
Genomic Chip
Non-Cancer Cell
cDNA
cDNA
A
Genomic Chip
Non-Cancer Cell
cDNA
cDNA
A
What if we incubated both of these
pools of cDNA on a microarray?
?
Genomic Chip
Non-Cancer Cell
cDNA
cDNA
A
What if we incubated both of these
pools of cDNA on a microarray?
Genomic Chip
Transcription in one tissue
Transcription in both
Transcription in another tissue
Transcription in one tissue
Transcription in both tissues
Transcription in another tissue
…dark spots = no transcription at all
Microarrays are
becoming very useful
in diagnosing whether
cancer cells are
malignant.
Bone Scan of a metastatic breast cancer patient.
Researchers can now
predict that a breast
tumor is malignant
with 83% accuracy.
2002.
cancer
BMC Nuclear Medicine, 2004, Vol. 4, p.3
Cancer Research, October 15, 2005
Called “Gene Expression Profiling” because
you are looking at lots of genes at once.
Almost fully predictive
Another example
2nd largest organ in the body (3 lbs)
Cytochrome P450 family of enzymes in
liver that breakdown medicines. There are
about 57 genes with each gene having
large numbers of alleles.
One Cytochrome P450 locus is particularly important in controlling how quickly we
metabolize drugs like anti-depressants, anti-psychotics, immuno-supressants,
cardiacs, pain-killers, and anti-cancer agents. For instance, Codeine gets converted
to morphine-like substances in your body due to this enzyme. Some people are fast
metabolizers while others are practically non-metabolizers, while most are
somewhere in the middle…regulates efficacy of medicine, toxic effects of medicine,
side effects.
There are 100,000 deaths in the U.S. every year due to adverse reactions to
medicines
The most important locus = CYP450-2D6 ….there are 33
possible alleles at this locus.
All you need is blood sample from patient…..
Microarray
Extra versions
First commercial example of
a personalized DNA Chip.
Switzerland
FDA approved for clinical
use in 2005.
What are some potential non-medical uses
for Microarrays?
Non-Cancer Cell
cDNA
cDNA
A
What if we incubated both of these
pools of cDNA on a microarray?
Genomic Chip