What technique would we use to determine

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What technique would we use to determine whether
a certain gene was transcribed in cancer cells?
A Northern Blot
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What technique would we use to determine which
of 10 different genes were transcribed in cancer
cells?
Lots of Northern Blots
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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
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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
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Microarray
DNA Array
DNA Chip
Bio Chip
Gene Chip
Genome Chips
Gene Array
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Can get 500,000 spots on one slide (representing
that many different sequences)
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Two basic kinds of microarrays Genomic
cDNA
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Genomic Microarray
Each spot is a single-stranded oligonucleotide
(25 bases long) that represents part of the
coding region of a gene.
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Robots are used to spot these DNA
oligonucleotides Click here to see a video
showing this..
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cDNA Microarray
Each spot is a single-stranded cDNA from a
specific tissue or organ.
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cDNA
Genomic Chip
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Non-Cancer Cell
cDNA
cDNA
?
?
Genomic Chip
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Non-Cancer Cell
cDNA
cDNA
Genomic Chip
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Non-Cancer Cell
cDNA
cDNA
What if we incubated both of these pools of cDNA
on a microarray?
?
Genomic Chip
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Non-Cancer Cell
cDNA
cDNA
What if we incubated both of these pools of cDNA
on a microarray?
Genomic Chip
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Transcription in one tissue
Transcription in both
Transcription in another tissue
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Transcription in one tissue
Transcription in both tissues
Transcription in another tissue
dark spots no transcription at all
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Microarrays are becoming very useful in
diagnosing whether cancer cells are malignant.
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Researchers can now predict that a breast tumor
is malignant with 83 accuracy. 2002.
Bone Scan of a metastatic breast cancer patient.
cancer
BMC Nuclear Medicine, 2004, Vol. 4, p.3
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Cancer Research, October 15, 2005
Called Gene Expression Profiling because you
are looking at lots of genes at once.
Almost fully predictive
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Another example
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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.
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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 middleregulates 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
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The most important locus CYP450-2D6 .there
are 33 possible alleles at this locus.
All you need is blood sample from patient..
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Microarray
Extra versions
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First commercial example of a personalized DNA
Chip.
Switzerland
FDA approved for clinical use in 2005.
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What are some potential non-medical uses for
Microarrays?
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Non-Cancer Cell
cDNA
cDNA
What if we incubated both of these pools of cDNA
on a microarray?
Genomic Chip