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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 - PowerPoint PPT Presentation
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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 DNA Chip
Bio ChipGene Chip
DNA Array
Gene ArrayGenome Chips
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 cDNAfrom a specific tissue or organ.
cDNA
Genomic Chip
Non-Cancer Cell
cDNA
?
A
cDNA
?
Genomic Chip
A
Non-Cancer Cell
cDNAcDNA
Genomic Chip
A
Non-Cancer Cell
cDNAcDNA
?
What if we incubated both of these pools of cDNA on a microarray?
Genomic Chip
A
Non-Cancer Cell
cDNAcDNA
Genomic Chip
What if we incubated both of these pools of cDNA on a microarray?
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 nowpredict that a breasttumor is malignantwith 83% accuracy.
2002.
cancer
BMC Nuclear Medicine, 2004, Vol. 4, p.3
Cancer Research, October 15, 2005
Called “Gene Expression Profiling” becauseyou are looking at lots of genes at once.
Almost fully predictive
Another example
Cytochrome P450 family of enzymes in liver that breakdown medicines. There are about 57 genes with each gene having large numbers of alleles.
2nd largest organ in the body (3 lbs)
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…..
Extra versions Microarray
FDA approved for clinicaluse in 2005.
First commercial example ofa personalized DNA Chip. Switzerland
What are some potential non-medical uses for Microarrays?
A
Non-Cancer Cell
cDNAcDNA
Genomic Chip
What if we incubated both of these pools of cDNA on a microarray?
