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 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 in your book

Microarray DNA Chip Bio Chip Gene Chip DNA Array Gene Array Genome 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…..here

cDNA Microarray Each spot is a single-stranded cDNA from a specific tissue or organ.

cDNA Genomic Chip

Non-Cancer Cell cDNA ? A ? Genomic Chip

A Non-Cancer Cell cDNA Genomic Chip

A Non-Cancer Cell cDNA ? What if we incubated both of these pools of cDNA on a microarray? Genomic Chip

A Non-Cancer Cell cDNA 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 now predict that a breast tumor is malignant with 83% accuracy 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

Cytochrome P450 family of enzymes in liver that breakdown medicines. There are about 57 genes with each gene having large numbers of alleles. 2 nd 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 clinical use in First commercial example of a personalized DNA Chip. Switzerland

What are some potential non-medical uses for Microarrays?

A Non-Cancer Cell cDNA Genomic Chip What if we incubated both of these pools of cDNA on a microarray?