DNA Microarray Activities

 

 

Activity 1:  Making your slide

 

You have a sheet with 15 different DNA sequences that are available. 

  1. Choose 4 sequences that you feel might be interesting. 
  2. Cut out the 4 sequences from the sheet. 
  3. Place each in one of the four squares on your DNA microarray sheet.

 

 

Activity 2:  Using your DNA microarray

 

Get together with two or three other people.  You will pool your DNA microchips for the next set of directions.

Each group should take a pair of envelopes of mRNA transcripts from the front table.  Each is labeled with the cell type. 

  1. Check to see if any of the normal envelope sequences would hybridize with the DNA sequences on your microarray.  Check the other DNA microarrays at your table. 
  2. Fill in the data table for normal cells.
  3. Check to see if any of the abnormal envelope sequences would hybridize with the DNA sequences on your microarray. 
  4. Fill in the table for cells.

 

Type of cell

Did you find RNA transcripts that matched your DNA microchip?

How many transcripts were in the cell type?

 

 

 

 

 

 

 

What can you conclude from your data?

 

 

 

 


Activity 2:  Analyzing DNA microarray results

 

Gene 1

Gene 2

Gene 3

Gene 4

Gene 5

Gene 6

Gene 7

Gene 8

Gene 9

Gene 10

Chip

Person 1

 

 

 

 

 

 

 

 

 

 

1

Person 2

 

 

 

 

 

 

 

 

 

 

2

Person 3

 

 

 

 

 

 

 

 

 

 

3

Person 4

 

 

 

 

 

 

 

 

 

 

4

Person 5

 

 

 

 

 

 

 

 

 

 

5

 

  1. Which genes are always expressed?  What might be their function?  How could you test your hypothesis?

 

 

 

 

 

 

 

  1. Which genes are never expressed?  What might be their function?  How could you test your hypothesis?

 

 

 

 

 

 

 

 

 

  1. Of the genes tested, which might play a role in cancer?  How could you test your hypothesis?

 

 

 

 

 

 

 

Additional Analysis

  1. Is the function of gene 4 required for cancer?  What additional experiments would help you determine this?

 

 

 

 

 

 

 

  1. What about gene 9?

 

 

 

 

 

 

 

  1. Are the patterns for genes 3, 5 and 10 relevant?

 

 

 

 

 

 

 
 

Homework:

 

A patient with cancer has the following gene expression (X means gene is ON).

 

Gene #         1        2        3        4        5        6        7        8        9        10

                   X                 X       X                 X                 X       X

 

This patientís cancer responds very well to Gleevec, a drug recently approved by the FDA for the treatment of chronic myeloid leukemia, a rare type of leukemia.  The drug has lower side effects and toxicity compared to standard cancer chemotherapy.  Doctors are therefore wondering which other types of cancers would respond well to treatment with Gleevec.  Rather than randomly testing the drug on other types of cancers, the doctors have decided to use DNA microarray experiments to predict which cancers are more likely to be susceptible to the drug.

 

The doctors test the tumors of five cancer patients and find the following results

 

Gene 1

Gene 2

Gene 3

Gene 4

Gene 5

Gene 6

Gene 7

Gene 8

Gene 9

Gene 10

Person 1

X

 

X

 

 

X

 

X

 

X

Person 2

X

X

 

X

X

X

 

X

X

X

Person 3

 

 

 

X

X

 

X

 

 

X

Person 4

X

X

 

X

X

X

 

X

X

 

Person 5

X

X

 

X

 

X

 

X

X

 

 

1. Can you tell from these preliminary results which type of cancer would be most likely to respond to Gleevec?

 

 

 

 

 

 

2. Are the results clear enough?

 

 

 

 

3.     How would you improve the accuracy of your predictions?

 

 

 

 

 

 

4.     As a physician, would you conclude with confidence which patient may be responsive to Gleevec?

 

 

 

 

 

 

5.     Which patients, if any, would you treat with Gleevec?