What technique would we use to determine whether a certain gene was transcribed in cancer cells?

1. What technique would we use to determine whether a certain gene was transcribed in cancer cells? A Northern Blot

2. What technique would we use to determine which of 10 different genes were transcribed in cancer cells? Lots of Northern Blots

3. 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

4. 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

5. Microarray DNA Array DNA Chip Bio Chip Gene Chip Genome Chips Gene Array

6. Can get 500,000 spots on one slide (representing that many different sequences)

8. Two basic kinds of microarrays: Genomic & cDNA

9. Genomic Microarray Each spot is a single-stranded oligonucleotide (25 bases long) that represents part of the coding region of a gene.

10. Robots are used to spot these DNA oligonucleotides Click here to see a video showing this…..

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

12. cDNA Genomic Chip

13. A Non-Cancer Cell cDNA cDNA ? ? Genomic Chip

14. A Non-Cancer Cell cDNA cDNA Genomic Chip

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

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

17. Transcription in one tissue Transcription in both Transcription in another tissue

18. Transcription in one tissue Transcription in both tissues Transcription in another tissue …dark spots = no transcription at all

19. Microarrays are becoming very useful in diagnosing whether cancer cells are malignant.

20. 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

21. Cancer Research, October 15, 2005 Called “Gene Expression Profiling” because you are looking at lots of genes at once. Almost fully predictive

22. Another example

23. 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.

24. 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

25. The most important locus = CYP450-2D6 ….there are 33 possible alleles at this locus. All you need is blood sample from patient…..

26. Microarray Extra versions

27. First commercial example of a personalized DNA Chip. Switzerland FDA approved for clinical use in 2005.

28. What are some potential non-medical uses for Microarrays?

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