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DNA Microarrays

DNA Microarrays. Examining Gene Expression. DNA MicroArrays. DNA MicroArrays use hybridization technology to examine gene expression Attach different DNAs onto a slide as a grid of small spots, one for each gene - up to 50,000 per slide

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DNA Microarrays

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  1. DNA Microarrays Examining Gene Expression

  2. DNA MicroArrays • DNA MicroArrays use hybridization technology to examine gene expression • Attach different DNAs onto a slide as a grid of small spots, one for each gene - up to 50,000 per slide • Hybridize a mixture of fluorescently labeled cDNAs extracted from cells after different treatments - control is green and experimental is red • Examine expression patterns by looking at levels of fluorescence for all genes in array

  3. DNA MicroArray Hybridization Data mRNAs at lower levels in treated cells are green, those at higher levels in treated cells are red, those that are unchanged are yellow. each spot corresponds to a different gene decreased expression increased expression

  4. Some Uses of DNA MicroArrays • Rapid scanning of DNA or RNA populations • Used for identifying bacterial infections in hospitals • Used in research on molecular biology of gene expression • Stanford MicroArray Database (SMD) - gene expression information and extensive database of results

  5. Tumor Subgroup Clusters Perou, et al Nature 406:747 (2000)

  6. Tumor Clusters basal expression normal breast-like Erb-B2+ Luminal epithelial/ER+ Perou, et al Nature 406:747 (2000)

  7. Tumor Portraits • Breast tumors are histologically diverse and differ in their responsiveness to treatments • The expression profiles provided a distinctive molecular portrait of each tumor subtype • Gene expression patterns in two tumor samples from the same individual were more similar to each other than either was to any other sample • Sets of co-expressed genes (portraits) were identified that were correlated with specific features or physiological variation • Metastases and primary tumors had similar expression profiles • Can lead to more effective chemotherapy decisions Perou, et al Nature 406:747 (2000)

  8. Pharmacogenomics • examine expression profile of patient • compare to known profiles • determine most effective treatment for this particular allele • designing drugs for individuals

  9. Some Questions • If pharmacogenomics tests are not done prior to treatment, can doctor/drug company be sued? • If tests are expensive, and patients pay for them, is this a kind of “economic” discrimination? • If patient pays for test is she/he “hiding” information from insurance company and subject to having policy cancelled? • If insurance company pays for test do they have a right to the results? • From a business perspective, doesn’t it make sense for an insurance company to pay for the tests since it might result in avoidance of cancer (a big bill!)? • Discover of “accidental” information in a gene expression profile analysis of a patient – should the patient be told?

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