#13 Microarrays

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AndreaCook
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136335
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#13 Microarrays
Updated:
2012-02-21 16:03:56
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Genomics #13 Microarrays
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  1. Gene Expression Profiling is used to assess ____________ within a sample simultaneously
    the expression of multiple genes
  2. Gene Expression Profiling uses a targeted set of __________
    mRNA
  3. __________ is a test of breast cancer tumor tissue to predict ___________ and ___________
    • Oncotype DX Breast Cancer Assay
    • Chemotherapy response
    • Recurrence
  4. CYP450 analysis uses a targeted set of ______________
    DNA sequences
  5. Genes selected for the Oncotype DX Breast Cancer Assay include ____________, ___________, & ___________
    • Her2/neu
    • estrogen receptor
    • progesterone receptor
  6. expression of a gene correlates with ___________ and/or ____________
    • progression
    • response to therapy
  7. PCR products are genenrally ____________ labelled and
    ____________ to the 21 gene chip.
    • fluorescently
    • hybridized
  8. Stage I & II cancer is _______ which means it is ________
    • node negative
    • localized
  9. Algorithms are created for ________ and ________
    • chemotherapy responsiveness
    • recurrence
  10. Tissue samples for the Oncotype DX Breast Cancer Assay do not need to be fresh. They can be taken from _____________
    formalin-fixed, paraffin embedded tumor samples
  11. PCR products are genenrally fluorescently labelled and hybridized to the _____________.
    21 gene chip
  12. The chip is read by laser for _____________
    relative binding for all genes
  13. One can analyze for a restricted set of genes at the _____ level using ________ __________ __________ __________.
    • DNA
    • specific DNA sequence analysis
  14. Amplichip CYP450 is a commercial chip to interrogate samples for _______ and ________ polymorphisms
    • CYP2D6
    • CYP2C19
  15. Amplichip CYP450 can use either _______ or _______ DNA samples.
    • blood
    • buccal
  16. Which DNA sample type is reccommended for Amplichip CYP450
    blood
  17. Amplichip CYP450 looks at ______CYP2D6 polymorphisms and ______ CYP2C19 polymorphisms
    • 90
    • 3
  18. ________ for the Amplichip CYP450 flow is extracted from the patient sample
    DNA
  19. DNA for the Amplichip CYP450 flow is amplified by ________
    PCR
  20. Products for the Amplichip CYP450 are _________ and __________ labelled
    • fragmented
    • fluorescently
  21. The sample _______ is __________ to the gene chip.
    • DNA
    • hybridized
  22. microRNA do not have ________
    polyadenylated tails
  23. Protein Expression Profiling uses a series of ________ fixed to a ______________ to detect the presence of ________ within a sample.
    • antibodies
    • solid substrate
    • proteins
  24. ____________ is useful for examining a number of signal transduction pathways simultaneously while exposing cells or tissues to drug
    Protein Expression Profiling
  25. ________ uses whole tissue instead of isolating proteins to detect where the ligand is bound and how much
    Tissue Microarray Fabrication
  26. ________ looks at 3 markers nad how the makers look different on different samples and at different _______
    • Tissue microarray analysis
    • stages
  27. Protein Expression Profiling is useful for examining a number of ___________ simultaneously while exposing cells or tissues to ___________
    • signal transduction pathways
    • drug
  28. CHiP stands for
    chromatin immunoprecipitation
  29. ChiP is an assay that is used to identify the ________ __________ and ________ _________
    associated with specific genes.
    • transcription factors
    • histone modifications
  30. ChIP-on-chip can label ________ products with ________ and _______ from two cell conditions and expose to a gene microarray
    • PCR
    • Cy3
    • Cy5
  31. What two parameters define microarray detectors
    • Resolution
    • Sensitivity
  32. A resolution of _______ is needed in a detector system to detect 1:500,000 copies
    5-10 μm
  33. The detector system needs a sensitivity of _______
    2-5 molecules/μm2
  34. What are the two types of detector systems
    • scanners
    • imagers
  35. What do the two types of detector systems have in common
    they both use laser light
  36. ___________ collect laser light on _________ and then reconstruct the entire field
    • Scanners
    • photomultiplier tubes
  37. _________ use a __________ to collect a picture of the light pattern
    • Imagers
    • charge-coupled device (CCD)
  38. Detection probes generally use a __________ tag, particularly the cyanine dyes ______ and ______
    • fluorescence
    • Cy3
    • Cy5
  39. Some problems with detection probes are ______ and _______
    • photobleaching
    • spectral overlap
  40. Dual fluorescence/chemiluminescence –
    here each spot contains two ______ , one labeled with _______ for chemiluminescnce, the second labeled with _____________.
    • oligimers
    • digoxigenin
    • fluorescent dye
  41. Dual fluorescence/chemiluminescence is used to compare _______ ________ to ensure reading spot correctly. This should decrease ________ ________
    • spot location
    • false negatives

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