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