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97% of the genome between any two individuals is identical. What accounts for the other 3%?
1% for SNPs
2% for copy number variations, deletions, etc.
Where can SNPs occur?
coding and noncoding region.
When SNPs are deleterious since they affect protein function, what are they called?
What happens where there are out-of-frame deletions?
it affects gene processing
Chrosome translocations can cause.... (4)
at site of translocation
4. create aneuploidy for sub chromosomal regions
T or F: hybridization only occurs in DNA-DNA pairs.
False, also RNA probes
CGH stands for
Comparative Genome Hybridization
What can CGH define?
deletions, losses, and gains of chromosomal material. NOT translocations.
In FISH, what does amplified green signal mean?
green- gene probe
Increased green signal defines level of amplification of gene probe.
If there is little to no green signal in FISH, what happened?
What do gene expression arrays define?
the expressio levels in a sample based on RNA abundances.
what are the three classifications of brain tumors?
proneural-young pts, good outcome
mesenchymal- older adults, mesenchymal differentiation w/poor outcome
proliferative- EGFR mutations, poor outcome
what are some ways that sequencing can be used clinically?
- genetic counseling
-defining the cause of a disease
-predicting appropriate therapy
-selecting pts for clinical trials
-defining response to a drug
How can overexpression of a cancerous/mutated gene be visualized?
When a gene is being overexpressed, sometimes it is not the gene that is mutated but the promoter. how is this visualized?
Gene expression arrays
Where can point mutations occur?
exons, splice sites, promoters, start ,stop sites
In frame deletion is
a deletion divisible by three
leukemia has chromosome translocation, t or f
what does the affymetrix determine?
it is a gene expression array that defines origin of metastatic tumors
exome sequencing involves enriching
protein-coding regions by designing biotin-nucleotides
Apply fundamental understanding of molecular biology to molecular events
-describe current treatment options
-provide examples of target therapy
-describe future of breast cancer treatment
Women are living longer. this increases prevalence of breast cancer.
many genetic mutations in breast cancer are druggable---
microarrays are used in breast cancer diagnosis type
into different biology, prognosis, etc.
There is a new class of breast cancer.
most women with breast cancer are diagnosed with early bc
Primary breast cancer highlights
pts age: 35
no oncogene amplification
What are some gene tests to help prognosis in borderline tumors?
-oncotype DX (21 genes, BAG-1)
-PAM 50, 50
Bone loss can be caused by AI (hormone therapy/ aromitase inhibitor)
HER family ligands/signals
4 molecules that are membrane-bound and is an oncogene, more expression associated with worse prognosis with breast cancer
Trastuzamab is an anti-HER2 drug
it binds HER2 to block it from binding
also blocks HER2 activation
T-DM1 selectively delivers a high toxic payload to HER2-positive tumor cells, very toxic
links with trastuzumab, and chemical is released into cell, only tumor cells
blocks development of blood supply to inhibit breast cancer cells
VEGF Trap, Bevacizumab, multikinase inhibitors, Mab and VEGFR, vascular disrupting drugs are all
moving away from "shotgun" approach to treating breast cancer
Cross-talks among signal transduction pathways aids cell resistance to chemotherapy
New targets for cancer therapy
growth factors, gf receptors, adaptor, phosphatases, ribsoeomes, histones, microtubules
IDO suppresses innative and adaptive immune responses
cancer cells use these and are correlated with reduced survival
tamoxifen has been largely replaced by
aromatase inhibitors, which directly inhibit estrogen production rather than competitively binding estrogen receptors
VEGF stands for
vascular endothelial growth factor
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