BME103:T930 Group 11 l2
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OUR TEAM: Group 11
LAB 2 WRITE-UP
Thermal Cycler Engineering
Our re-design is based upon the Open PCR system originally designed by Josh Perfetto and Tito Jankowski. Our new design incorporates some new designs such as software, screen zize, number of testing tube lots, as well as size of heating lid. All of these alterations are made to make the Open PCR system more efficient in terms of its operating system and user-friendly features.
Our most major change to the Open PCR System is the change we made to the read-out screen on the top of the device near the heating lid. This change actually affects a few major components of our system. Not only did we move the screen to the side of the machine, rather than the top, but we also optimized the size of it. This size-change allows users to see the read-outs clearer. We also eliminated the need for a computer (or any outside device, that is) as this new larger screen will also be able to control the machine. Now the user is able to input cycles, temperature, etc. right on the screen instead of needing to plug it into a separate system. This allows for better portability and easier use.
We also changed the space of the testing tubes so now more tubes can be tested at once. To do this we lengthened the plate as well as the heating lid entirely across the top of the machine. Removing the screen from this part of the Open PCR System also allowed for this change.
DNA Measurement Protocol
Research and Development
Background on Disease Markers
Prostate Cancer: androgen receptor
"Prostate Cancer is cancer that starts in the prostate gland. The prostate is a small walnut-sized structure that makes up part of a man's reproductive system. It wraps around the urethra, the tube that carries urine out of the body." Prostate Cancer is the most common cause of death from cancer in men over age 75. It's very rare to find it in men younger than 40. In fact, the most common problem in almost all men as they grow older is an enlarged prostate. More information can be found regarding Prostate cancer is here.
An image of a normal prostate and cancer prostate
The marker that is being use was rs137852593.
The Dna Sequence is CTCTGCCTCTTCTTCTCCAGGCTTCC[G/T]CAACTTACACGTGGACGACCAGATG and found in chromosome 13.
Retinoblastoma is a rare, cancerous tumor of a part of the eye called the retina. The disease is caused by a mutation in a gene controlling cell division, causing cells to grow out of control and become cancerous. The cancer generally affects children under the age of 6. It is most commonly diagnosed in children aged 1-2 years. The information regarding this disease is here.
An image of the eye is here. 
The marker that is being use is rs121913297. 
The DNA sequence is TCAAACGTGTTTTGATCAAAGAAGAG[G/T]AGTATGATTCTATTATAGTATTCTA  and found in chromosome 13.
Forward Primer: 5' ATCAAAGAAGAGTAGTATGA 3'
There is a mutation from a G to a T
Reverse Primer: 3' TAGTTTCTTCTCATCATACT 5'
Forward Primer: 5' AGGCTTCCTCAACTTACACG 3'
There is a mutation from a G to a T
Reverse Primer: 3' TCCGAAGGAGTTGAATGTGC 5'
If the sample carries the mutation, then the sample would test positive. If it does not, then the sample would test negative because the primers would not be able to bind to the DNA because it does not contain the proper sequence.
These are the primers for the Retinoblastoma sample binding:
These are the primers for the Prostate Cancer sample binding:
This is the process of DNA amplification:
P(A | B) represents the probability that cancer will produce a positive outcome in the test (when the primer binds to the mutated gene).
P(B | A) represents the probability a person will yield a positive result for the cancer test.
P(A) represents the probability of carrying the mutated gene.
P(B)represents the probability of people who would yield a positive result in the test without really having cancer.