BME100 s2014:T Group12 L6
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Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
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Company: GMP (Genetics Made Possible)
LAB 6 WRITE-UP
TinkerCAD is a design software that allows a person to create a 3-D model of anything they need/want to. We used this program to model the sides of the original PCR machine so as to determine a new model for it. The new model using this program provides a new perspective on an older idea.
Feature 1: Disease SNP-Specific Primers
Background on the disease-associated mutation
How the primers work:
This is done to detect the disease and also have as a control in the test to ensure accuracy. The reverse primer will bind to the DNA 100% of the time (both not diseased and diseased DNA sequences). when this happens the DNA will not exponentially amplify. For the case of a not diseased DNA sample the test will render minimal amplification. If the reverse primer does not bind to the DNA sequence then the test is considered to be a not valid. The forward primer will only bind to the diseased DNA sequences along with the forward primer. This will result in an exponentially amplified DNA that contains the disease-associated SNP.
Feature 2: Consumables Kit
Self-contained Green Magazine
All of these items will be loaded into a container, or "magazine." There will be specific compartments for the different types of items. One side of the magazine will have compartments for the more generic items, including: PCR reaction mix, SYBR Green I dye, disposable pipette tips, test tubes, and rough superhydrophobic slides (for the fluorimetery test). The other side of the magazine will have compartments for items more specific to the test, including: positive DNA, negative DNA, and subject DNA. Additionally, there will be a compartment which houses a compartment that will collect the disposable pipette tips and the other used items when they are ready to be disposed of. All of these items, generic and specific, will be in their own container when inserted into the magazine. The magazine will be such that it slides into the Green Machine. Inside the Green Machine, a simple automated robotic system will prepare solutions using the items in the magazine and it will also move the prepared solutions to their proper compartment for PCR and fluorimetery testing.
This way of packaging the consumables creates a more organized method of performing PCR and fluorimetery. Instead of having a researcher working with multiple solutions scattered around, this system is more contained and controlled, which helps speed up the testing process and reduce contamination. This packaging method helps eliminate human error as well.
Feature 3: Hardware - PCR Machine & Fluorimeter
Included in the Green Machine will be the PCR machine and fluorimetery system along with the simple automated robotic system that prepares solutions, transports them, and tests them. Both the PCR machine and fluorimetery system will be integrated into the Green Machine so that they can be controlled by the Green Machine's computer. Both the PCR thermal cycler and fluorimeter system will be above the inserted magazine and on opposite sides of the Green Machine.
Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach
The PCR results can sometimes be misleading and it is better not to rely entirely on it to predict whether a person has cancer or not because in the PCR results it showed an either positve or negative response.This will cause cancer misdiagnosis as a patient who doesn't have cancer may think he has it while a patient who has cancer may think he doesn't have cancer and will never have cancer.The Bayesian statistics verifies that the fact that you are tested positive to cancer doesn't mean you have it, it is probable you may develop the disease and the fact that a patient is tested negative to cancer doesn't mean he will never get cancer.So the Bayesian statistics uses a very logical interpretation to tell you an accurate probability of developing cancer after you have been tested positive.Calculation 3 and 4 shows that a person who has tested positive may have a lower probability of developing cancer while a person who has been tested negative may have a higher probability of developing cancer.This makes sense because the fact that a person has family history of cancer doesn't mean he is going to get cancer.People with no family history of cancer also develop cancer.