BME100 f2013:W1200 Group3 L6: Difference between revisions
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==Feature 1: Cancer SNP-Specific Primers== | ==Feature 1: Cancer SNP-Specific Primers== | ||
'' | '''Background on the cancer-associated mutation''' <br> | ||
rs17879961 is a pathogenic mutation that is found in homo sapiens on the 22nd of the 23 chromosomes. This mutation affects the single nucleotide polymorphisms in the CHEK 2 gene which has been found in both hereditary and non-hereditary cancers. This gene's primary function is to produce checkpoint kinase which is a protein that works to repress tumors. Nucleotides are the building blocks or sub-unites of nucleic acids that are also organic molecules that serve as monomers. Polymorphism is two or more clearly different phenotypes that exist within the same population of a species. | |||
'''Primer design'''<br> | '''Primer design'''<br> | ||
* Forward Primer: ' | * Forward Primer: 5'-A C T C A C T T A A A C C A T A T T C T | ||
* Cancer-specific Reverse Primer: ' | * Cancer-specific Reverse Primer: 5'- G G T C C T A A A A A C T C T T A C A C | ||
How the primers work: '' | '''How the primers work:'''<br> | ||
Primers are specifically sequenced DNA that work to produce specific genetic material.Primers do this by attaching to a specific area of the gene on two strands. These strands are not exactly the same and compliment each other. The primer then works to extend only the specific area of the gene it attached to. If the primer is not an exact compliment to the other strand the DNA will not replicate. When this happens only the cancer containing DNA will be replicated. In our lab the DNA containing the cancer SNP rs17879961 will be amplified by the primers. | |||
==Feature 2: Consumables Kit== | ==Feature 2: Consumables Kit== | ||
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==Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach== | [[Media:Instruction manual for PCR.docx]]==Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach== | ||
The results from calculation 3 give the probability of a person with cancerous DNA receiving a positive PCR diagnosis. This calculation has very low percentage meaning that the cancerous DNA will most likely not return a positive result from the PCR machine. The PCR instrument may not be the best device to use for this experiment. Calculation 4 tests specificity, giving the probability that a non-cancerous DNA sample will test negative using the PCR test. The calculated percentage for calculation 4 was also very small meaning that the PCR diagnosis test will likely return a positive result for a non-cancerous DNA sample. This suggests that the PCR machine would not be a good instrument to use to test for a non-cancerous negative result. | The results from calculation 3 give the probability of a person with cancerous DNA receiving a positive PCR diagnosis. This calculation has very low percentage meaning that the cancerous DNA will most likely not return a positive result from the PCR machine. The PCR instrument may not be the best device to use for this experiment. Calculation 4 tests specificity, giving the probability that a non-cancerous DNA sample will test negative using the PCR test. The calculated percentage for calculation 4 was also very small meaning that the PCR diagnosis test will likely return a positive result for a non-cancerous DNA sample. This suggests that the PCR machine would not be a good instrument to use to test for a non-cancerous negative result. |
Latest revision as of 11:03, 27 November 2013
BME 100 Fall 2013 | Home People Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3 Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6 Course Logistics For Instructors Photos Wiki Editing Help | |||||
OUR COMPANY
LAB 6 WRITE-UPComputer-Aided DesignTinkerCAD
Implications of Using TinkerCAD for Design
Feature 1: Cancer SNP-Specific PrimersBackground on the cancer-associated mutation rs17879961 is a pathogenic mutation that is found in homo sapiens on the 22nd of the 23 chromosomes. This mutation affects the single nucleotide polymorphisms in the CHEK 2 gene which has been found in both hereditary and non-hereditary cancers. This gene's primary function is to produce checkpoint kinase which is a protein that works to repress tumors. Nucleotides are the building blocks or sub-unites of nucleic acids that are also organic molecules that serve as monomers. Polymorphism is two or more clearly different phenotypes that exist within the same population of a species.
How the primers work: Feature 2: Consumables KitThe small tubes are typically placed all together in a plastic bag. Instead the tubes would be placed in a holder similar to the one the micro-pipette tips are in. This makes for a more convenient set-up and organization. As well the tubes would be perforated so that the there could be any amount in a set, not just four. Lastly, to secure all of the tubes there would be lid to go over the container to help prevent spillage. Feature 3: PCR Machine HardwareThe PCR machine will be redesigned to address a few small issues that were found with the original version. Using the original version of the PCR machine was a large time consuming processes, so we are redesigning our PCR machine to reduce the run time. Another problem we saw with the PCR machine was that the performance was not reliable. Our redesigned machine aims to be accurate 100% of the time. We did not see a problem with the PC software; most people interested in using a PCR machine will have access to a computer. By putting the software on the computer, we are able to minimize the size of the machine. The last change that we are going to make to the machine is the size of the sample tray. Originally the PCR machine was only able to use 16 samples, but we thought this number was much too low. The improved PCR machine will be able to run 96 samples in each run."
Feature 4: Fluorimeter HardwareAfter using the fluorimeter hardware in another system, we have decided to make several changes that we see necessary. These changes will mainly be concerning the amount of variables in operation. The original fluorimeter hardware was very difficult to set up because of the large quantity of variables. We place on creating a more effective camera stand that is adjustable for different cellular phones that may be used by the consumers. The camera stand will also be attached to the device so that the distance from the camera to the lights will become constant. We hope to improve the results of the machine by making the product more user-friendly and by reducing the chance of user error.
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