BME100 f2013:W1200 Group5 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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Contents

OUR TEAM

Name: Dominick Cocciola
Name: Dominick Cocciola
Name: Hany Arafa
Name: Hany Arafa
Name: Wendy Gray
Name: Wendy Gray
Name: Kristina Roscher
Name: Kristina Roscher
Name: Estefania Meza
Name: Estefania Meza

LAB 6 WRITE-UP

Computer-Aided Design

TinkerCAD

TinkerCAD is a computer aided design tool that can be used to design, create, alter, or optimize a model. It is quite intuitive and user friendly website due to the simplicity of the tools and controls available. In addition, it is compatible with a number of 3D printers and even offers printing services built into the software. TinkerCAD was utilized in this project to modify the design of the samply tubes in order to eliminate confusion and cross contamination. The template containing the sample tubes was downloaded and was modified in a number of ways. To begin with, all the sample tubes were placed into one fixture to eliminate any possible confusion. This fixture had labels included for both the positive and negative samples. It also had partitions or sections for the control and three separate sections for each sample. This design was implemented to be to be used in a PCR machine, eliminating the need for labeling and potentially decreasing the chance of cross contamination. Lastly, the labels were given bright colors to eliminate user error.

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Implications of Using TinkerCAD for Design


There are many ways to use TinkerCAD to alter the function of a variety of models which allow them to work in a more convenient and elaborate fashion. With TinkerCAD, a researcher could upload a 3D image of a smoke detector, for example, and do a complete analysis of the device's flaws. After these flaws have been identified, he can then redesign the smoke detector in a more practical manner so that all the flaws can be worked out. After the smoke detector is finished, he could then print out the design he has created, have the circuit board and various part of it implemented and put into use. TinkerCAD allows anyone to fully view a device and recreate it how ever they please.

Feature 1: Cancer SNP-Specific Primers

Background on the cancer-associated mutation
A nucleotide is the basic building blocks of nucleic acids. A polymorphism is a common variance in the sequence of DNA. A single nucleotide polymorphism or SNP is a difference in a single nucleotide in the DNA of an individual. The SNP rs17879961 is a cancer associated mutation that is found in the homosapien species and is pathogenic in its clinical significance. This SNP is located on the 22nd chromosome and the affected gene is called CHEK2, which stands for checkpoint kinase 2. When this gene is active, it inhibits cancer cells from replicating.



Primer design

  • Forward Primer: 5' - T G T A A G G A C A G G A C A A A T T T
  • Cancer-specific Reverse Primer: 5' - C A C T A G A A G A T A C A T A C G T C

How the primers work: The reverse primer will bind to a complementary cancer-SNP containing template that was taken from a patient sample. The reverse primer will only bind to the complementary sequence if it 100% matches just as the forward primer will also bind to its complement given it matches 100%. When the primer does not match the sequence completely, it will not be replicated. This makes it so only the DNA with the cancer-associated SNP will be replicated and any DNA that has the non-cancer allele will not be replicated.



Feature 2: Consumables Kit

The Eazee Baike PCR system comes complete with a micropipettor, pipette tips, PCR sample tubes, PCR mix, and primers. In addition to having all ingredients of the experiment readily available, the PCR tubes come pre-labeled and sorted which allows the user to begin the experiment immediately after opening the package. Other kits force the user to separate the tubes from large connected groups, down to a manageable size while also requiring the user to label the individual tubes. We find that pre-labeling and grouping the PCR tubes can save the user time and hassle.



Feature 3: PCR Machine Hardware

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The Eazee Baike PCR machine is nearly identical in design to the Open PCR machine used in BME lab. The main design change happens internally, in the PCR Machine software. Eazee Baike PCR's new software will ensure that all cycles running through the machine, are uniform in both time and temperature. This means that the user simply has to put the PCR tubes into the machine and start it. The machine will take care of the rest, displaying a time of completion so the user knows the total duration to complete all cycles. In addition, the PCR machine will include a USB drive which will allow the user to either connect the machine to a computer, or download the data onto a flash drive (flash drive included in kit).

Feature 4: Fluorimeter Hardware

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The Eazee Baike PCR Fluorimeter is designed with a smartphone compatible dock that is attached to the base at a fixed position. This will reduce drop analysis error due to varied camera distances. There will also be an insert included with the kit that gives instructions on how to download the Eazee Baike PCR Camera App to your smartphone. This app is customized to take pictures in the dark and allows the user to manually focus the camera which will reduce errors related to camera quality.


Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach

[Instructions This section is OPTIONAL, and will get bonus points if answered thoroughly and correctly. Here is a chance to flex some intellectual muscle. In your own words, discuss what the results for calculations 3 and 4 imply about the reliability of CHEK2 PCR for predicting cancer. Please do NOT type the actual numerical values here. Just refer to them as being "less than one" or "very small." The instructors will ask you to submit your actual calculations via e-mail. We are doing so for the sake of academic integrity and to curb any temptation to cheat.]

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