BME100 s2015:Group14 12pmL6

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BME 100 Spring 2015 Home
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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Name: Nathan Francois
Name: Lexi Bounds
Name: Dakota Graham
Name: Thor Kissman
Name: Justin Mieth


Bayesian Statistics

Overview of the Original Diagnosis System

The BME 100 Lab was separated into 34 groups of 6 students. Each group was given the task of testing 2 different patients for a disease SNP using a PCR method and analysis with a fluorimeter. In total, 68 patients were tested for a disease SNP. In order to prevent error in this experiment, 3 samples of DNA were given for each patient. This ensured that positive results would not be flukes. During the PCR portion of the lab, certain measures were taken to make sure that DNA was able to be replicated accurately. Disease specific primers were used to locate DNA strands containing the disease SNP. This ensured that only disease specific DNA could be replicated. The number of cycles of PCR, as well as the heating and cooling for each cycle, were both controlled to ensure that PCR results were run to completion. During the ImageJ calibration, measures were taken to eliminate background "noise" that would make it seem as if more DNA was present in a sample than there actually was. Finally, 3 images for each of the three samples tested, as well as the positive and negative samples, were taken so that strong values for calibration could be obtained.

Overall, the class data was not 100% reliable for predicting presence or absence of the disease. In some cases, patients with the disease would test positive for the SNP, which would be expected. Likewise, some negative test results corresponded to negative patient diagnoses. In addition to the positive-positive, negative-negative results, some groups had results that contradicted the patient diagnoses. This says that perhaps the tests were not performed accurately, or perhaps that the tests are not wholly accurate at predicting disease diagnosis. Finally, some of the groups did not have conclusive data, while other groups did not complete the test in time to contribute to overall class data.

What Bayes Statistics Imply about This Diagnostic Approach

Using Bayesian statistics, it was found that almost 100% of people with the disease SNP would test positive for the SNP through the PCR test. Likewise, it was found that almost 100% of people without the disease SNP would test negative through the PCR test. These results show that the test is accurate and precise for detecting the disease SNP. Errors that may negatively affect the PCR test results and Bayesian statistics include false positives and false negatives. These could possibly be caused by improper calibration of the fluorimeter test, improper handling of SYBR green dye which would lead to false negatives, and a reliance on data from all groups in the class. The final cause might lead to error because it increases the chances that samples would be mishandled and calibrations would be done improperly.

As for the accuracy with which the test can predict the development of the disease from the presence of the disease SNP, about 86% of people with positive PCR test results can be expected to develop the disease. About 86% of people with negative PCR test results can expect a negative diagnosis in regards to disease development.

Overall, these results say that the test can be used to predict the development of the disease from the presence of the disease SNP. However, since the reliability of using the test as a diagnostic tool is only 86%, other confirmatory tests should be used in conjunction with this test. Additionally, these results indicate that the disease SNP is most likely not the only factor contributing to the development of the disease in question. More research needs to go into determining these additional factors.

Computer-Aided Design

TinkerCAD is an online tool which lets the user edit 3D designs and share the designs with team members. It is browser-based, allowing a designer to use different devices to work on their project. It is easy-to-use and has a built-in tutorial. It is also a free program, while similar programs like AutoCAD are not.

Our Design

Internal of the revised OpenPCR


Extra USB port
There are a few differences between our design and that of the original OpenPCR. The first is the size. Our design uses the same base parts to make our machine as the original OpenPCR, but at a 1.25:1 scale, as to increase heating and cooling units, the fan, and the motherboard. The second difference is the added camera. Having a camera integrated with the machine makes using the machine much more efficient, as it will stay in the same position with the same results. The last addition is the extra USB port, which would be used to plug the machine into a separate device.

Feature 1: Consumables Kit

Strengths and Weaknesses of Current Consumables Kit

  • Strength: The micropipettor was accurate in measuring the proper amounts of solutions needed for the lab experiment.
  • Weakness: The main weakness of the consumables kit was the amount of plastic wasted. For instance, the tips of the pipettor could not be used more than once and, thus, had to be replaced each time solutions were measured in order to reduce the risk of contamination. This led to a great amount of plastic waste.

Our Company's Improvements on the Consumables Kit

In order to embrace the strengths of the consumables kit and offset the weaknesses, our company has developed a micropipettor with an internal disinfectant system that allows the user to reduce the number of tips used during an experiment. When an individual presses down in order to attach or release a tip, the press engages with a button that causes the disinfectant spray to release from its chamber. Once released, the spray cleanses both the plastic tip and the pipettor. The spray is formulated so as to not contaminate samples. Additionally, it contains a hydrophobic component that will decrease the possibility of water retention. With this new system, our kit produces less waste and reduces the cost. This, in turn, reduces the overall price of the product. Additionally, there is little to no risk of contamination. The liquid reagents will be packaged in a less costly material that still provides the same assurance that no leakage can occur. The entire consumables kit will then be packaged into a recyclable container that doubles as a waste container, so as to reduce the cost of use for each customer.

Feature 2: Hardware - PCR Machine & Fluorimeter

Strengths and Weaknesses of Current PCR Machine and Fluorimeter

  • Strengths: The OpenPCR machine is user friendly and easy to use.
  • Weakness: The OpenPCR machine is slow at getting results back to the user. Additionally, the heating and cooling system can lead to inefficiency. Finally, the camera for the fluorimeter is hard to keep in place.

Our Innovations for the PCR Machine and Fluorimeter

We will include the PCR machine and fluorimeter in our system by using them to analyze DNA samples that were inputted into the device. The PCR machine will heat and cool the samples to get the desired effects out of the DNA samples, and the camera for the fluorimeter will take pictures of the samples for analysis.

The group decided to change the design of the PCR machine and fluorimeter to address problems in the system. The first change is that the PCR machine is larger in overall size. This allows for a larger and more effective heating and cooling system to increase efficiency and effectiveness. The next change was the inclusion of a camera on the inside of the fluorimeter to be able to take more accurate and precise images of the samples during the fluorimeter portion of the work process. The PCR machine is already connected to a computer, so including a camera in the fluorimeter would just involve adding a USB plug-in so an additional connection can be established. The result is a 2-in-1 technology.