BME100 f2016:Group12 W1030AM L6

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BME 100 Fall 2016 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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Aly CarlsonGroup Member
Aly Carlson
Group Member
Ryan ShannonGroup Member
Ryan Shannon
Group Member
Ryan FaustGroup Member
Ryan Faust
Group Member
Adin RoemerGroup Member
Adin Roemer
Group Member
Kyle TappendorfGroup Member
Kyle Tappendorf
Group Member

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Bayesian Statistics

Overview of the Original Diagnosis System In the lab there are 15 groups each consisting of 5 students. Each of these groups were given two patients to test for the disease associated SNP. The groups used three samples from each patient in order to eliminate error. The groups also tested a positive and negative control to have something to compare the patients' results to. A calibration curve was created using known concentrations of DNA. The positive, negative, and patient samples were analyzed using florescence to detect DNA. Three pictures of each sample were taken to avoid error. We analyzed a total of eight samples using florescence--a positive, a negative, three samples of the first patient, and three samples of the second patient. In the final class data, there were twenty three successful conclusions, three inconclusive results, and two groups with no data.

What Bayes Statistics Imply about This Diagnostic Approach

Calculation 1 tells the probability that the the sample actually has the DNA sequence given by the positive diagnosis. This rate was around 80%. The second calculation tells the probability that the sample does not have the DNA sequence, with the negative diagnosis agreeing. This value is very close to 100%. Overall, the negative diagnosis is more likely than the positive diagnosis to tell whether the sample contains the DNA sequence or not.

Calculation 3 tells whether the patient is actually positive, given a positive test result. This number was very low, around 40%. Calculation 4 tells the probability that the patient is negative, given a negative test result. This result was very high, near 100%. Given these results, and the results from calculations 1 and 2, the sensitivity of the diagnosis is very poor, while the specificity of the diagnosis is very high. This means that the positive predictive value is low, and the negative predictive value is high.

There could have been several sources of error. First, the volumes of liquid could have been measured incorrectly. This would especially cause error during dilutions. Also, when analyzing the images in ImageJ, the area of the drop could have been selected wrong, which would lead to differing calibration values. Finally, the pictures taken of the liquids may not have been well-defined, leading to difficulties in determining whether the sample was positive or negative.

Intro to Computer-Aided Design

3D Modeling
Our team used the Solidworks software to design the new PCR machine. Solidworks is an intermediate software meant for comprehensive 3D design that has applications in the professional world. With this advanced software almost any object can be 3D modeled and used for things like schematics, design concepts, and 3D printing. Our team figured out this software in order to make a new design. We added new sub-assembly parts, we changed object dimensions, and we modified parts. We had a generally easy experience with using Solidworks to create a new design.

Our Design

For the design of our PCR machine, we have added 16 additional slots in order to put more micro tubules in. With more space for tubules, more runs can be done in the same amount of time. With the more experiments that can be done, the quicker we will be able to compare the results. With double the number of slots for tubules, our new design will be much more efficient than its predecessor.

Feature 1: Consumables

In our prepackaged consumables kit, we will include: company manufactured PCR tubes, mircopipettor and tips, PCR mix, primer solution, SYBR Green solution, buffer, and glass slides. The mircopipettor will be used to transfer solutions to the PCR tubes. The PCR mix, primer solution, SYBR Green solution, and buffer will be used to create the solutions. The glass slides are for the fluorimeter. One problem we had with the consumables was the size of the tubes. It was very hard to get the solution in the tubes because the opening of the PCR tubes were very small. It was inconvenient and time consuming. Our company will develop a tube with a detachable funnel part so the transferring of liquids to the tubes is easier to do and requires like time and precision. The funnel will attach to the tube and the before it is placed in the PRC machine the funnel is removed. The funnel is disposed of after it is used so the samples do not become contaminated. See picture below for example of the tubes and funnel.

Picture from:

Picture from:

Feature 2: Hardware - PCR Machine & Fluorimeter

Our company will include both the PCR machine and fluorimeter in our system. Both parts of the system are required to ensure that the PCR experiment can be run successfully. The PCR machine will be used to run the major part of the experiment: copying and emphasizing the strand of DNA we want to enhance. The fluorimeter should be used to help us take pictures of our finished PCR experiments and use that to determine if the patient has whatever detail we are looking for in the experiment.

In order for the PCR machine to be more expedient, we will design it to have more tube holders so that more PCR experiments can be run at once. This will speed up how many experiments can be done and will also allow the user to see if the experiment was accurate by comparing more of the same experiment to each other. The fluorimeter will have a webcam attached to it so that the operator will not need to use their own phone. This webcam will also send the photos it takes to the various data storages of the operator, which will allow the user to access the photos from their computer or phone. Because of this, the user will be able to get the pictures onto ImageJ and find any important details within the DNA. The webcam will speed up the process because the pictures will be directly transferred to the computer. Also the webcam won't have to be moved so the pictures can be taken from the same place every time. See picture below for webcam.

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