BME100 f2018:Group11 T1030 L6

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Owwnotebook icon.png BME 100 Fall 2018 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
Course Logistics For Instructors
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B.B. BioMed

Name: Reyna Armbrust
Name: Justin Pettit
Name: Luis Vazquez
Name: Lauren Ospina
Name: Karen Lopez


Bayesian Statistics

Overview of the Original Diagnosis System
In the PCR lab, 17 groups were responsible for diagnosing a total of 34 patients. Every group tested two patients with unique ID numbers. To prevent error, replicates and controls were used. There were three replicates of each patient's DNA sample along with a positive and negative control for each pair of patients. In addition to the PCR drops, drops with initial DNA concentrations ranging from .25 to 5 in SYBR Green solution were placed in the fluorimeter. For each DNA concentration, each disease control and each replicate, three images were taken and used for ImageJ calculations. For the 34 patients, the class results included 31 successful conclusions yielding clear positive or negative results. There were also two blank results and one inconclusive result. In the initial set-up for the PCR reaction, our group had a pipetting error. The pipettor accidentally pulled the solution back up into the tip after transferring it to the final tube. The tip was then placed into the cup with the other disposable tips without any group members noticing. The empty tube was noticed and the tip was then taken out of the disposal cup and the solution was properly transferred. It is possible that the exposure of this tip to the tips used for other samples resulted in cross-contamination.

What Bayes Statistics Imply about This Diagnostic Approach

The results from calculations 1 and 2 imply that using individual PCR replicates to conclude that a person has a disease SNP is reliable. This is seen by both of the calculations being so close to one. The first shows that if a person has a positive result they have a high probability of having the SNP. The second calculation shows that having a negative result will have a high probability of not having the SNP.

The results from calculations 3 and 4 imply that PCR is pretty reliable. For calculation 3, the reliability was really low, closer to 50%, when the PCR test was used for positive specimens. When PCR is used to test for a negative result, then the results are very reliable and can generally be used to correctly predict the results.

Possible sources of error could have occured in transferring the liquid from the PCR tubes into the big Buffer tubes. Remaining liquid could have been dicarded along with the used micropipette tip. Human error that could have occured in the detection steps would be placing the SYBR Green 1 drop on the wrong side of the glass slide. The drop of SYBR Green 1 would disperse if placed on the wrong side. This would affect the analysis using ImageJ because an innacurate area recording would be taken since the shape of the drop would be changed. A third possible source of error could have occured in aligning the drop and the blue LED light. Failure to do this would not ensure a high emission of light when a high concentration of DNA was added to the SYBR Green 1.

Intro to Computer-Aided Design

3D Modeling
The software used to design our product was Solid Works 2018. The experience with the software was somewhat challenging due to our lack of experience with the program. A lot of extrusions and cuts were used in order to make the product. One issue was getting the chamfer to work for the top container of the product. Another issue was trying to align all of the pieces perfectly and mating them to the appropriate surfaces. Overall the experience using Solid Works went well.

Our Design

Exploded View Closed View

This design was chosen as we believed that the main issue with the original product was the use of the phone camera as well as the intrusion of light into the system due to the design of the storage unit. We virtually eliminated this by using a camera that can be connected to a computer through a wireless connection. This along with the seal from the lid makes it so that there is no extra light when taking the picture. This leads to a more accurate result. Another way to help improve the design is by making a container that stores the SYBR Green when in use. This container is solid so that no light can come through and will automatically pipette the appropriate amount of solution when it is told to do so. This process is another step to prevent light from affecting the data.

Feature 1: Consumables

Side View of Slide Holder Dimensions of Tip

The only products that would be added and/or created by our company would be the glass slides that go with the machine as well as specifically made tips for the SYBR Green dispenser. The manufactured glass slides are due to the specifications of the machine creating specific dimensions for the slit that holds the glass slides. The manufactured tubes are also due to the specifications created for the machine and are necessary in case of blockage or forms of possible wear on the tips. The tips were designed with a wider point of exit in order to help prevent this, but extra should be included if for any odd reason there is an issue with it.

Feature 2: Hardware - PCR Machine & Fluorimeter

In our system, both the Open PCR machine and the fluorimeter will be used and are extremely important and relevant to the accuracy of the test. Both of these individual part have a particular job and help develop the test results. The Open PCR machine and the fluorimeter have very specific jobs that are necessary to complete the system. Our system does have several changes that were made to the fluorimeter to improve the process and system. This being said, it is important to mentions the weaknesses of the original fluorimeter and the improvement made.

The problems we ran into were the instability of the setup of the fluorimeter. The setup was very unstructured and was easy disturbed. The new and improved fluorimeter will have a built in camera to ensure that the more precise picture is taken. The fluorimeter will also have a disposable SYBR green dispenser. This will help avoid spills and inaccuracies the data. In our experience, it was extremely difficult to take a clear picture and send it to someone else to use ImageJ to find the results. In order to solve this issue, we added a wireless transmitter that will instantly and accurately transmit the results from the fluorimeter to the healthcare providers. These changes will help create an easier and more accurate testing procedure, while providing the patient with more precise results in a timely manner.