BME100 f2014:Group29 L6

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Owwnotebook icon.png BME 100 Fall 2014 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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Name: Amanda Smith
Name: Blake Morrow
Name: Mitchell Durbin
Name: Julian Bertrandt
Name: Zied Alghamdi
Name: Gergey Mousa



Bayesian Statistics

Overview of the Original Diagnosis System

In this investigation, there was 68 patients that were tested for the disease-associated SNP through replicating their DNA. Patients were split among 34 teams which mean each team was assigned 2 patients to test for the SNP. Each team consist of 6 members. In order to ensure accuracy and to prevent error, 3 samples of DNA were given for each group to be tested in addition to two control samples, one is positive and the other is negative. This prevented error by giving three samples to analyzed and compare with ImageJ instead of just one. Furthermore, for ImageJ calculations, 3 drop images were used to confirm the results and eliminate any possible error. After doing the ImageJ and seeing the results, it is easy to tell that the three different pictures were essential to getting a more accurate result. Every 2-3 groups used the same PCR machine to replicate their samples and then used fluorimetery to analyzed the samples against the positive and negative controls. After the data was analyzed, everything was collected in one spreadsheet for the all teams to use. In general, the final data was accurate. Out of 68 patients, 6 were not submitted (blank), and 8 patients were inconclusive.

What Bayes Statistics Imply about This Diagnostic Approach

Calculations 1 and 2 were both close to 1.00 (100%). Having these calculations close to 1 imply that the reliability of the individual PCR replication for concluding that a person has the SNP disease or not is high. This shows that there is likely a correlation between a positive/negative final test conclusion and a positive/negative PCR reaction, respectively. This is essentially showing that there is a high probability of having a positive final test conclusion (A) given a positive PCR reaction (B), and vise verse, as shown with the high percentages of P(AB).

There were many sources of possible human or device error that could have occurred during the PCR & detection steps that could have affected the Bayes values in a negative way. The solutions in the PCR tubes may have not been precise, the PCR machine may not have taken the solutions to the proper cold and hot temperatures, the PCR machine may have not gone on for the precise time, the pictures taken may have not been of the high quality needed for the image processing, and there may have been complications with the image processing causing inaccurate results.

Calculations 3 and 4 were both very small. Having these calculations so small imply that the reliability of the individual PCR replication for concluding that a person has the SNP disease or not is low. This shows that there is likely a correlation between a positive/negative final test conclusion and a positive/negative PCR reaction, respectively. This is essentially showing that there is a low probability of the patient developing the disease (A) given a positive final test conclusion (B), and vise verse, as shown with the low percentages of P(AB).

Computer-Aided Design


TinkerCAD, the browser based 3D design lab was instrumental in displaying what improvements would be made to the PRC and fluorimeter machines. With the provided PCR parts, a quick model was generated and gave a baseline design on how to modify the initial design to fit the improvements that were proposed. The interface was not an advanced program with all the bells and whistles of a program like Solid-works, but it's simple enough to not have a high barrier of entry in order to use TinkerCAD effectively. Additionally, being a directly online design lab it was possible to have multiple people interacting with designs without having to constantly upload and update after each modification.

Our Design

Complete Device.jpg Sample Tray.jpg

The improvements made to the OpenPCR is that the Flourimeter is now combined and attached to the PCR machine. The PCR machine is a closed box and the samples are placed on a tray and then slid into the machine from the side and not placed on top like the previous design. Having the samples completely enclosed by the machine allows the process to happen more quickly because the samples will be heated and cooled from all sides, and not just the bottom like with the previous design. Once the PCR is done, the tray can be removed and then placed onto the attached Flourimeter. The Flourimeter will have light already shining on the samples, and the lid of the Flourimeter will have cameras that will be already calibrated and have a standard distance. The Flourimeter will also be able to be connected to a computer so the imagines can be processed. The only changes that will have to be made to the lab is that the SBYRGreen can be added prior to the PCR machine, or it can be added right after, but before the Flourimeter. Also, once the samples have gone through the PCR machine, their lids will need to be removed so that the cameras on the lid of the Flourimeter can have a clear unobstructed view of the samples.

Feature 2: Consumables Kit

Our consumables will be packaged in a plastic tray in a styrofoam block to ensure they are not damaged in transport. The consumables in the kit will consist of:

  • Gloves
  • SYBR Green
  • Taq Polymerase
  • Micropipette
  • Tips for Micropipette
  • Primer

The plastic tray will also be labelled so as the materials can be placed back in it when they are not in use. This will prevent any mixing up of the reagents. The reagents will be pre-measured in small plastic tubes.

The pre-measurement of the reagents will prevent human error during mixing. One would simply have to pipette all of the reagent from the plastic tube to the tube being used for the PCR.

Feature 3: Hardware - PCR Machine & Fluorimeter

For this product, both the fluorimeter and PCR machines have been combined into one, easy to run system. The way this device is set up, is that the test tubes with the DNA are inserted into a rack in the first box labelled PCR. After all of the essential parts have been added to the samples, including the parts needed for the fluorimeter, and the PCR has been completed, the tubes are then moved to the subsequent box labelled Fluorimeter. The tubes are placed into a rack on the side of the device, just like the PCR machine, and individual cameras are attached to the top of the rack. Blue light illuminates every sample from the sides. After the hatch is shut and the device is turned on, the camera's will take three individual photos of every tube and download them to a file on the computer that the device is attached to.

This change in design eliminates human error because the device is completely machine operated. There is no pipetting, and, really, no area for error other than a malfunction in the device. The only possible human error could come from the initial step of the samples being added to the test tubes before the samples enter the device at all. Also, this design cuts down on time because nothing has to really be set up for the fluorimeter. Everything comes pre-calibrated and everything is already set up in the device.