BME100 f2014:Group21 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: Dustin D. Burley
Name: Mackenzie Konves
Name: Scott Boege
Name: Nicholas Goettl
Name: Travis Tibbs
Name: Lionel Davis


Bayesian Statistics

Overview of the Original Diagnosis System

The PCR reactions that were done in the BME100 lab were designed to mitigate error. Each group tested 2 patients, meaning a total of 68 tests were done (there were 34 groups). Since each patient had their DNA ran three times there was little chance for error (a total of 208 PCRs were run!). Even after this was done there were still things put in place to reduce the risk of error. When it came time to do the image processing there were three ImageJ tests done on each of the DNA samples (3 samples per patient would mean a total of 9 tests were run for one patient) to ensure accuracy in the diagnosis. Not only where the quantity of tests a way to prevent error, but the quality of the ImageJ calibrations served as a check on error. These photos were also taken multiple times to ensure that the images would produce a good calibration. Since it was so closely calibrated it would be hard to misread the image and give the wrong diagnosis. Since there was so much data in the final spread sheet the Bayesian statistics could be used effectively. A large sample size made determining the actual likelihood of a false positive or negative much easier.

What Bayes Statistics Imply about This Diagnostic Approach

The Bayesian statistic calculations 1 and 2 conclude that the individual PCR replicates are reliable in detecting whether or not patients have a disease SNP. For both calculation 1 and calculation 2, the Bayes values were close to 1.00 (100%). The high Bayes values indicate that the tests were reliable. Error could have been from the SYBR Green being exposed to light before being used in the fluorimeter, the method of adding primers or transferring liquids, mistakes in the use of the ImageJ software, or a flaw of the Open PCR machine. If the SYBR Green was exposed to light before use in the fluorimeter, the fluorescence of the drop could change. False positives or negatives could occur because of the exposure to the light. Error could occur from the process of transferring primers and enzymes, as the liquids could not be mixed properly and the target gene may not have been copied enough. Human error in calculations using the ImageJ software could lead to either wrong calibration results or wrong values for the patients. A wrong calibration line would skew the results of the two patients even if the patients' drops are analyzed correctly. The Open PCR machine could have had errors, but groups were allowed to leave before the process was complete. There could have been temperature control problems, but the group was not present to identify the issues.

The Bayesian statistic calculations 3 and 4 conclude that individual PCR replicates are not reliable in diagnosing or predicting the disease. The Bayes values for calculations 3 and 4 were very small. The small Bayes values indicate that the tests were not reliable. Overall, the Bayes values show that the PCR tests are reliable in detecting a disease but not reliable in predicting a disease. This is important, because it shows the limitations of the applications of PCR testing. It can only be used to confirm not to infer.

Computer-Aided Design


Boat made with TinkerCAD Boat made with TinkerCAD

Using the TinkerCAD ruler tool helped us see how precise designing in a virtual setting can be done efficiently and quickly. The shape tools made it easier to combine small details into one overall product. The shapes also made it easier to put on the computer what you were originally visioning in your mind. The boat that was made was a simple design, but it incorporated many of the features of TinkerCAD. Making the boat in TinkerCAD helped us better design a better version of the PCR machine.

Our Design

PCR machine made with TinkerCAD

TinkerCAD helped us change the design of the PCR machine. We used the parts of the PCR machine that were already made by Dr. Haynes and changed some of the parts of the machine. Instead of having a bulky lid with the PCR tubes underneath, we decided to put a slot in the side for an easier way to access the PCR tubes. We also got rid of the bulky lid that was on top. The PCR machine is less bulky and the PCR tubes are more accessable.

Feature 1: Consumables Kit

All liquids will be shipped in small test tubes. Micro test tubes and micro-pipette tips will also be included in the package. Our consumables kit will include the standard liquids:

  • SYBR Green
  • buffer
  • nucleotides
  • primers (with some restrictions)
  • hydrophobic glass slides

Any other additional liquids can be ordered separately. The SYBR Green liquid reacts to light, so the small test tube it will be shipped in will be black to avoid contamination and the use of foil. The primers will be available for purchase, but since each gene has a different coding, the customer will have to select the primer specific to their target. All of the other tubes will be labeled with their contents to eliminate confusion.

Black micro test tube

Citation: Catolla. Image of Arm In Glove And Tube. Digital image. FeaturePics. FeaturePics and FeatureImage, 2014. Web. 25 Nov. 2014.

Feature 2: Hardware - PCR Machine & Fluorimeter

PCR machine made with TinkerCAD

The PCR machine is very bulky and has a lot of pieces that could be removed and the machine as a whole could be improved.The PCR machine was changed so there were an increased number of test tube slots and there was only one thing that had to be moved in order to work the new PCR machine.

A major weakness of the improved PCR machine, is that it is possible that heat will be lost when the process goes on. Therefore the PCR machine would need to be in the process of heating for a little longer than normal time.

Right side view of an improved iPhone stand Left side view of an improved iPhone stand

The set-up of the Fluorimeter stayed the same, other than the stand that the phone rested in. As we completed the lab, we noticed that the phone kept toppling over in the stand that was given to us. This not only could damage the user's phone, but can also create error as the phone will not be the same distance away from the drop during each trial. We changed the shape of the base of the stand from a rectangle to a circle in order to make its center of gravity lower than the previous design, thus making it harder to topple over. There is also more support to hold the back of the phone and prevent it from falling. The PCR machine has the removable tray as described in the Our Device section.