BME100 s2016:Group2 W1030AM L6

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OUR COMPANY: LIBEDE TECH

Name: Bailey Gasvoda
Name: Ishitha Jagadish
Name: Destinee Martin-Karim
Name: Earl Brown
Name: Erik Drager
Name: Logan Luke

Name of team's company: LIBEDE TECH

Brand name of product: LibedePCRMachine

LAB 6 WRITE-UP

Bayesian Statistics

Overview of the Original Diagnosis System

For the analysis of patients’ DNA in order to make diagnoses, 16 groups from 16 different companies with each group containing six employees tested 32 patient samples using the process of PCR for the sake of division of labor. Therefore, each group tested two patient samples. Each group tested each patient sample three times by taking three drop images of each patient sample in order to prevent errors by attempting to increase the accuracy of the PCR results. One challenge that was faced was that the pictures were not of high quality, since they were taken with an iPhone 6 camera.


In the class data that was obtained, 12 trials had positive final results, 18 trials had negative final results, and 2 trials had inconclusive final results. 68.8% of class data correctly corresponded with the doctor's diagnosis, meaning that either both tests yielded that the patient did not have the disease or both yielded that the patient did have the disease. Consequently, 31.3% of class data incorrectly corresponded with the doctor's diagnosis.


What Bayes Statistics Imply about This Diagnostic Approach

The probability of a patient getting a positive final test conclusion given a positive PCR reaction was close to 1.00 (100%). The probability of a patient getting a positive PCR reaction given a positive final test conclusion was close to 1.00 (100%). These results from calculation 1 mean that the individual PCR replicates were reliable for concluding whether or not a patient has the disease SNP.


The probability of a patient getting a negative final test conclusion given a negative PCR reaction was close to 1.00 (100%). The probability of a patient getting a negative PCR reaction, given a negative final test conclusion was close to 1.00 (100%). These results from calculation 2 also mean that the individual PCR replicates were reliable for concluding whether or not a patient has the disease SNP.


The probability of a patient developing the disease given a positive final test conclusion was slightly below 0.5 (50%). The probability of a patient being given a positive final test conclusion given that the patient will develop the disease was 0.5 (50%). These results from calculation 3 mean that the PCR test is not very reliable to use in order to diagnose the disease.


The probability of a patient not developing the disease given a negative final test conclusion was above 1.00 (100%). The probability of a patient being given a negative final test conclusion given that the patient will not develop the disease was close to 1.00 (100%). Even though the latter had a good result of near 1.00 (100%), the former had an impossible result of over 1.00 (100%). Therefore, it must be concluded that the results from calculation 4 also support the idea that the PCR test is not very reliable to use to predict whether the disease will develop or not.


Sources of Error

1) Inaccurate pictures: Since the pictures were taken with an iPhone 6 camera, the colors of the drop images may not have been accurate. Also, the dim lighting cause the pictures to be a little blurry. This error could be minimized by using a professional camera. While all groups used ImageJ to analyze the drop images from the fluorimeter, some used webcam cameras to take the pictures while others used phone cameras. The use of different cameras probably contributed to the error in the experiment, because the type of camera that was used should have been controlled.

2) Small number of trials: Each patient sample was tested only three times. In order to increase the possible accuracy of the results, more trials could be performed in the future.

3) Concentration of DNA: If the concentration of DNA was very low, it is possible that tests performed on the DNA would not be accurate.

Intro to Computer-Aided Design

TinkerCAD
First, the prepared body of the PCR machine was uploaded using the import tool. Each piece had to be rotated and moved to be in the right angle and place. The heating chamber was uploaded next. It had to be copied so that four were in the workplane. They were then moved together to be one continuous piece. The four were grouped together to make for easier movement later. The ruler was used to measure the side of length of the new enlarged heating chamber. Therefore, it was possible to know how much space was needed on the top of the PCR body. A new hole for the heating chamber to fit in was created, and the piece was moved into place.

Our Design

Openpcrmachinegroup2.png
LIBEDE Tech resigned the standard PCR Machine to increase efficiency. Previous models held only 16 samples, meaning researchers had to wait for runs to finish before running that next sample. Now they can run 64 samples at once. This image is shown without the lid to showcase this new design feature. This means the results are ready in 1/4 of the time.


Feature 1: Consumables

The LibedeTech consumables kit will include:

  • 1 Micropipetter
  • Pipette tips (100)
  • 80 empty PCR tubes
  • 80 test tubes that can hold 25-50 μL of the mixed solution
  • SYBR Green Solution
  • PCR Mixed solution
  • Primer Solution
  • Buffer Solution
  • Glass Slides for Fluorimeter

The packaging of the consumables will contain all of the needed supplies packaged separately, there will also be a full list of instructions for when the subject is setting up the PCR machine. Each of the separately packaged supplies will also have a label, addressing the name of the supply and what it is used for. Among other things, there will be a disposable bag that can be used when disposing the equipment, especially the pipette tips. Pictures and diagrams will also be provided for a visual view of the PCR machine after it is set up. The PCR tubes rack will also be in the kit along with the necessary mixtures to perform the experiment. The test tube rack will be larger compared to others to minimize the previously stated problem with not having enough sample space.

Feature 2: Hardware - PCR Machine & Fluorimeter

The PCR Machine that was used for the experiment was very limiting in that it only allowed 16 slots for PCR samples to be placed into the machine. For this reason, the new and improved LibedePCRMachine was upgraded to have 64 slots which makes the machine more efficient.


One of the ways to redesign the Fluorimeter system would be to make a built in stand. The stand itself should be adjustable both forward and backwards, as well as adjustable in height. With this kind of stand that is actually attached to the system, there won’t be any errors or differences in the distance or the height of the pictures. The built in stand will just make everything more consistent.