BME100 f2014:Group30 L6

BME 100 Fall 2014	Home People 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 Photos Wiki Editing Help
OUR COMPANY Name: Megan Wieser Name: Brittney Wong Name: student Name: student Name: student Name: student LAB 6 WRITE-UP Bayesian Statistics Overview of the Original Diagnosis System In the PCR lab experiment, the DNA of 68 patients total was amplified and analyzed for a specific disease indicator in order to predict the group's probability of disease detection. To divide the work for this experiment, 34 groups of 6 people each tested 2 patients to determine the likelihood that either patient would contract the disease. As with any experiment, steps were taken to prevent error. For example, 3 total replicates were tested for each patient as a way to minimize the likelihood that the patient will be misdiagnosed. In addition, the PCR mix had positive and negative control solutions, which helped to make sure that the PCR machines and fluorimeters produced the expected results for the known positive and negative solutions. Regarding the Image J processing, calibration controls of positive and negative solutions were utilized to prevent error in the sense that they provided a baseline for what was supposed to happen in patient samples with negative and positive test results. In other words, the positive control showed the SYBR green, which indicated that the PCR and fluorimeter machines worked to produce expected, controlled results, and it also indicates that other patient samples with the same green color test positive. To increase the accuracy of the Image J processing values, 3 drop images were taken per PCR sample and averaged together. Although the class's final data contained a majority of successful conclusions, there were discrepancies within the data collection that affected the overall Bayesian calculations for the specificity and sensitivity that a patient has a disease. For example, 8 out of the 68 patient results were inconclusive, which means that the calculated Bayesian probability statistics were higher or lower than the actual probability depending on whether the inconclusive results should have been positive or negative. Blank data was also discrepancy within the data collection, as the 6 blank conclusions decreased the total PCR conclusions that were used to calculate Bayesian probabilities. Since the total number of conclusions was decreased due to the number of blank conclusions, the statistics were higher than what they should have been if there had been 68 total conclusions. For example, if 20 out 68 people had a positive conclusion, there would be a higher probability of a positive test conclusion than if 20 out of 62 people had a positive test conclusion. Measures were taken to obtain the most accurate data collection, but there are things like inconclusive and blank test results that can still affect the data analysis. What Bayes Statistics Imply about This Diagnostic Approach Computer-Aided Design TinkerCAD TinkerCAD is an easy tool used to create designs that can be 3D printed later on. On the website there are many different features which include shapes, planes, numbers, letters, and the ability to import, this allows the ability for a team to easily create designs. In creating the OpenPCR machine, multiple STL files holding the various parts were imported into TinkerCAD for quick assembly. This was then used to dissect how the parts functioned and was a basis for the new design of the OpenPCR machine. Our Design The newly designed OpenPCR machine implements a hyper-speed fan that will cool down the reaction quicker than the regular fan that contributes to the lengthy 2 hour PCR reaction duration time. In addition to the increased efficiency, Feature 1: Consumables Kit One major weakness of the plastic vile consumables is that they were clear and allowed light to pass through to the SYBR green solution. To avoid light exposure, the SYBR green solutions had to be wrapped and stored in aluminum foil, which made it risky and inconvenient to transport the SYBR green. To address this major weakness, Group 30 has designed dark plastic test vials as a way to prevent the SYBR green from being exposed to the light in the room. This makes the solution more convenient to transport during the lab without the aluminum foil, and it also helps to decrease the risk that the SYBR green will be affected from light exposure. Feature 2: Hardware - PCR Machine & Fluorimeter One aspect of the PCR machine that Group 30 has redesigned was the fan system that is used to cool down the PCR reaction. In order to speed up the reaction in general, the group has redesigned the PCR machine to implement a hyper-speed fan that will cool down the reaction quicker than the regular fan that contributes to the lengthy 2 hour PCR reaction duration time. A weakness of the Fluorimeter system that was improved was the method for taking pictures. With the regular fluorimeter system, a phone camera had to be placed into a cradle, and it had to be adjusted or moved several times throughout the experiment to take the best quality of pictures possible. Thus, with the redesigned system, Group 30 has implemented a built-in camera into the side of the fluorimeter, which can be controlled by a smart phone app that allows the group to see inside the fluorimeter without moving the fluorimeter door. The features of the app also allow the experimenter to control zoom and camera resolution.