The BME 100 Lab class all worked together to test 16 difference patients for the disease-associated SNP. The 8 groups of 4 students were each responsible for two different patients. Each patient had three samples that were tested separately. Each sample was observed in the fluorimeter after varying concentrations of SYBR GREEN were added to the sample. Pictures were taken for all of the samples including the positive control, the negative control, and water in every concentration that was used. For all 3 samples from each patient, the positive control, the negative control, and the water sample three different pictures for each of the 5 concentrations were taken. ImageJ measured the mean area and the integrated density. All of these values were then used to obtain the PCR concentrations. From these numbers, we can see that 3 patients were positive for the disease-associated SNP, 6 patients were negative and 5 patients were inconclusive. Data could have been affected by having to readjust the camera when the phone that was being used would time out, or just improper calculations being carried out.
What Bayes Statistics Imply about This Diagnostic Approach
For the first calculation, there was about a 50% probability that a patient will get a positive final test conclusion given a positive PCR reaction. This is just over half which is not ideal. For the second calculation, there was a close to 75% probability that a patient will get a negative final test conclusion given a negative diagnostic signal. This percentage was closer to 100%, showing us that it was more reliable.
For calculation 3, it was found that there was a probability greater than 100% that the patient will develop the disease given a positive final test conclusion. This can most likely be attributed to the inconclusive results that were obtained from some of the tests. For calculation 4, there was a probability also greater than 100% that the patient will not develop the disease given a negative final test conclusion. This can also be attributed to the inconclusive results that were obtained from some of the tests.
The first possible source of error is how we set up the camera. The setup could have cause the drop itself to be too blurry or the camera could have been in a different spot as we did each new concentration and such. There also could have been an error in how ImageJ analyzed the photo. When selecting the part of the drop for ImageJ to analyze, it was important to exclude the really bright spots there were being hit directly by the light. Attempting to do this was difficult and some of the brighter parts may have ended up in the area that was found. Finally error could have occurred in just doing the calculations. The numbers could have been graphed wrong and then the line with the best fit would not be accurate which would skew all of our results in the end.
Intro to Computer-Aided Design
3D Modeling
The software we used to create our computer aided design was Solidworks. The program was extremely useful for the purposes of our design, because we were able to delete the parts that held the old screen in place and replace it with the new touch screen and the computer hard drive, while still keeping the other parts of the PCR in their original space. Solidworks enabled us to easily display our design in a 3D format, and contains many features that are beneficial in product design. By continuing to practice the use of Solidworks and programs like it, we are preparing for any future product design courses we may take. Once the use of Solidworks is mastered, the program can also be used in a professional setting, to design actual products.
Our Design
Front View Top View
Isometric View
Our improved design includes an internal computer hard drive and a touch screen, to eliminate the need to hook the PCR up to an external computer. We chose this design because during our lab, we noticed that while using the PCR our TA had to set the parameters and display the results on an external computer. By having this internal computer system and screen, the PCR is easier to use and more mobile than the original PCR. All of the parts that enable the PCR to be used by an external device are still in place; so should the internal drive malfunction, or the touch screen break, the PCR can still function.
Feature 1: Consumables
The consumables would remain the same and will continue to use the same products for the lab. There were no changes regarding the consumables, only to the machine itself which did not impact the use of consumables. However the kit would include the smaller items to avoid any loss in the products. The items would be the pipette tips, PCR tubes, and the PCR reaction mix. The DNA will be separate as well as the micropettor, coat, gloves, waste bin and machine. This would eliminate the bulk and the extra packaging. Use less plastic and supplies to complete the lab.
Feature 2: Hardware - PCR Machine & Fluorimeter
The fluorimeter will not be changed and still be included in our system. The PCR machine will function the same way, but instead of connecting the machine to a computer, the machine will have a touchscreen. The touch screen will make the system more efficient for set-up and completely get rid of the need of a computer hook-up.
BME 100 Spring 2018
