BME100 f2016:Group16 W8AM L6

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Owwnotebook icon.png BME 100 Fall 2016 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
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Name: Nandini Sharma
Name: Brandon Gandalf
Name: Christian Forbus
Name: TJ Smith
Name: Jared Macanas

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Bayesian Statistics

Overview of the Original Diagnosis System

For this PCR lab, 32 patients were tested for the disease-associated SNP by have 16 teams of 4-5 students test two patients each. To prevent error, each team was to create triplicates of each patient sample and PCR control. Then for the analysis with ImageJ three pictures were taken for each drop and each calibration control. This provided us with a enough data to ensure that we could conduct a reliable analysis and receive reliable results. The biggest challenge in collecting data was taking the photos of the droplets in the fluorimeter. The camera we utilized was light sensitive and would refocus after the lid was closed. This resulted in blurry photos. Also for a few photos the lid could not be completely closed because in order to take the photo someones had had to be in the box to take the photo. This meant that not all the light was completely blocked making it harder to detect the blue light and the green glow of the dot. Even though, we were able to diagnosis that patients successfully. Majority of the patient data was used for the bayesian statistics. Four patients had no data because the analysis of their results was not completed and not ready for statistics to be conducted. Therefore only 28 patients analyzed with Bayesian stats. Four of the patients analyzed had inconclusive results. 7 of the 28 patients diagnosis did not match the doctor's diagnosis. 21 of the patients were successfully diagnosed.

What Bayes Statistics Imply about This Diagnostic Approach

An individual PCR test is pretty reliable in coming to a conclusion. About half of all tested patients received a positive final test conclusion and about half of all PCR reactions ran were positive. Since most of all tests ran that result in a positive conclusion were positive, by using bayesian statistics, it can be determined that there is a pretty high probability that a patient will receive a positive final test conclusion given a positive PCR reaction. By using bayesian statistics, it can also be determined that there is a high probability that a patient will receive a negative final test conclusion given a negative PCR reaction since about half of all tested patient received a negative final conclusion, half of all PCR reactions are negative, an most of all PCR tests that result in a negative final test conclusion are negative.

The conclusions themselves however, are not very reliable. Using Bayesian statistics again, there is only a little more than 50% chance in a patient developing the disease given a positive final test conclusion. There is a slightly higher probability in a patient not developing the disease after receiving a negative final conclusion.

One error could be a result of possible errors in concentrations of solutions needed to run the PCR. Another error could result from errors in collecting images of using a smartphone. The newer models of popular smartphone auto-focus all images, which results in a decreased sensitivity of the detection. A third error could result from surrounding light getting in the fluorimeter, affecting the sensitivity of the sensitivity of the flourimeter as well.

Intro to Computer-Aided Design

3D Modeling
TO design our fluorimeter we utilized Solidworks. Since we have already utilized it once it was far easier the second time. For the box part of the fluorimeter we created a 10 in by 10 in square and extruded it 10 in. Then we shelled it with 0.1 in remaining. For the door we created a 10 in by 10 in square and extruded it 0.35 in. Then we created an extruded cut that is 4 in by 7 in by 0.3 in where a phone will be placed. The hardest part was assembling the product. Mating it in a way that allowed the door to remain open involved mating faces not edges. Overall, the fluorimeter was very simple to make in solid work and the end product matched our idea well.

Our Design

Fluorimeter11.png Fluorimeter

We did alter the OpenPCR design rather the fluorimeter. We choose to design the fluorimeter with a door that had a camera/phone stand to ensure better data collection. While utilizing the fluorimeter in lab we had difficulty focusing our camera and ensuring that all of the light was blocked. Our design consists of a door that has a magnetic lock, similar to a bathroom mirror. This ensures the door will close completely and majority of excess light will be blocked. The camera stand in the middle of the door will be adjustable to fit multiple phones. A phone can be placed in the stand with the back camera facing the drop and the front screen facing you. You can then make sure that the image is focused and can take the photo yourself.

Feature 1: Consumables

What will be included in the package: 1) PCR solution 2) Patient samples 3) PCR test tubes 4) Micropipettte 5) Micropipette tips

The consumables package will include the PCR solution, the patient samples, PCR test tubes, micropipettes, and micropipette tips. These will be clearly labeled. The PCR solution and the patient samples are important because they are need to conduct the OpenPCR. PCR test tubes because the samples and PCR solution will be placed in these tubes and then put in the OpenPCR. Additionally, the micropipette and micropipette tips will be used to to put the solution in the tubes.

Feature 2: Hardware - PCR Machine & Fluorimeter

In our new design we will still incorporate the Open PCR machine and the fluorimeter. The Open PCR machine isn't getting changed but when it comes to the fluorimeter, we've decided to add an adjustable holding slot to support the camera in the right position while it takes the pictures. Along with that we decided to include a magnetic door that will close to keep out light and get the most accurate pictures possible. We'll also have a hole in the door that meets up with the screen of the phone, and allows access to the screen to be able to still use it while keeping the door shut and keeping all light out.