BME100 f2015:Group13 8amL6

BME 100 Fall 2015	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: Derek Scott Name: Parker Storry Name: Alexander Dasilva Name: Luis Morales Name: Shivanshi Shukla Name: Ksenia Poujlivaia

LAB 6 WRITE-UP

Bayesian Statistics

Overview of the Original Diagnosis System To begin this lab,we firstly as a class broke into 17 teams containing at least 6 people each. A total of 34 patients were tested by the different groups. Which basically added up to the teams studying two patients each. The main goal was to determine whether or not the patients were positive or not for the SNP. The process was done using PCR and Image J to help us collect some data to analyze it using the Bayesian statistics. In order to make sure there were no errors, we all wore proper lab attire, and tested the patient's samples multiple times to give us multiple results to compare and ensure our data collected was correct.However, ensuring that all the materials were underneath the tin foil could have also been the possible cause of error. Due to the fact that mistakes were made in always keeping the collected samples covered at all time and avoid light exposure. After all the proper precautions were taken we started running the lab. Each patients samples were tested at least 3 times, so that we could ensure the test was more accurate.Also so we had a better idea of what the outcome of the results should be. Once the entire class's data they collected and results were on the shared spreadsheet, it helped us collect our final data. Having to see every groups data was a bit challenging and unreliable because some didn't do the lab correctly. While they did the lab their results seemed inaccurate possibly due to the errors in their ImageJ process, or other environmental errors. However, it overall didn't have that much affect on our groups results.

What Bayes Statistics Imply about This Diagnostic Approach

Calculations one and two are used to determine the accuracy of being able to detect the disease SNP. When looking at the statistics it is very clear that there is a definite correlation between the PCR replicate and the conclusion of whether a patient has a disease or not. Both the diseased and non-diseased patients came back either positive if they had the disease SNP or negative if they didn't. The results that came back both were extremely close to almost perfect results. This means this method is a fairly reliable way of testing whether you carry the disease SNP or not.

Calculations three and four describe your possibilities of developing the disease given either a positive or negative conclusion. Both of the possibilities for each of the tests are not very appealing. Together they average around at about 30% for successfully predicting whether you will develop the disease. The chances of you developing the disease does come at a smaller risk fortunately. If a positive conclusion is returned, the odds of the disease further developing is quite low and the chances of the disease won't develop if a negative conclusion was returned is pretty high. Overall this lab doesn't really help predict the development of the disease, instead it more accurately reads if the disease is currently present.

One of the biggest hindrances of this lab was the fact that we didn't have any sort of professional way of capturing images. We had to use the cameras off of our phones that were very faulty throughout the lab. The camera never seemed to be able to captured a fair enough image without it being out of focus. Going along with this, the method of keeping the light out was putting down a flap which had drawbacks in and of itself. We had to close it carefully or else that would shake the inside of the PCR which would alter the phone by shaking it and going out of focus. One final possibility error comes from the chance of improperly using the ImageJ program. The operators could've very easily have caused an accident by doing something as simple as improperly making a circle that didn't fit the drop. ImageJ was a tedious program that left great room for mistake.

Intro to Computer-Aided Design

TinkerCAD

Our company made use of TinkerCAD for improving the design of the OpenPCR. TinkerCAD is an online computer aided design software that allowed us to quickly model and adjust parameters of the original OpenPCR design. TinkerCAD was chosen over Solid Works due to the ease at which various group members could access the design online, and due to the tendency of Solid Works to often crash when saving designs. Our company used TinkerCAD to assemble the OpenPCR using components provided by the lab, and to then easily create and change any dimensions of the product. Our team chose to improve the capacity of the OpenPCR, which was easily accomplished using TinkerCAD.

Specifically, our team decided that the original OpenPCR design's limited number of microtube placements was one of the most glaring limitations of the machine. Thus, we wanted to address this issue by increasing the microtube capacity of the OpenPCR. Using TinkerCAD, we uploaded the OpenPCR shell, filled in the current holes that were designed for the lid and display. We then used the cube tool to create the correct opening size for the hinge and microtube tray and created two areas that each will hold 16 tubes for a total of 32 tubes. We also used the functionality of TinkerCAD to create a display screen for the front of the unit.

Our Design

Feature 1: Consumables

A major weakness in the plastic tubes used was that it was very difficult to open and close the tube without the fear of spilling the solution inside. This pertains to our re-designing of the lid, as the plastic tubes come into close contact with the lid. These plastic tubes, as well as the pipettor and reagents will be included in our re-vamped PCR kit. Due to the light sensitivity of SYBR Green solution, this will not be included in our consumables kit.

Consumables Included in Redesigned OpenPCR Kit

1. Redesigned plastic microtubes attached in groups of 4 (108 total tubes included)

• • Tube colors alternate between yellow, red, blue, and violet

1. Micropipetter, 250 μL capacity

• Micropipetter tips, pack of 100

1. Reagents

• • PCR Mix (100 mL)
  • Primer solution (100 mL)
  • Buffer solution (100 mL)

Feature 2: Hardware - PCR Machine & Fluorimeter

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