BME100 s2016:Group5 W1030AM L6

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BME 100 Spring 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: Tudor Sasaran
Name: Nathan Grass
Name: Devin Lillegaard
Name: Jaffalie Twaibu
Name: Jagannath Pandarinathan
Name: Stephan Mendez


Bayesian Statistics

Overview of the Original Diagnosis System In BME 100, 17 groups of six students each, tested for the disease associated SNP. Three samples of each patient were given to the 17 groups, along with a buffer, calibration solutions, a positive and negative control, and green fluorescence. The calibration solutions were imaged through PCR and analyzed in the software imageJ. The patient DNA samples were then imaged through PCR and put in imageJ. To prevent error, the pipette tips were changed every time they came in contact with one of the solutions. The green fluorescence was covered immediately to prevent it from absorbing light. In total, 96 PCRs with 36 total positive PCRs and 56 negative PCRs. In total, 32 tests were run with 12 positive, 18 negative, and 2 inconclusives out of those 32 tests. Some problems that occurred were that the images were tough to analyze in imageJ. Also, not all the pictures were probably taken at the exact same angle. This could be another source of error.

What Bayes Statistics Imply about This Diagnostic Approach Calculation 1 was relatively close to 1. This means that if a patient has a positive test diagnosis, then they will have a positive pcr reaction. The patient will develop the disease. Calculation 2 shows that if a patient has a negative test result, they will have a negative pcr reaction. So the patient will not develop the disease. Calculation 3 shows us that if a patient received a positive test diagnosis, there is still a low chance of developing a disease, less than 50%. The result for calculation 4 indicates that if a patient recieved a negative diagnosis, there is no chance of developing the disease. 0% chance of developing the disease. Some possible sources of error could be rounding errors, incorrect use of the pipette, and the limitation of the measurement. Another possible error could be an incorrect interpretation when analyzing the tests.

Intro to Computer-Aided Design

TinkerCAD was a relatively easy online application to use. The tutorials helped in learning the different features of the design program. It is a less sophisticated design program when compared to Solidworks so the designs can't be as specific/detail oriented, but it is also much easier to use, especially when using TinkerCAD for the first time. We created a design of the openPCR machine but the primary design change we made was to the fluorimeter, specifically the portable light box and camera set up. This is what you will see in our image below.

Our Design

Our new design for the light box includes a mounted camera which eliminates focusing and re-focusing in between samples. It also will give us more consistent positioning of the camera relative to the slide, which should lead to more accurate data collection. There is also a USB cable coming from the box, linking the camera to the computer. This makes for easier data collection when compared to transferring images from a smart phone into a computer. The analysis would also become quicker by eliminating this extra step. Finally, we would want to run our camera through a computer application that could be pre-set to automatically perform the color split of the pictures being taken as well as automatically analyze the pixels.

Feature 1: Consumables

Our Consumables kit : PCR mix, primer, pre-labeled plastic tubes and SYBR Green solution

The biggest weakness for the general consumables kit is in the plastic tubes. Our team encountered difficulties to stay organized because of the plastic tubes, therefore, we thought it would be a good idea to improve them by pre-labeling so there will be no confusion or accidents like clearing the marker from the plastic material that they are made of. We thought increasing the size with 15% will make them easier to operate. The reagents are playing the main part of the PCR reaction, therefore these reagents will have their own space in the kit and will have the name written above them, to keep things organized.

Feature 2: Hardware - PCR Machine & Fluorimeter

The Open PCR machine will not see any changes in our system but there will be changes made to the light box and camera cradle for the fluorimeter. Both fluorimeter and the Open PCR will be included in our system, but the main focus will be the easier to use fluorimeter.

The biggest change comes from the light box used with the fluorimeter. The light box now includes brackets that hold a camera mounted in place and it remains focused on the slide stand. This will allow for much easier and more consistent set up, as well as easier calibration. There is a USB cable connected to the box that will allow for faster image transfer into the computer software program.