BME100 f2016:Group2 W8AM L6

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Owwnotebook icon.png BME 100 Fall 2016 Home
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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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OUR COMPANY

Yesenia Barrera Millan
Mariam El Sheikha
Tori Johnson
Vishvak Rangarajan

PCR 4 U

LAB 6 WRITE-UP

Calculation 1 describes the sensitivity regarding the system's ability to detect the disease SNP.

Calculation 3 describes the sensitivity regarding the system's ability to detect the disease

Calculation 2 describes the specificity regarding the system's ability to detect the disease SNP.

Calculation 4 describes the specificity regarding the system's ability to detect the disease

Bayesian Statistics

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Overview of the Original Diagnosis System
There were 14 teams of 4-5 students and each diagnosed two patients with a total of 28 patients. Several things were done to prevent error. The first thing that was done was to use 3 replicates of the patient's DNA as well as 3 replicates of a positive and a negative control. Multiple images of each sample were analyzed using ImageJ. We used the aseptic technique to prevent contamination of the samples. For example, we used gloves when handling the DNA samples and discarding the micropipette tips after every use. The final data revealed that there was near an equal amount of positive and negative conclusions. There was also a few inconclusive conclusions that were omitted when calculating the probability of a disease testing positive or negative. A challenge that was encountered was with the Iphone 6 camera. The timer would cause the camera's flash to turn on too early which would ruin the SYBRgreen because it was light sensitive

What Bayes Statistics Imply about This Diagnostic Approach
The results for calculation 1 implies that the PCR reaction is reliable given that the probability that a patient will get a positive final test conclusion for the disease SNP given a positive PCR reaction is about 0.9. The results of calculation 2 imply that the PCR replicate is reliable given that the probability that a patient will get a negative final test conclusion given a negative PCR reaction is about 1.00 (100%).
The results of calculation 3 imply that the PCR is unreliable given that the probability that someone will develop the disease given a positive final test conclusion is about 0.6. The results of calculation 4 imply that the PCR is reliable because the probability that someone will not develop the disease givena negative conclusion is about 0.8.
One source of possible human error is inaccurate measurements. A possible machine error is using incorrect temperatures in the PCR cycles. Another possible error is using the flash on the camera when taking the picture. The sample was light sensitive so it could ruin the sample itself.

Intro to Computer-Aided Design

3D Modeling
During the computer-aided design, there were many different discussions about what the new PCR machine should specifically contain. After a consensus was reached, a design was drafted on paper. The designs were then made on the computer program TinkerClad. Three different designs were crafted, each depicting a different aspect of the design. There were difficulties of downloading the different images, so screenshots were taken and then uploaded onto the lab report.
Our Design
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This design was chosen in order to allow more PCR samples to be placed in the machine and make it easier to close. The original OpenPCR design allowed 16, but the new design will allow for 48 samples. The new design will include a lever which will make it easier to close.

Feature 1: Consumables


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The new micropipette is more accurate and will collect liquids at a more precise measurement. This will decrease any possible error from the micropipette.


Feature 2: Hardware - PCR Machine & Fluorimeter

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As mentioned before, this new design will be able to hold 48 DNA samples rather than 16 DNA samples. This will be efficient in the sense that more samples will be able to be held in one PCR machines as opposed to using many PCR machines. This is beneficial because then all of the DNA samples will be run at the same time and will finish at the same time. Also, it allows more DNA samples to be tested if we had multiple of these PCR machines. For example, if we had the original PCR machine design, we would have to use 6 PCR machines to test 96 DNA samples, as opposed to using the 2 of the newly designed PCR machines to test 96 samples.
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This fluorimeter will be one machine with a separate part that slides into the box. The sliding compartment will include a place to properly hold the camera and the fluorimeter itself will be attached at a set distance that is best for the camera. This will resolve the original fluorimeter's inability to stay in the same place and the inconvenience of setting both objects into position.