BME100 f2017:Group16 W1030 L6
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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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LAB 6 WRITE-UP
Overview of the Original Diagnosis System
In 16 groups of 4-6 people, BME students were given two patients samples which had to be tested for a particular disease (SNP). Each patient sample was then divided into 3 smaller tubes using a micropipette into a primer mix that diluted the DNA and allowed it to be tested in a PCR Machine. Along with the given patient samples, students were also given a sample that tested positive (positive control) for the disease and a sample that tested negative (negative control). The negative and positive control were also diluted with the primer mix. Then the 8 samples of DNA (3 from each patient, the negative control, and the positive control) were mixed with buffer and SYBR green in order to test them with the fluorimeter device. Each of the samples was also mixed with Calf Thymus DNA of varying concentrations. The samples were then photographed using a fluriometer device. In order to avoid potential errors, three pictures were taken of each sample. The images were then analyzed on ImageJ, in which the brightness of the samples was analyzed to determine whether or not the patient was negative or positive for the "disease". For the most part, the class was accurate in their final assessments of whether their patients were positive or not, although there were some inconclusive results which could have come from mistakes in calculations or errors in analyzing the images.
Calculation 1 represents the probability that a patient would receive a positive final result given that a positive PCR result was also obtained. The number calculated in this part was close to 1, meaning that the experiment has high sensitivity in predicting if the patient is positive or negative for the disease. Calculation 2 represents the probability of the patient receiving a negative test conclusion given a negative PCR reaction. Since this number is close to 1, this shows a high specificity in predicting whether the patient is positive or negative for the disease. Therefore, since both numbers of sensitivity and specificity are close to 1, it is reasonable to believe that the PCR replicates are good sources when determining whether or not a patient has a certain disease.
Calculation 3 represents the probability that a patient who is given a positive final test result will develop the disease. The number calculated for this part was about 55% which shows a low sensitivity in detecting the disease. Calculation 4 represents the probability that a patient who is given a negative final test result will not develop the disease. The number calculated for this part is close to 1, showing that there is a high specificity in the experiment detecting the disease. While the specificity is high, the sensitivity is significantly low, meaning that the accuracy of the PCR experiment is doubtful due the possibility of giving inaccurate readings (specifically negative results).
One possible source of error during the PCR and detection steps could have been the image analysis on ImageJ. When placing the oval on the droplet, it may have been inconsistent with the area of the droplet or shifted slightly in the process of analyzing. Additionally, the pictures analyzed could have been blurry, therefore making it harder to distinguish the area of the droplet against the background.
Intro to Computer-Aided Design
Feature 1: Consumables
Our packaged kit will include the following consumables -
The labeled tubes would be important for this particular procedure because it reduces the time spent on labeling the positive and negative controls and the patients' ID. Glass slides are an added benefit because they help visualize the fluorescence and of the droplet and its shape better. Gloves and googles help when handling these chemicals and protecting them from entering your eyes.
Feature 2: Hardware - PCR Machine & Fluorimeter
The design of the open PCR machine will be the same as it was for the experiment in the previous lab. The one part of the hardware for this system that is changing is the fluorimeter. The new type of hardware that this part of the system will be utilizing is a built in camera. This camera will be able to capture a clearer image of the contents in the box and record this information in a chip that can then be connected to a computer where the photos can be downloaded.