BME100 f2015:Group3 8amL6

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Contents

OUR COMPANY

Name: Rachel Hagan
Name: Rachel Hagan
Name: David Busch
Name: David Busch
Name: Shahzadi Aimen
Name: Shahzadi Aimen
Name: Michele Dekker
Name: Michele Dekker
Name: Amellali Gamez
Name: Amellali Gamez
Name: Jose Moreno
Name: Jose Moreno

Our Company: Simple Tech

LAB 6 WRITE-UP

Bayesian Statistics

Overview of the Original Diagnosis System


A group of 34 students was divided among 17 groups of students. Each group received two patients that they tested to find if they were positive or negative for albinism (disease associated SNP). Along with the three samples from each patients, groups also received PCR mix including Taq DNA Polymerase, MgCl2, and dNTP’s and DNA primer mix that included forward primers, reverse primers, and template DNA. Once we labeled the test tubes and calibrated the micropipette to 50microliters we combined the DNA to corresponding test tubes and tested them in the PCR machine. Possible error was prevented by having three samples for each patient. This greatly prevented the likelihood of a false positive or a false negative. Error was further prevented by having the groups take three pictures of each drop sample. This would reduce the likelihood of an inconclusive result.


What Bayes Statistics Imply about This Diagnostic Approach


For calculation 1, the probability that a patient will get a final positive test conclusion for albinism, given a positive PCR reaction, is close to 1.00. The test is showing a high reliability rate when detecting that a person has albinism.

For calculation 2, the probability that a patient will get a negative final test conclusion for albinism, given a negative PCR reaction is much closer to 1.00. This indicates that the PCR test has a higher reliability rate when detecting the absence of albinism than even the positive PCR test.

Therefore, given a positive PCR result and a final positive test conclusion, and a negative final test conclusion, the PCR test is showing a high reliability rate of success for either positive or negative results.

For calculation 3, the probability that a patient will develop albinism given a positive final test conclusion is much less than one, indicating that there is a disparity between the PCR resullts and a diagnosis of albinism.

For calculation 4, the probability that a patient will not develop albinism given a negative final test conclusion indicates a mid-range value of over fifty percent. Again, the negative PCR results and negative diagnosis results are much closer, but still indicates that a diagnosis may require more investigation to determine if albinism is present.

The overall results of both tests when compared, indicates that the diagnosis of albinism cannot be determined only from the PCR. Determining the outcome of albinism through PCR results cannot be relied upon as the only way of diagnosing albinism. Other tests should be done for a comprehensive and inclusive outcome of negative or a positive diagnosis.

One error that could have occurred is the amount of light within the box when taking the picture of the drop, causing an error in the illumination of the drop. Another error that could have occurred is the angle at which the picture was taken, causing the amount of SYBR Green1 to be false in ImageJ. The cellphone that is used with the fluorimeter process is not standardized, so errors can occur due to the operating ranges of different manufacturers for the standard controls of the camera. One of the other errors that could have occurred in the very beginning was with the labeling of the test tubes with patient's samples which could have lead to a false result at the end.

Intro to Computer-Aided Design

TinkerCAD
Working with TinkerCAD was simple and effective. It allowed us to get to create our design quickly but did not seem to be as accurate as Solid Works. When working with Solid Works I felt that my design was more precise and to my exact specifications whereas the TinkerCAD felt as if I was just throwing different shapes together to make it look like the design in mind. TinkerCAD is a great tool to use when you are trying to get a quick and more realistic view of a product design that has been on your mind. TinkerCAD was a simple and more straight-forward tool to get a design done fairly quickly and efficiently.

Our Design

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Our design:


Our product and company’s name is Simple Tech. This device is handheld and can be easily transmitted from place to another. Our device has a number of components; a test strip that already has PCR mix and DNA primer mix and just needs the patient’s sample to be added when it is ready to be used, a metal heating plate slot where the test strip is put in, this plate slot is heated and cooled for PCR reaction by using electric circuits and a battery. Our device includes a black box that has the properties similar to a fluorimeter, this black box resides on top of the test strip compartment in the device, this black box also has small cell for SYBR green which is refillable and this cell uses a very small and precise amount of SYBR green that is dropped on the already processed PCR DNA. The next step in the design of this product includes a camera which takes few shots of the DNA sample with SYBR green added to it. These pictures are transferred through the circuitry within the device that has microprocessors that makes this transfer quick and efficient. This device also has a USB port that can be connected to the computer for the final analyzing and finalizing of the results. The device is turned on and off by a switch. Lastly, our device is simply and has the ability to store about 64 GB of data. Our design is more focused on individual results rather than results for a group of people. This design helps lower the cause of error by making it more personalized for each patient. It is different from the original OpenPCR because it eliminates the need of labeling the tubes with different patient IDs and then placing up to 16 of those tubes at once in the PCR that can lead to error in reading the results if the tubes weren't labeled correctly in the first place. We chose to design a device to test individuals to reduce the possibilities of error and have quick and simple results. Our design is mainly used for testing only one particular kind of disease and for appropriate audience. The disease that our device detects using the test strip containing all the mixes, PCR reaction, and flourimeter is albinism.


Feature 1: Consumables

Consumables that will be included in out packing plan include:

  • PCR Mix
  • Primer Solution
  • SYBR Green Solution
  • Buffer
  • Glass test strips

The test strips that are included will have the necessary mixes on the strip prior to packaging and distribution to make it more simpler for users. Each package will contain 100 disposable strips that are able to be purchased at a later time if needed. SYBR green solution comes in a small cell that is put on the black box to be added to the DNA sample after the PCR reaction. This cell is refillable and disposable.

Feature 2: Hardware - PCR Machine & Fluorimeter

Our device is portable and small in size. The device comes with up to hundred test strips, these test strips already have PCR mix, DNA primer mix, buffer in it and when the patient's DNA sample is added to it then this strip is placed in the main device. The other components of the device include a metal slot where the test strip is put it, this metal slot is connected to a circuitry and battery that helps with the heating and cooling of this strip to carry out PCR reaction. A black box that is placed on top of this metal slot with the test strip works as a fluorimeter, this black box has the blue LED light that passes through the sample of DNA after the PCR reaction has been completed and SYBR green is added to that DNA sample, this SYBR green solution is added to the sample from a cell that is refillable and is on top of the black box. The camera placed at the other end captures the shots of the sample to be further analyzed and finalized for the results. The image is provided in the design section with labels on the components. Our device is mainly designed to detect particular SNP in the gene that is associated with albinism. The DNA primer mix present in the strips have particular forward and reverse primers associated with this disease.


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