BME100 f2017:Group3 W0800 L6

BME 100 Fall 2017	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: Joey Green Name: Julian Klein Name: Kenny Le Name: Beerjas Bath Name: Nathan Atwood The People of PCR LAB 6 WRITE-UP Bayesian Statistics Overview of the Original Diagnosis System During our time in the lab, 17 teams of roughly 6 students per team each tested 2 patients, creating a total of 34 diagnosed patients, for single nucleotide polymorphisms present in their DNA related to the Alzheimers disease. Because this was such a large task, there was a lot of room for error; however, many different steps were taken to minimize and eliminate error throughout the lab. To begin with, there were many different trials done for the initial PCR reactions. Rather than testing each patient only once, each team tested both of their patients three times. Also, the use of controls allowed each team to have a better understanding of what their results might come out to and further helping the team to correctly identify whether or not their patient had the gene for the disease. Furthermore, there were five calibration bubbles used before inputting any information into Image J, simply to ensure that the results were accurate. Lastly, each team took three different photos of their micropipette bubbles to make sure that each picture was the best quality to again enable the best results. The lab as a whole concurred that their patient tested negatively, with a few positives and inconclusive patients sprinkled in there. A few of the "inconclusive" results stemmed from the fact that their patient was not positive or negative with every trial. This could be due to personal error. There was also a group with no data input for themselves, which makes the lab slightly less accurate as a whole. A few teams got inconclusive results on their individual PCR tests. This could just be because they added too much solution to their dot or because of human error again. All-in-all, the lab results were primarily negative. What Bayes Statistics Imply about This Diagnostic Approach The Bayesian Statistics revealed that about 79% of people that had the disease SNP would test positive through the PCR test. Likewise, about 46% of people who did not have the disease SNP would not test positive through the PCR test. These statistics infer that the PCR test is inaccurate in identifying the disease SNP; However, the PCR machine is proven accurate and precise, so we have to take into account the errors that affected our data. First, the fluorimeter could have been improperly calibrated. Also, the pictures might have been taken at different distances from the machine each trial, and you could also consider the picture quality as a source of error. Lastly, relying on an entire class for collective data increases the possibility of error for all of the previously listed sources. Given a positive positive final test conclusion, the PCR test predicted that about 57% of people will develop the SNP disease. Likewise, given a negative final test conclusion, the PCR test predicted that about 84% of people will not develop the disease. These statistics shed light on how accurate the PCR test is in predicting the development of a disease. We can conclude that there should be other tests in collaboration for predicting the development of the disease SNP. Since the reliability of the PCR test is only about 84%, it is evident that it cannot fully predict the disease. It also demonstrates the disease SNP is not the only factor in the development of the disease we were given. Intro to Computer-Aided Design 3D Modeling We used TInkerCad for this project design because we found it to be a more user-friendly platform when it comes to designing new models. When it comes to inserting and cutting out certain shapes, TinkerCad was easier to use because it gives its users premade shapes that they can insert instead of having to cut out and design your own shapes. It is definitely less proactive that SolidWorks because the user does not have to do nearly as much to familiarize themselves with the software. TinkerCad was a better choice for us because of the use of different colors in the design as well. The colors helped us better distinguish the orientation of the objects we were adding or cutting out. TinkerCad also has the ability to be shared with other users. Rather than heading to a computer for one person at a time to work on a design, multiple people can work on a design in TinkerCad if the design is shared with them. Our Design The choice of this design was based on convenience, efficiency, and price point. The flaws we identified in the original design of the OpenPCR was that it was very inconvenient to have to operate two different machines in order to get the results. We designed a PCR Fluorimeter, a machine that houses both the PCR and fluorimeter machines in one. This is more convenient simply because since both machines are together by design, the search or inconvenience of not having the second part of the machine is no longer a problem. This is also more cost-efficient. Because both machines are combined into one, there is no reason to buy both separately since they will be manufactured as one machine at a lower cost. Although our new machine does not involve any major redesigns of the original machines, we believe it to be a better option. Feature 1: Consumables Our product will come with a consumables kit that will look somewhat different than the usual kit. Our newly-designed incubator comes with an attachable box that will contain test tubes; However, these test tubes will have to be modified - they are reusable. Also, storage boxes will no longer be included in the consumables package because the attached box takes over its function. In a regular consumables kit, a stand may be provided to take pictures of the reagents being tested in a fluorometer. However, our kit will not provide a stand because the box attached to the incubator contains an attachable stand. This also eliminates margin of error regarding the distance at which a picture was taken. Lastly, the attachable box has a small, safe compartment for glass slides so that it doesn't have to be included in the consumables kit. Essentially, the consumables kit for our product is, except for a few products, being replaced by the diverse attachable box on the incubator. Feature 2: Hardware - PCR Machine & Fluorimeter We decided to incorporate both machines into our system for efficiency and cost purposes. We felt that not incorporating either the fluorimeter or the PCR Machine would increase the cost and possibly inhibit the ability for someone to purchase one of the items or the other based on their budget. We created a PCR Fluorimeter in one. By adding a platform lateral to the original PCR machine, we combined both machines into one. As far as the taking photos of the fluorimeter, it becomes easy to place a phone to take pictures because the fluorimeter is already level with the average smartphone camera after placing it on top of the PCR machine. Increasing convenience and efficiency, it's easier for anyone to get their hands on both machines, and they can be used together better. Although a downside to this is that the machine becomes even bulkier, we think that it is a necessary sacrifice for the convenience of having both machines right next to each other. Additionally, we incorporated a half-circle that will be raised over the droplet in the fluorimeter so that it will be easier for the users to see the CYBR Green illumination for photos and analysis, rather than having to place a large, bulky box over the entire fluorimeter system as a whole.