BME100 s2015:Group9 12pmL6

BME 100 Spring 2015	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: Brianna Chavez Name: Johnathon Ruiz Name: Josh Quick Name: Maria Guzman Name: Taylor Little Lelouch of Fate Zero Dynasty LAB 6 WRITE-UP Bayesian Statistics Overview of the Original Diagnosis System For this experiment, 68 patients were tested for a disease via a disease-associated SNP. These patients were asked for two samples each of their DNA. The DNA sample pairs were kept together, and a number that was associated with the patient was attached to them. These pairs were distributed amongst 34 teams for testing, amounting to two subjects or four DNA samples per team. The reason for asking each patient for two samples of DNA is to prevent error. That requirement, along with other steps, assures that any anomalies in a single sample will not skew an entire data set. Also, the results from a single patient's samples can be compared to each other and conclusions can be drawn concerning the validity of the test based on the similarity in their results. This is same reasoning behind using multiple drops of DNA solution from each individual sample. Other actions taken to reduce error include positive and negative controls, and the precision of using ImageJ. Adding positive and negative controls established a baseline range for our results, and allowed for direct comparison analysis. This comparison was completed by ImageJ software. The pixel color analysis feature on ImageJ allowed for more accurate, mathematical results as compared to, say, teams visually comparing the color the images side by side. These precautions were necessary to accurately analyze the validity of the chosen test using Bayesian statistics. What Bayes Statistics Imply about This Diagnostic Approach Both the final results for calculation 1 and 2 were above .5, nearing 1.00. This indicates that a negative or positive result would be reliable. The final result for calculation 2 is higher than calculation 1, indicating that the test would be more reliable if the result it read was negative as opposed to positive. Errors that had a notable affect on the accuracy of these results include the quality of the camera that imaged the sample, the probably that some amount of light from outside the dark room permeated the image, and human errors. Human error of this kind is a factor in any experiment and can include typing in a wrong number during analysis, or accidentally adding an incorrect amount of solution. The results for calculations 3 and 4 differ more so from each other than calculations 1 and 2. The reliability that a patient with a positive test result will develop the disease is just about .5, which is not very reliable and this result should be followed up with other tests. A negative test result would be much more reliable, and a patient receiving this result would be more sure in knowing they will not develop the disease. Computer-Aided Design TinkerCAD The TinkerCAD tool was used in creating a 3D design of the fluorimeter setup. On a square platform three objects were created representative of a base (stand for a phone/camera device) and fluorimeter light. The base was placed four centimeters away from the fluorimeter light. A three millimeter cut was made in the bottom of the box at the phone stand and ran to the edge of the box. A cylinder was drawn leading up to the base of the box to represent a cord. The box was created with a cross-sectional cut of the box to allow for viewing the inner contents. Our Design The chosen design was similar to the basic fluorimeter setup. This included a phone base placed four centimeters away from the fluorimeter light placed within a box. A cut was made at the bottom of the box to allow a cord to pass through. This design was chosen for greater simplicity and ease of use of the typical fluorimeter design. This aids in completing the intended use more efficiently and in less time. The differences in the designed fluorimeter setup include an anchored base and fluorimeter light to always allot for proper positioning of the pictures at a four centimeter distance. The cut at the bottom of the box will allow a cord to adapt to the phone/camera device for external imaging of the specimen. Feature 1: Consumables Kit The liquid reagents and mixing fluids will be packaged within their respective tubes which can be labeled easily with any writing utensil. Both the tips for the micropipettor and the tubes containing SYBR Green liquid will be tinted black in order to reduce the affect of light interacting with the SYBR Green liquid, which is highly light-sensitive. All consumables will be packaged in small containers that can be shipped conveniently. Corrections: Even though it is tinted, it only reduces the possible error of the SYBR Green being affected which leads to a more accurate and precise reading of the nucleotides going through the PCR process. This modification does NOT elimnate all error due to light contamination. It is simply a tool used to allow the experimenter more time and leniency when working with this consumable, while also improving the accuracy in their outcome. Feature 2: Hardware - PCR Machine & Fluorimeter The new diagnostic system will have the PCR machine and have included software be integrated into the box that way all of the circuitry and programming will overlap each other with no disturbances or electrical and technical difficulties occurring during the process. For the software that will be appplicable to the PCR, there will be a design cellphone app that is programmed to only run PCR images on a ImageJ similar app. It will function and run the algorithm automatically when a picture is imported from the phone's camera via high-powered bluetooth technology. Extracting the data will be done with a usb drive. The fluorimeter system will be vastly improved in shape and size where the box will be a safe lock box where one of its sides can attach itself by an interlocking puzzle and be un-attached in order to to put in the whole PCR experiment. The box is also customized with a customized stand for the phone where it will be at a perfect distance of 4 centimeters from the droplets on the fluorimeteer slides. There will be a usb camera clicker that will connect to the phone's camera and be able to take pictures when the box is completely sealed with all of the consumables.