BME100 f2017:Group8 W1030 L6
|BME 100 Fall 2017|| Home |
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
Wiki Editing Help
LAB 6 WRITE-UP
Overview of the Original Diagnosis System
Thirty four patients were tested by, 16 groups of 5 students, for the disease-associated SNP through multiple PCR experiments. Each group was assigned two patients, and given 3 replicates of DNA for each patient. The DNA was then put inside a thermocycler which replicated the DNA multiple times. Photos of the DNA samples were taken with a fluorometer, and were amplified for analyzation. Two group members combined the PCR with SYBR Green, and used the fluorometer to capture images of the droplets of each sample. Then, one member used the program ImageJ to enhance, manipulate and calculate the pictures of each droplet. ImageJ provided both qualitative and quantitative data which was used to determine if the patient had the disease-associated SNP.
What Bayes Statistics Imply about This Diagnostic Approach
Calculations one and two analyze how probable it would be to get a positive or negative final test conclusion, given a positive or negative PCR reaction. Seeing that the probability of the patient getting a positive final test conclusion, given a positive PCR reaction, was calculated to occur about 75% of the time, it is pretty reliable to infer that a positive PCR reaction will result in a positive final test conclusion. On the other hand, a patient getting a negative final test result, given a negative diagnostic signal, occurred closer to 90% of the time, implying that a negative diagnostic test signal almost always guarantees a negative final test conclusion. Seeing that the probability for receiving a negative test conclusion was higher than that of a positive final test conclusion based off of the PCR reactions, the negative results could be considered more reliable.
Calculation 3 determines the probability that a patient will develop the disease, given a positive final test conclusion. Based on the results the probability that the patient tests positive given the patient develops the disease was around 60%. The probability that the patient develops the disease given the patient tests positive was also around 60%. Calculation 4 determines the probability that a patient will not develop the disease, given a negative final test conclusion. The probability that the patient tests negative given that the patient will not develop the disease was about 80%. While the probability that the patient does not develop the disease given the patient tests negative was close to 100%. Overall, the results for both calculations proved that the reliability for predicting the development of the disease was accurate.
Intro to Computer-Aided Design
Feature 1: Consumables
GaugeCo.'s PCR machine comes with a consumable kit that includes various liquids as well as tools used to complete the reaction. The liquids include PCR mix (concentrated taq DNA polymerase, 200 µl), primer solution (200 µl), SYBR Green solution (200 µl), and buffer (500 µl). Twenty plastic tubes will be provided: 8 tubes of buffer solution, 2 tubes of SYBR Green, and 10 empty tubes. These tubes will be small enough to fit inside the PCR machine. Extra empty tubes are provided for back up in case an error were to occur. Thinly glass slides will be found in the kit, which will be used to examine the DNA and SYBR Green drops under the fluorimeter. The kit itself will consist of a light box which will be used when examining the fluorimeter.
A micropipette, as well as micropipette tips, will not be included. These must be purchased by the customer in order to achieve accuracy in measurements.
The glass slides were modified to be more thin than the original slides. The purpose of this is to prevent error when examining the DNA and SYBR Green drops. Because the previous glass slides had a greater height, they had to slide tightly against the sides of the fluorimeter. The surface tension of the liquid sample broke, causing the sample to lose its shape. This led to examination difficulties. Altering the glass slides to be thinner will allow for a smooth slide into the fluorimeter, which will ultimately prevent error during the sample examination process.
Feature 2: Hardware - PCR Machine & Fluorimeter
GaugeCo is creating our DNA-analyzing machine even better and more convenient than ever. By combining an Open PCR machine and fluorimeter into the body a single machine. An automated system within the body of our new, combined design, will allow our customers ease during experimentation. The two cones under the lid is a mechanized pipetting system that minimizes human error and pipetting mistakes while also reduces the cost of pipetting tips. In order to address a major weakness in the consistency of pictures taken during experimentation, our team designed a camera rig within the fluorimeter-side of our combined design that accommodates a wide range of smart-phone sizes and our compatible iPhone and Android app syncs with our combined design's system to maximize photo consistency.