BME100 s2015:Group8 9amL6

From OpenWetWare
Jump to navigationJump to search
BME 100 Spring 2015 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


Name: An Tran
Name: Robert Culibrk
Name: Austin Lehew
Name: Molly Golek
Name: Anthony G.


Bayesian Statistics

Overview of the Original Diagnosis System

-Patients were tested for SNP through the usage and implementation of PCR. Multiple DNA samples were taken from each of the two patients involved in the experiment to ensure a greater amount of accuracy in determining whether they exhibited the genetic mutation. The DNA samples were then placed into a primer and subsequently placed into a thermocycler, initiating the process of replicating a specific, targeted sequence of DNA, provided the specific sequence existed. The DNA was warmed to approximately 94 degrees Celsius so that the DNA double-helixes unraveled into straight strands and disconnected from each other, a step in the PCR amplification process also known as "denaturization". Next, the DNA was cooled to approximately 54 degrees Celsius to initiate the annealing process, during which the primers and Taq polymerase worked into conjunction to continuously replicate a predetermined strand of the DNA. Finally, the thermocycler heated to 72 degrees for about 120 seconds, allowing the newly formed DNA to come together. Once the DNA samples had been sufficiently amplified, a flourimeter was used to check for the presence of the SNP in droplets of the DNA sample. If the strands of DNA were present, they reacted with the SYBR Green solution to produce an observable green hue.

-To minimize the amount of error propagated throughout the process of the lab, multiple DNA samples were taken from each patient, various PCR controls were created and analyzed in order to establish a control for both the positive and negative cases. Additionally, a Java program known as ImageJ was used, which mathematically calculated the presence of a green hue in the droplets created through a series of photos that were taken. Finally, two to three images PER TRIAL were analyzed in ImageJ, eliminating the possibility of arriving at erroneous conclusions based on the data accrued.

What Bayes Statistics Imply about This Diagnostic Approach

-Calculations 1 and 2 center on the probability of whether a positive or negative final test conclusion will be rendered from either a positive or negative PCR reaction. The values obtained from Calculations 1 and 2 were reasonably close to 1, allaying that there is a fairly high probability of a positive final test conclusion given a positive PCR reaction; a similar probability holds for the negative case.

-Calculations 3 and 4 involve the probability of whether the patient will develop SNP given a positive or negative final test conclusion. For the positive case - the probability that a patient would develop SNP if a positive final test solution reached - was 100%. Given this data, a positive final test conclusion definitively states that the patient will develop SNP. Alternatively, in the negative case, it was slightly less probable that a patient would NOT develop the disease given a negative final test conclusion.

Computer-Aided Design


Our Design

Feature 1: Consumables Kit

-The tubes will be packaged in a very dark casing that reflects light

-The reagents will also be packaged in dark casing to reflect light

-The plastics will be made of a stronger polymer to ensure that they do not break in transport

-Storage compartments for the tubes and tips will be added to the outside of the PCR machine. They will be stored in an air-tight and tight container so that they will not get exposed to any unnecessary light or contaminants.

The problems with the consumables used in lab was that they didn't protect the reagents from light, and the plastic tubes and tips seemed a little weak. The packaging of the tubes will be very dark so that when the reagents and DNA are mixed in the tubes, the package will provide shielding from light interference. Also, the reagents will be enclosed in a dark casing so tin foil won't have to be used to prevent light from coming in. The storage compartments on the PCR machine will be the same way to prevent light interference as well. Lastly, the plastics will be made stronger to prevent cracking.

Feature 2: Hardware - PCR Machine & Fluorimeter

Hardware:PCR Machine

To make the PCR process more efficient, the PCR machine could be manipulated to complete the PCR process in less than 24 hours. Also, more sample ports could be added so that more than 4 samples could be processed at once. The big change that will be made is the incorporation of real-time video analysis of the PCR process. This video will then be streamed real-time to an added spectrophotometer. The spectrophotometer will analyze the percent transmittance of light through the PCR sample.


The spectrophotometer will measure percent transmittance at certain frequencies to check for the presence of a certain colored bioindicator. The spectrophotometer will measure the percent transmittance of light from the real-time video streaming from the PCR machine. This will make the process real-time, and will take only as long as the PCR machine machine takes to get through the process. This will eliminate the need of image J, which is very tedious and time-consuming.